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BC 2- > Lecture 1 > Flashcards

Lecture 1 Flashcards

1
Q

What are the steps of biosignaling

A

Signal, transduction, response

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2
Q

What is a signal?

A

NON-COVALENT interaction between ligand and receptor

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3
Q

What is a receptor?

A

Membrane-bound or soluble protein or protein complex, which exerts an intrinsic effect after binding to its endogenous/natural ligand

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4
Q

What are the features of signal transduction? (6)

A
  • Specificity
  • Amplification
  • Modularity
  • Desensitization/adaptation
  • Integration
  • Localization
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5
Q

What are the 4 features of specificity?

A
  • Complementarity
  • Non-covalent bond
  • Tissue specific receptor
  • Tissue-specific receptor target
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6
Q

Can there be a permanent interaction between a ligand and a receptor?

A

No

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7
Q

Give an example of tissue-specific receptor target

A

E.g. adrenalin. Both liver and adipose tissues have adrenaline receptors. However, receptor in liver results in a different response (hepatocyte interaction with adrenaline stimulates glycogen breakdown) than receptor in adipose tissue (triglyceride breakdown)

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8
Q

Does amplification occur downstream or upstream?

A

Downstream- from a signal down the cascade

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9
Q

What is a domain of a protein?

A

Domain or a module is a part of a protein that has a specific role

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10
Q

What is modularity?

A

Signaling proteins are somewhat modular. This allows cell to mix and match different complexes to have different functions

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11
Q

Are all modules of proteins catalytic?

A

No, they can just fulfil 3D function

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12
Q

When does desensitization occur and what is it?

A

When a signal is present continuously, desensitization of the receptor system results
- Blocking of the receptor
or
- Removal of it from the cell surface.

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13
Q

What is integration?

A

When 2 signals have opposite effects on a metabolic characteristic, the regulatory outcome results from the integrated input from both receptors

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14
Q

What is localisation?

A

When the enzyme that destroys an intracellular message is clustered with the message producer, the message is degraded before it can diffuse to distant points, so the response if only local and brief

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15
Q

What does interaction of ligand and receptor increase?

A

Interaction of L & R increases the activity of effectors/ mediators of signal transduction

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16
Q

What are the 4 classes of receptors?

A
  • G-protein coupled receptors
  • Receptor enzyme (tyrosine kinase)
  • Gated ion channel
  • Nuclear receptor
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17
Q

What are the steps of G-coupled receptor?

A
  1. Ligand interacts with receptor, which is a transmembrane protein
    Transmembrane protein interacts with G proteins–modularity
    When Gsα is bound to GDP, it is inactive
  2. As soon ligand binds to receptor, it causes Gsα to become activated by replacing GDP to GTP.
  3. Gsα dissociates and is an enzyme. It moves to adenylyl cyclase and activates it.
  4. Adenylyl cyclase catalyzes formation of cAMP
  5. cAMP activates protein kinase A (PKA)
  6. PKA can phosphorylate cellular proteins, resulting in cellular response
  7. cAMP is degraded to AMP, reversing the activation of PKA
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18
Q

What is the most druggable class of proteins?

A

G-coupled

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19
Q

Which protein is self-inhibitory? Explain

A

G protein has an unique ability to self deactivate

Gsα is also known as GTPase. It can convert GTP to GDP, deactivating itself.

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20
Q

What happens when Gsα is deactivated?

A

Gsα goes back to Gsβ

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21
Q

___ is the most common second messenger

A

cAMP is the most common second messenger

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22
Q

How is ATP converted into cAMP?

A

ATP is converted by adenylyl cyclase to cAMP by removal of 2 phosphate groups and cycling the remaining phosphate within the sugar

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23
Q

What is a second messenger?

A

Second messenger is a substance that is released after a ligand-receptor interaction and which brings about a response by the cell.

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24
Q

Are second messneger and mediators the same?

A

No, as only proteins can be mediators. Second messengers are not proteins

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25
Q

What are the 2 PKA subunits?

A
  • Regulatory subunit regulates catalytic subunit

- Catalytic subunit- has enzymatic function

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26
Q

What are the 2 PKA subunits held together by?

A

AKAP

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27
Q

How is PKA activated?

A
  • Regulatory subunit needs to be activated. It blocks substrate binding cleft which is at the catalytic subunit
  • Needs 4 cAMP to activate 2 regulating subunits
  • This opens substrate binding clefts which can now bind ligands
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28
Q

How is PKA disactivated?

