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

Lecture 18 (exam 3) Flashcards

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
Q

Ex. of GPCRs

A

Glucagon, sensory receptors

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26
Q

Enzyme coupled receptors (kinase receptors)

A

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

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27
Q

Ex. of Enzyme coupled receptors

A

receptors for insulin, growth hormone, growth factors, cytokines

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28
Q

Nuclear hormone receptors

A

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.

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29
Q

EX. of nuclear hormone receptors

A

glucocorticoid receptors, estrogen receptor, peroxisome proliferator activated receptors

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30
Q

Different signaling strategies

A

Contact dependent, paracirne/autocrine, synaptic, endocrine

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31
Q

Contact dependent signaling

A

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

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32
Q

Paracrine signaling

A

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

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33
Q

local mediators

A

have a very short halflife

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34
Q

Autocrine signaling

A

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
Q

Synaptic signaling

A

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
Q

Endocrine Signaling

A

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
Q

Major steps in Signaling

A
  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
Q

Major features of signaling systems

A

specificity, affinity, sensitivity, amplification, integration, desensitization/adaptation

39
Q

specificity

A

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
Q

Affinity

A

high affinity binding is exhibited by most receptors (Kd =< 10^-8 M)

41
Q

Sensitivity

A

Most receptors are exquisitely sensitive to the signal, meaning they respond robustly to its binding

42
Q

Amplification

A

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
Q

Integration

A

when multiple signals activate a pathway or elicit a response, there is coordination of the signals

44
Q

Desensitization/adaptation

A

receptor activation leads to a feedback system that turns off the receptor or removes it from the cell surface or nucleus

45
Q

half life of hydrophilic signaling molecules

A

are short (seconds to minutes), so that signaling terminates rapidly when the stimulus is no longer present to stimulate its secretion

46
Q

Desensitization of receptors mechanisms

A

Receptor sequestration, Receptor down-regulation, Receptor inactivation, inactivation of an intracellular signaling protein, production/activation of an inhibitory protein

47
Q

Receptor sequestration

A

the receptor is internalized into an endosome but often recycles back into the membrane once the amount of the signal molecule has dropped

48
Q

Receptor down-regulation

A

the receptor is internalized into an endosome, trafficked to a lysosome, and then degraded. New synthesis is required to restore receptor levels

49
Q

Receptor inactivation

A

the receptor is inactivated, often by modification such as by phosphorylation or dephosphorylation

50
Q

Inactivation of an intracellular signaling protein

A

a signaling protein closely associated with the receptor is inactivated

51
Q

Production/activation of an inhibitory protein

A

an inhibitory protein prevents the receptor from signaling event tough the signal is there

52
Q

Relay system

A

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
Q

A sequence of two inhibitory signals produce….

A

a positive signal (a double negative)

54
Q

Intracellular mediators (second messengers) are often used…..

A

early in membrane signaling pathways

55
Q

Common intracellular mediators

A

(second messengers)
cAMP, cGMP, DAG, IP3

56
Q

How are the proteins in the relays/cascades regulated? (state changes of proteins)

A
  • covalent modification by phosphorylation or dephosphorylation
  • Allosteric modification (guanine nucleotide, GTP/GDP, binding)
  • protein protein interactions
57
Q

Covalent modification by phosphorylation or dephosphorylation

A
  • 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
Q

Principal mechanisms of state change: signaling currency

A

binding/dissociation, post-translationals modification, conformational change, localization

59
Q

changes in protein state kinetics

A

protein protein interactions

Association/dissociation rates, dissociation constant

60
Q

Association rate

A

Kon[A][B]

61
Q

Dissociation rate

A

Koff[AB]

62
Q

At equilibrium

A

Kon[A][B] = Koff[AB]

63
Q

Dissociation constant

A

Kd = Koff/Kon = ([A][B]) / [AB]

64
Q

Changes in protein state: conformational changes

A

conformational change, allosteric regulation

65
Q

conformational change

A

a change in the three dimensional arrangement or shape of a protein

66
Q

allosteric regulation

A

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
Q

Changes in protein state: Subcellular localization

A

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
Q

Changes in protein state: post translational modification

A

Logic behind PTM:
- fast
- energetically cheap
- reversible (usually)
- combinational

  • Glycosylation (sugars)
  • S-palmitoylation (lipids)
  • Isomerization (proline residues)
  • Ubiquitination/sumoylation (proteins)
  • degradation
69
Q

chemical effects: post translational modification

A
  • size, shape, charge of amino acid side chains
  • hydrophobicity
70
Q

Changes in protein state: post translational phosphorylation

A

effect can be stabilizing or destabilizing

71
Q

Changes in protein state: Post-translational modification
Effects of modification on cell signaling

A
  • change conformation, activity
  • promote protein binding
  • prevent protein binding
  • change subcellular localization
  • change proteolytic stability
72
Q

Protein kinases

A

catalyze the transfer of the y-phosphoryl from ATP to a hydroxyl group on serine, threonine, or tyrosine.

73
Q

Two major groups of protein kinases

A
  1. Serine/threonine protein kinases
  2. Tyrosine protein kinases
74
Q

Serine/threonine protein kinases

A

put phosphates on serine or threonine

75
Q

Tyrosine protein kinases

A

put phosphates on tyrosine

76
Q

Protein phosphatases

A

remove the phosphates.

there are more than 150 protein phosphatases

77
Q

GAP

A

GTPase activating proteins

speed up protein inactivation by promoting the hydrolysis of GTP

78
Q

GEF

A

Guanine exchange factors

speed up protein activation by promoting the exchange of the GDP to GTP

79
Q

Signaling cascades/Relays rely on signaling complexes

A
  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
Q

scaffolds proteins

A

are essential for the accurate coordination of signaling pathways

81
Q

binding domain

A

PH = Pleckstrin homology domain
PTB = phosphotyrosine-binding domain
SH2 = Src homology 2 domain
SH3 = Src homology 3 domain

82
Q

Phosphorylated inositol phopholipid

A

PH

83
Q

Phosphotyrosine

A

SH2, PTB

84
Q

Proline-rich motif

A

SH3

Biochem II Self Study (10 decks)

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