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Biochem II Self Study > Lecture 18 (exam 3) > Flashcards

Lecture 18 (exam 3) Flashcards

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1
Q

Cell signaling

A

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

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2
Q

signal transduction

A

the conversion of an extracellular input to an intracellular output

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3
Q

RSV

A

rous sarcoma virus

the Src sequence was discovered and analyzed, and it turned out to be a cytoplasmic tyrosine kinase

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4
Q

RSV Src protein

A

is oncogenic because its activity is unregulated in the infected cells

Src, could increase cell growth, and learned a lot about cell signaling

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5
Q

Proto-oncogene

A

a normal cellular gene that promotes cell growth and/or proliferation and/or survival as part of its normal funciton

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6
Q

oncogene

A

a proto-oncogene that becomes cancer-promoting due to genetic or epigenetic changes that alter the activity or mass of the resultant protein

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7
Q

oncogenes are proto-oncogenes….

A

whose protein products are expressed abnormally or have abnormal activities

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8
Q

Tumor suppressor gene

A

a gene that opposes cell proliferation, and/or cell growth, and/or promotes DNA repair

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9
Q

Agonist

A

a ligand (signal) that activates a receptor

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10
Q

Antagonist

A

a ligand that blocks the actions of the agonist by competitively binding to the receptor (a competitive inhibitior)

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11
Q

Desensitization

A

inactivation of the receptor or its’ signaling pathway

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12
Q

What are the signals (ligands) that cells might respond to?

A
  • Hormones/growth factors
  • Antigens
  • Neurotransmitters
  • Environmental
  • Medicial and recretional drugs (antihistamines, THC, CBD)
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13
Q

Hormone/growth factors that cells might respond to

A
  • peptide/protein (ex. insulin, glucagon)
  • steroid (ex. estrogen, testosterone)
  • amines (epinephrine, norepinephrine, thyroxine) = adrenaline, noradrenalin (older terms)
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14
Q

Environmental signals cells might respond to

A

light, sound
mechanical touch/pressure/stretch
nutrients/metabolites (fatty acids, bile acids)
odorants, pheromones
tastants

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15
Q

Hydrophilic ligands

A

cant pass though membranes

  • proteins or polypeptides
  • derivates of amino acids: epinephrine, norepinephrine
  • charged or polar molecules at neutral pH
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16
Q

Hydrophobic ligands

A

can pass through membranes

  • derivatives of cholesterol: steroid hormones, Vit D, thyroxine
  • derivatives of fatty acids: retinoids, eicosanoids
  • uncharged at neutral pH
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17
Q

Hydrophilic/Hydrophobic ligands

A

unique exceptions to the rule

  • Dissolved gases: NO, CO
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18
Q

What type of ligands (signals) need Cell surface receptors?

A

hydrophilic molecules cannot pass though the cell membrane and need cell-surface receptors to relay information

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19
Q

What type of ligands (signals) need Intracellular receptors?

A

Hydrophobic molecules can pass through the cell membrane to intracellular receptors

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20
Q

General features of receptors

A

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

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21
Q

Major classes of cell surface receptors

A
  • Ion-channel coupled receptors
  • G protein coupled receptors
  • Enzyme coupled receptors (kinase receptors)
  • Nuclear hormone receptors
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22
Q

Ion-channel coupled receptors

A

(transmitter-gated ion channels)
open or close specific ion-gated channels in response to binding of the signal molecule, which is typically a neurotransmitter