A

Removal of cAMP disactivates PKA

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29
Q

What are the 2 method of G-protein signal termination?

A
  • cAMP is catalyzed by cyclic nucleotide phosphodiesterase, which emoves phosphodiester bond to produce AMP
    This results in deactivation of PKA
  • Modulators of GTPase activity deactivate Ga protein
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30
Q

What are modulators of GTPase activity?

A

different classes of proteins that can speed up or slow down the process of conversion of GTP to GDP (deactivation of G alpha)

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31
Q

Describe desentization of g-protein

A
  1. When G alpha leaves, the receptor is only associated with beta and gamma
    Free beta and gamma subunits can attract another protein called βARK, which adds phosphate groups
  2. βARK phosphorylates Ser residues at carboxyl end (cytoplasmic end) o
  3. β-arrestin (βarr) protein binds to the phosphorylated receptor
  4. βarr associated receptor is taken in by endocytosis and is now inside the cell. It is no longer available for binding with the ligand
  5. Inside the cell βarr is removed and the receptor is dephosphorylated
    Dephosphorylated receptor can go back to the membrane again and is available for his ligand
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32
Q

Can G protein also be inhibitory?

A

Yes- Gi instead of Gs

Active Gi inhibits Adenylyl cyclase, reducing cAMP concentration and supressign protein phosphorylation

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33
Q

Describe G-protein localization/nucleation

A

AKAP proteins e.g. AKAP5 are A kinase anchoring proteins
Adaptor proteins
They physically holds receptor, PKA and adenylyl cyclase
Thus, anything that can happen has to happen within the vicinity of this anchoring protein - localization of the signal

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34
Q

What are the 4 classes of G proteins?

A
  1. Gs-alpha- activates adenylyl cyclase
  2. Gi-alpha - inhibitory to adenylyl cyclase
  3. Gq-alpha - stimulates phospholipase protein
  4. G12,13 family - is associated with cytoskeleton
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35
Q

Steps of GPCR signaling through IP3 and Ca

A
  1. Hormone (H) binds to a specific receptor.
  2. Binding results in replacement of GDP by GTP and dissociation of Gq bound to GTP
  3. Gq moves to PLC and activates it
  4. PLC cleaves a phospholipid called PIP2 into two products: IP3 and Diacylglycerol (DAG)
  5. IP3 binds to a specific receptor- calcium channel that is present on endoplasmic reticulum, releasing
    sequestered Ca2+
  6. Diacylglycerol and Ca2+ activate protein kinase C at the surface of the plasma membrane
  7. Phosphorylation of cellular proteins by protein kinase C produces some of the cellular responses to the hormone.
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36
Q

What is PLC?

A

Phospholipase C

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37
Q

What are the second messengers in GPCR pathways that uses Gq? What qualifies them as second messengers?

A

Calcium, IP3 and Diacylglycerol. They are not proteins and their concentration can be measured

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38
Q

Where’s calcium stored?

A

In endoplasmic reticulum

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39
Q

Neurotransmitters usually act through GPCR by ___ signaling pathway

A

Neurotransmitters usually act through GPCR by IP3 signaling pathway

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40
Q

What is the common structure shared by GPCRs?

A

They 7 helical domains that pass through the membrane 7 times- transmembrane proteins that cross the membrane 7 times

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41
Q

What does PKA stand for?

A

Protein kinase A

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42
Q

G-alpha either ___ or ___ an effector enzyme (AC) changing local ___ ____ concentration thus modulating ____

A

G-alpha either activates or inhibits an effector enzyme (AC) changing local second messenger concentration thus modulating PKA

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43
Q

Adaptors like ___ ensure localization of the signal

A

Adaptors like AKAP ensure localization of the signal

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44
Q

Some G-alpha (Gq) activate ___ that signals through ___ and ___ thus activating ___

A

Some G-alpha (Gq) activate PLC that signals through Ca and diacylglycerol thus activating PLC

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45
Q

What else acts through GPCRs apart from hormone receptors?

A

Vision, olfaction and gustation

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46
Q

What is the process of PIP2 cleavage? Products?

A

PIP2 is cleaved in two by phospholipase C.

The ring part is IP3 and the CHO chain is DAG

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47
Q

What does phospholipase C do?

A

Cleaves PIP2 into DAG and IP3

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48
Q

What does RTK snad for?

A

Receptor tyrosine kinase

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49
Q

What does RTK always act as?

A

Always acts as a dimer

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50
Q

What are the 3 important features of RTK?

