Lecture 18 (exam 3) Flashcards
Cell signaling
refers to the biochemical mechanisms by which cells receive information from another cell or from the environment and utilize this information to cause a cell function
signal transduction
the conversion of an extracellular input to an intracellular output
RSV
rous sarcoma virus
the Src sequence was discovered and analyzed, and it turned out to be a cytoplasmic tyrosine kinase
RSV Src protein
is oncogenic because its activity is unregulated in the infected cells
Src, could increase cell growth, and learned a lot about cell signaling
Proto-oncogene
a normal cellular gene that promotes cell growth and/or proliferation and/or survival as part of its normal funciton
oncogene
a proto-oncogene that becomes cancer-promoting due to genetic or epigenetic changes that alter the activity or mass of the resultant protein
oncogenes are proto-oncogenes….
whose protein products are expressed abnormally or have abnormal activities
Tumor suppressor gene
a gene that opposes cell proliferation, and/or cell growth, and/or promotes DNA repair
Agonist
a ligand (signal) that activates a receptor
Antagonist
a ligand that blocks the actions of the agonist by competitively binding to the receptor (a competitive inhibitior)
Desensitization
inactivation of the receptor or its’ signaling pathway
What are the signals (ligands) that cells might respond to?
- Hormones/growth factors
- Antigens
- Neurotransmitters
- Environmental
- Medicial and recretional drugs (antihistamines, THC, CBD)
Hormone/growth factors that cells might respond to
- peptide/protein (ex. insulin, glucagon)
- steroid (ex. estrogen, testosterone)
- amines (epinephrine, norepinephrine, thyroxine) = adrenaline, noradrenalin (older terms)
Environmental signals cells might respond to
light, sound
mechanical touch/pressure/stretch
nutrients/metabolites (fatty acids, bile acids)
odorants, pheromones
tastants
Hydrophilic ligands
cant pass though membranes
- proteins or polypeptides
- derivates of amino acids: epinephrine, norepinephrine
- charged or polar molecules at neutral pH
Hydrophobic ligands
can pass through membranes
- derivatives of cholesterol: steroid hormones, Vit D, thyroxine
- derivatives of fatty acids: retinoids, eicosanoids
- uncharged at neutral pH
Hydrophilic/Hydrophobic ligands
unique exceptions to the rule
- Dissolved gases: NO, CO
What type of ligands (signals) need Cell surface receptors?
hydrophilic molecules cannot pass though the cell membrane and need cell-surface receptors to relay information
What type of ligands (signals) need Intracellular receptors?
Hydrophobic molecules can pass through the cell membrane to intracellular receptors
General features of receptors
target cells respond to an extracellular signal by means of receptor proteins. (no response if no receptor)
receptors have multiple functional domains (ex. ligand binding response)
The physical organization of receptors is an important area for biochemical study. No two cells are likely to have the same physical organization
Major classes of cell surface receptors
- Ion-channel coupled receptors
- G protein coupled receptors
- Enzyme coupled receptors (kinase receptors)
- Nuclear hormone receptors
Ion-channel coupled receptors
(transmitter-gated ion channels)
open or close specific ion-gated channels in response to binding of the signal molecule, which is typically a neurotransmitter
Ex. of Ion-channel coupled receptors
Acetylcholine nicotinic receptor
G protein coupled receptors
GPCRs interact with G (guanine nucleotide binding) proteins in the presence of the signal molecule to promote GDP/GTP exchange
the active G protein ACTIVATES a membrane enzyme and/or ion channel
Ex. of GPCRs
Glucagon, sensory receptors
Enzyme coupled receptors (kinase receptors)
have intrinsic enzymatic activity in their cytoplasmic domain or are tightly associated with an enzyme.
in either case, enzyme activity is activated by BINDING of the signal molecule to the receptor
Ex. of Enzyme coupled receptors
receptors for insulin, growth hormone, growth factors, cytokines
Nuclear hormone receptors
have no intrinsic enzymatic activity but undergo a conformational change once ligand-bound.
such changes enables their DNA binding domains to RECOGNIZE specific DNA sequences and often INITIATE transcription.
EX. of nuclear hormone receptors
glucocorticoid receptors, estrogen receptor, peroxisome proliferator activated receptors
Different signaling strategies
Contact dependent, paracirne/autocrine, synaptic, endocrine
Contact dependent signaling
the signal molecule is displayed on the cell surface and can only influence the recipient cell with direct membrane to membrane contact
specificity comes from the receptor and proximity
Ex. Notch signaling
Paracrine signaling
local mediators (ex. cytokines) are secreted into the extracellular space by one cell type and act locally on/in different nearby cell types
specificity lies with receptor and proximity.
displayed a gradient effect (based on proximity)
Ex. TGFbeta, Wnt signaling
local mediators
have a very short halflife
Autocrine signaling
is a specialized form of paracrine signaling.
involves local mediators that act on the same cell (same type of cell) that released the signal molecule)
Ex. Cancer
Synaptic signaling
neurons release neurotransmitters at synapses, often far from the cell body.
specificity comes from receptors and from one-to-one communication between the axon of the signaling neuron and the target cell
Ex. Acetylcholine signaling
Endocrine Signaling
hormones secreted by endocrine glands into the blood and can affect any cell or tissue in the body at great distances from endocrine cell.