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23
Q

Ex. of Ion-channel coupled receptors

A

Acetylcholine nicotinic receptor

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24
Q

G protein coupled receptors

A

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

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25
Ex. of GPCRs
Glucagon, sensory receptors
26
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
27
Ex. of Enzyme coupled receptors
receptors for insulin, growth hormone, growth factors, cytokines
28
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.
29
EX. of nuclear hormone receptors
glucocorticoid receptors, estrogen receptor, peroxisome proliferator activated receptors
30
Different signaling strategies
Contact dependent, paracirne/autocrine, synaptic, endocrine
31
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
32
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
33
local mediators
have a very short halflife
34
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
35
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
36
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
37
Major steps in Signaling
1. Binding to a specific receptor protein 2. receptor activation and eliciting the response to the signal 3. Removal of the signal 4. Termination of the response
38
Major features of signaling systems
specificity, affinity, sensitivity, amplification, integration, desensitization/adaptation
39
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
40
Affinity
high affinity binding is exhibited by most receptors (Kd =< 10^-8 M)
41
Sensitivity
Most receptors are exquisitely sensitive to the signal, meaning they respond robustly to its binding
42
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
43
Integration
when multiple signals activate a pathway or elicit a response, there is coordination of the signals
44
Desensitization/adaptation
receptor activation leads to a feedback system that turns off the receptor or removes it from the cell surface or nucleus
45
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
46
Desensitization of receptors mechanisms
Receptor sequestration, Receptor down-regulation, Receptor inactivation, inactivation of an intracellular signaling protein, production/activation of an inhibitory protein
47
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
48
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
49
Receptor inactivation
the receptor is inactivated, often by modification such as by phosphorylation or dephosphorylation
50
Inactivation of an intracellular signaling protein
a signaling protein closely associated with the receptor is inactivated
51
Production/activation of an inhibitory protein
an inhibitory protein prevents the receptor from signaling event tough the signal is there
52
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
53
A sequence of two inhibitory signals produce....
a positive signal (a double negative)
54
Intracellular mediators (second messengers) are often used.....
early in membrane signaling pathways
55
Common intracellular mediators
(second messengers) cAMP, cGMP, DAG, IP3
56
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
57
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
58
Principal mechanisms of state change: signaling currency
binding/dissociation, post-translationals modification, conformational change, localization
59
changes in protein state kinetics
protein protein interactions Association/dissociation rates, dissociation constant
60
Association rate
Kon[A][B]
61
Dissociation rate
Koff[AB]
62
At equilibrium
Kon[A][B] = Koff[AB]
63
Dissociation constant
Kd = Koff/Kon = ([A][B]) / [AB]
64
Changes in protein state: conformational changes
conformational change, allosteric regulation
65
conformational change
a change in the three dimensional arrangement or shape of a protein
66
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
67
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
68
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
69
chemical effects: post translational modification
- size, shape, charge of amino acid side chains - hydrophobicity
70
Changes in protein state: post translational phosphorylation
effect can be stabilizing or destabilizing
71
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
72
Protein kinases
catalyze the transfer of the y-phosphoryl from ATP to a hydroxyl group on serine, threonine, or tyrosine.
73
Two major groups of protein kinases
1. Serine/threonine protein kinases 2. Tyrosine protein kinases
74
Serine/threonine protein kinases
put phosphates on serine or threonine
75
Tyrosine protein kinases
put phosphates on tyrosine
76
Protein phosphatases
remove the phosphates. there are more than 150 protein phosphatases
77
GAP
GTPase activating proteins speed up protein inactivation by promoting the hydrolysis of GTP
78
GEF
Guanine exchange factors speed up protein activation by promoting the exchange of the GDP to GTP
79
Signaling cascades/Relays rely on signaling complexes
1. performed signaling cascade: scaffold proteins 2. Assembly of a signaling complex on an activated receptor 3. Assembly of the signaling complex on membrane phosphoinositide (PIs)
80
scaffolds proteins
are essential for the accurate coordination of signaling pathways
81
binding domain
PH = Pleckstrin homology domain PTB = phosphotyrosine-binding domain SH2 = Src homology 2 domain SH3 = Src homology 3 domain
82
Phosphorylated inositol phopholipid
PH
83
Phosphotyrosine
SH2, PTB
84
Proline-rich motif
SH3

Biochem II Self Study (10 decks)

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