A
  • Receptors themselves are kinases
  • Always act in a dimer
  • Activate multiple signaling pathways.
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51
Q

What are the 2 most important multiple signaling pathways activated by RTK?

A

MAPK and PIP3

52
Q

Steps of MAPK pathway with insulin as an example

A
  1. Insulin binds to RTK. Results in phosphorylation of cytoplasmic domain of the receptor on its carboxyl-terminal Tyr residues
  2. This phosphorylation results in another phosphorylation of IRS-1 protein on its Tyr residues, activating it
  3. IRS-1 now acts as a docking protein. It binds to SH2 domain of Grb2.
  4. Irs-1> Grb2->Sos-> Ras-> Raf-1
  5. Raf-1 phosphorylates MEK on two Ser residues, activating it. MEK phosphorylates ERK on a Thr and a Tyr residue, activating it.
    Activated ERK can act as kinase
  6. ERK moves into the nucleus and phosphorylates nuclear transcription factors such as Elk1, activating them
  7. Elk1 joins SRF to stimulate the transcription and translation of a set of genes
53
Q

On which residues does MEK phosphorylate ERK?

A

On Thr and Tyr

54
Q

Mnemonic to remember MAPK pathway

A 
rigRRmet
Receptor
IRS-1
Grb2
Ras
Raf-1
MEK
ERK
Transcription factors or target
55
Q

MAPK pathways involves cascade of _____

A

MAPK pathways involves cascade of phosphorylation

56
Q

Steps of signaling through PIP3- insulin example

A
  1. Ligand binds to a receptor, IRS-1 is phosphorylated and acts as a docking protein
  2. IRS1 allows for PI3K (PI3 kinase) to bind
  3. PI3K converts PIP2 to PIP3 by adding a phosphate group- phosphorylation of 3rd carbon
  4. PIP3 allows for docking of PKB (protein kinase B)
  5. PKB is activated by phosphorylation
  6. One target of PKB is GSK3. Phosphate group is added to GSK3 on Ser residue, INACTIVATING it.
  7. GSK3 is a GS (glycogen synthase) kinase. It is active only when it is not phosphorylated. In its active state can add phosphate to glycogen synthase- GS. GS converts glucose to glycogen. GS is active when it is NOT phosphorylated. The moment it is phosphorylated, it becomes inactive. - remover of an activator step
  8. When GSK3 is phosphorylated, GS remains active. PKB stimulates movement of glucose transporter GLUT4 from internal vesicles to the plasma membrane, increasing the uptake of glucose
57
Q

Does phosphorylation always activate?

A

No, phosphorylation is a modulation step - can both activate & deactivate

58
Q

How is glucose taken up from circulation?

A

Using GLUT- glucose transporter proteins- e.g. GLUT4

PKB helps in opening of GLUT4

59
Q

How is PIP3 made?

A

It is converted by PI3K from PIP2

60
Q

Which is the most studied RTK?

A

Insulin receptor

61
Q

What activates TRK activity?

A

Phosphorylation of the receptor due to the binding of the ligand

62
Q

What activates MAPK signaling cascade?

A

Multiple adaptive protein

63
Q

What PIP3 serves as?

A

As an activator of PKB

64
Q

How does TRK and β-adrenergic receptor interact?

A

When RTK is activated, it phosphorylates and activates IRS-1.
IRS-1 in turn can activate PKB. PKB can phosphorylate Tyr and Ser on GPCR
RTK can lead to multiple phosphorylations of Tyr and Ser of GPCR tail
And these multiple phosphorylations lead to internalization of GPCR.
GPCR is taken into the cytoplasm thus GPSR become non-available for signaling
RTK can inhibit GPCR signal

65
Q

What is β-adrenergic receptor?

A

Class of G protein-coupled receptors that are targets of many neurotransmitters

66
Q

How does TRK and GPCR interact?

A

RTK is activated and it can phosphorylate instead of multiple sites, just one Tyr on cytoplasmic domain on GPCR
This one Tyr acts as activator protein, providing a docking site for multiple proteins
This complex proteins ultimately lead to MEK and ERK -> altered gene expression
Multiple MEKs and ERKs are activated-leading to multiple gene expressions

67
Q

What is the usual name of hormones that trigger RTK? What do they do?

A

Hormones that trigger RTK are usually called cytokines

Cytokines inhibit other ligand function

68
Q

What is IRS-1 function?

A

IRS-1 provides a docking site for many proteins

These complex protein ultimately lead to MAPK

69
Q

What is protein phosphorylation?