specificity lies with the receptor and with the location of receptor, i.e. not all cells have all receptors
Ex. insulin, glucagon, steroid hormone signaling
Major steps in Signaling
- Binding to a specific receptor protein
- receptor activation and eliciting the response to the signal
- Removal of the signal
- Termination of the response
Major features of signaling systems
specificity, affinity, sensitivity, amplification, integration, desensitization/adaptation
specificity
determined by:
- complementarity between the signal and the receptor
- tissue and cell specific distribution of receptors
- tissue and cell specific distribution of the intracellular response systems
- proximity of signal
Affinity
high affinity binding is exhibited by most receptors (Kd =< 10^-8 M)
Sensitivity
Most receptors are exquisitely sensitive to the signal, meaning they respond robustly to its binding
Amplification
the signal of ligand binding is often geometrically increased as a result of an enzyme cascade
- increase the intensity of the signal
- prolongs the duration of the signal
Integration
when multiple signals activate a pathway or elicit a response, there is coordination of the signals
Desensitization/adaptation
receptor activation leads to a feedback system that turns off the receptor or removes it from the cell surface or nucleus
half life of hydrophilic signaling molecules
are short (seconds to minutes), so that signaling terminates rapidly when the stimulus is no longer present to stimulate its secretion
Desensitization of receptors mechanisms
Receptor sequestration, Receptor down-regulation, Receptor inactivation, inactivation of an intracellular signaling protein, production/activation of an inhibitory protein
Receptor sequestration
the receptor is internalized into an endosome but often recycles back into the membrane once the amount of the signal molecule has dropped
Receptor down-regulation
the receptor is internalized into an endosome, trafficked to a lysosome, and then degraded. New synthesis is required to restore receptor levels
Receptor inactivation
the receptor is inactivated, often by modification such as by phosphorylation or dephosphorylation
Inactivation of an intracellular signaling protein
a signaling protein closely associated with the receptor is inactivated
Production/activation of an inhibitory protein
an inhibitory protein prevents the receptor from signaling event tough the signal is there
Relay system
many membrane receptor use a relay system
- transduce the signal to the correct form
- integrate the signal with other pathways
- provide specificity
- increase duration of the response
A sequence of two inhibitory signals produce….
a positive signal (a double negative)
Intracellular mediators (second messengers) are often used…..
early in membrane signaling pathways
Common intracellular mediators
(second messengers)
cAMP, cGMP, DAG, IP3
How are the proteins in the relays/cascades regulated? (state changes of proteins)
- covalent modification by phosphorylation or dephosphorylation
- Allosteric modification (guanine nucleotide, GTP/GDP, binding)
- protein protein interactions
Covalent modification by phosphorylation or dephosphorylation
- addition of a phosphate group with its 2 negative charges can change the conformation of the protein, which can affect protein activity
- the phosphate group can serve as a recognition signal
- the phosphate group can mask a binding site and thus disrupt protein protein interactions
- cellular localization
Principal mechanisms of state change: signaling currency
binding/dissociation, post-translationals modification, conformational change, localization
changes in protein state kinetics
protein protein interactions
Association/dissociation rates, dissociation constant
Association rate
Kon[A][B]
Dissociation rate
Koff[AB]
At equilibrium
Kon[A][B] = Koff[AB]
Dissociation constant
Kd = Koff/Kon = ([A][B]) / [AB]
Changes in protein state: conformational changes
conformational change, allosteric regulation
conformational change
a change in the three dimensional arrangement or shape of a protein
allosteric regulation
a state change to a protein caused by binding of a ligand outside of the active site
the binding event is typically communicated to the active site via conformational change
Changes in protein state: Subcellular localization
cell-cell junction
determine the environments in which proteins operate. As such, subcellular localization influences protein function by controlling access to and availability of all types of molecular interaction partners
Changes in protein state: post translational modification
Logic behind PTM:
- fast
- energetically cheap
- reversible (usually)
- combinational
- Glycosylation (sugars)
- S-palmitoylation (lipids)
- Isomerization (proline residues)
- Ubiquitination/sumoylation (proteins)
- degradation
chemical effects: post translational modification
- size, shape, charge of amino acid side chains
- hydrophobicity
Changes in protein state: post translational phosphorylation
effect can be stabilizing or destabilizing
Changes in protein state: Post-translational modification
Effects of modification on cell signaling
- change conformation, activity
- promote protein binding
- prevent protein binding
- change subcellular localization
- change proteolytic stability
Protein kinases
catalyze the transfer of the y-phosphoryl from ATP to a hydroxyl group on serine, threonine, or tyrosine.
Two major groups of protein kinases
- Serine/threonine protein kinases
- Tyrosine protein kinases
Serine/threonine protein kinases
put phosphates on serine or threonine
Tyrosine protein kinases
put phosphates on tyrosine
Protein phosphatases
remove the phosphates.
there are more than 150 protein phosphatases
GAP
GTPase activating proteins
speed up protein inactivation by promoting the hydrolysis of GTP
GEF
Guanine exchange factors
speed up protein activation by promoting the exchange of the GDP to GTP
Signaling cascades/Relays rely on signaling complexes
- performed signaling cascade: scaffold proteins
- Assembly of a signaling complex on an activated receptor
- Assembly of the signaling complex on membrane phosphoinositide (PIs)
scaffolds proteins
are essential for the accurate coordination of signaling pathways
binding domain
PH = Pleckstrin homology domain
PTB = phosphotyrosine-binding domain
SH2 = Src homology 2 domain
SH3 = Src homology 3 domain
Phosphorylated inositol phopholipid
PH
Phosphotyrosine
SH2, PTB
Proline-rich motif
SH3