A

It’s the process in which a phosphoryl group (phosphate), donated by ATP, is transferred to an acceptor protein. The reaction is catalysed by a protein kinase

70
Q

What are the 3 most common AA phosphorylated?

A

Serine, Threonine and Tyrosine

71
Q

Why do we why say that kinases have specificity?

A

They only target only specific AA

72
Q

Which AA is target of RTK?

A

Tyr

73
Q

What are the 2 characteristic that all kinases have?

A
  • ATP binding site

- Catalytic cleft

74
Q

What do Raf-1, MEK, and ERK all have in common?

A

They are all protein kinases

75
Q

How can ion gated channels be opened or closed?

A

they may be open or closed, by a specific ligand (a neurotransmitter, for example) or by a change in the transmembrane electrical potential, Vm.

76
Q

What is the cytosolic calcium concentration normally?

A

It is usually kept very low

77
Q

What drives Na+ and Ca2+ movement and in which direction? What effect does it have?

A

The chemical gradient drives Na+ and Ca2+ inward producing depolarization

78
Q

What drives K+ movement and in which direction? What effect does it have?

A

The chemical gradient drives K+ outward producing hyperpolarization

79
Q

What drives Cl- movement and in which direction? What effect does it have?

A

The electrical gradient drives Cl- outward, against its concentration gradient (producing depolarization).

80
Q

What are the ionic movements across plasma membrane and what drives them?

A

Chemical gradient moves Na+ and Ca2+ inward, and K+ outward

Electrical gradient drives Cl- outward against it’s gradient

81
Q

What does NaK ATPase? How?

A

Creates a resting membrane potential (Vm) of -50 to -70 mV by carrying 3 Na+ out of the cell for every 2 K+ carried in making the inside negative relative to the outside. As both of the ions go against their gradient, their movement requires ATP

82
Q

What dictates the random flow of ions through the membrane via ion channels?

A

Electrochemical gradient potential across the membrane

83
Q

Is [Na+] and [K+] higher on the outside or inside?

A

[Na+] is higher on the outside

[K+] is higher on the inside

84
Q

Flow of each ion and in which direction can alter the cytosolic concentration of it? Why

A

As the intracellular concentration of Ca2+ is generally very low (∼10^7M), inward flow of Ca2+ can significantly alter the cytosolic [Ca2+].

85
Q

Is Ca2+ a second messenger?

A

Yes, as it is not a protein and has a very low concentration

86
Q

What is a nicotinic acetylcholine receptor?

A

This receptor is found in the postsynaptic membrane of neurons and opens in response to the neurotransmitter acetylcholine

87
Q

Give 2 examples of excitable cells

A

Neurons

Muscles

88
Q

What are excitable cells + example

A

Thus, excitable cells are any cells that secrete hormones e.g hormone insulin that are produced by beta cells in the pancreas

89
Q

Which side of membrane is positive and which is negative?

A

Outside is positive

Inside is negative

90
Q

What is the value of resting membrane potential?

A

-70 to -50 mV

91
Q

Name and describe 3 states of membrane potential

A
  1. Polarized- When cell is in resting membrane potential - polar membrane
  2. Depolarized- When is a bit more positive compared to resting membrane potential e.g when sodium or calcium goes from outside to inside, or calcium goes from outside to inside
  3. Hyperpolarized- when membrane becomes more negative than the resting membrane potential e.g. when chloride goes from inside to outside, the negative charge goes to outside, which might create further negative voltage difference
92
Q

What are the other ion transporters that can be found in the membrane?

A

Sodium, chloride and potassium channels

93
Q

What do sodium, chloride, potassium channels do?

A

When they are open, they allow ions to move down the electrochemical gradient

94
Q

Why does chloride move against the electrochemical gradient?

A

The amount of force created by electrical differential takes over the amount of force created by chemical difference, thus chloride comes from inside to outside, down the electrical gradient (negative chloride moves from negative inside to positive outside)

95
Q

Describe the process of propagation of neural signal

A

There are sodium gated ion channels along the axon which are gated by voltage difference
If there is any change in the voltage, they open
When this occurs, sodium goes in from outside to inside which creates less negativity/more positivity on the inside. Thus, wherever these channels are, the membrane becomes depolarized
When this happens, potassium channels open up and potassium leaves due to chemical gradient
This repolarizes the membrane
Opening of potassium channels is slightly delayed compared to sodium channels
This creates the direction for action potential propagation
Once sodium channels open, the membrane becomes depolarized, this is followed by repolarized by opening of potassium channels. However, by then there’s a slight difference in the action potential which opens sodium channels next to that-> Action potential keeps going forward

96
Q

Describe how is the signal passed from one neuron to another one

A

This is achieved by voltage gated calcium channels
They are opened by changes in membrane potential and allow calcium to move from outside to inside.
Calcium comes in and due to normally very low concentration, it not only causes depolarization, but also acts as a second messenger
Secretory granule that contain neurotransmitters come to the membrane and are exocytosed into the synaptic cleft in response to calcium concentration changes
Across the synaptic cleft there are receptors for neurotransmitters which are gated ion channels that are gated by a ligand- e.g. acetylcholine
Acetylcholine channels allow cations to go from outside to inside like sodium or calcium
This movement of positive ions from outside to inside depolarizes the membrane and begins the propagation of signal

97
Q

Is there more calcium on the inside or outside?

A

Normally there are more calcium on the outside

98
Q

Where does calcium act as a second messenger

A
  • IP3

- Signal transduction in neurons

99
Q

Neurotransmitters are ___ substances

A

Neurotransmitters are hormone substance

100
Q

How many acetylcholine molecules bind to acetylcholine receptor?

A

2

101
Q

What does binding of acetylcholine to its receptor do?

A

It induces a conformational change in acetylcholine receptor which opens the channel
This allows for influx of ions from outside to inside

102
Q

Which ions (+ or -) move through acetylcholine receptor

A

Cations (+ive)

103
Q

What is the purpose of the intrinsic ability of gated ion channels to close?

A

Allows for a short window of time during which movement of ions occurs

104
Q

Name cation gated receptors

A

Serotonin, acetylcholine, glutamate receptors

105
Q

Name anion gated receptor

A

Glycine

106
Q

Which receptors are not membrane bound? Where are they found

A

Nuclear receptors
Mostly found in the nucleus
5-10% of them can be in the plasma membrane

107
Q

Describe ligands of nuclear receptors

A

They are lipid soluble as they have to be able to move across the cell membrane
Have to be transported by a protein in aqueous environments

108
Q

Steps of nuclear receptors

A
  1. Ligands (usually hormones) carried by serum binding proteins diffuse across the plasma membrane and bind to its specific receptor in the nucleus
  2. Ligand binding changes conformation of the receptor;; it forms homo- or heterodimers with the other hormone-receptor complexes and binds specific regulatory regions-HREs in the DNA adjacent to specific genes
  3. Receptor attracts coactivator or corepressor protein(s) and, with them, regulates transcription of the adjacent gene(s), increasign or decreasign the rate of mRNA formation
  4. Altered levels of the hormone-regulated gene produce the cellular response to the hormone
109
Q

Describe the 2 types of possible dimers formed by nuclear receptors

A 
Homodimerization- 2 receptors of the same class come together and dimerize
Heterodimer- 2 different types of nuclear receptors that are activated by 2 different ligands come together.
110
Q

Which substances can use nuclear receptors to regulate gene expression?

A

Steroid and thyroid hormones, retinoids, and vitamin D

111
Q

Nuclear receptors act as ___ factors

A

Nuclear receptors act as transcription factors

112
Q

How fast is the signal transduction by nuclear receptors?

A

Slow

113
Q

Are steroid receptors cytoplasmic or nuclear?

A

Both

114
Q

What are the 3 essential components that define signal transduction through GPCR?

A
  • a plasma membrane receptor with seven transmembrane helical segments,
  • an enzyme in the plasma membrane that generates
    an intracellular second messenger,
  • a guanosine nucleotide–binding protein (G protein)
115
Q

What does the enzyme, bound by G-alpha generate?

A

Second messenger

116
Q

Define agonist

A

Agonists are structural analogs that bind to a receptor and mimic the effects of its natural ligand

117
Q

Define antagonist

A

antagonists are analogs that bind without triggering the normal effect and thereby block the effects of agonist

118
Q

What does S stand for in G coupled proteins?

A

S stands for stimulatory

119
Q

What are the G proteins that G receptor is made up of?

A

G proteins are composed of Gs alpha, Gs beta and Gs gamma

120
Q

The interaction between Gsa and adenylyl cyclase is possible only when Gsa i bound to ___

A

The interaction between Gsa and adenylyl cyclase is possible only when Gsa i bound to GTP

121
Q

Which residues does PKA phosphorylate?

A

Ser or Thr

122
Q

Describe amplification in G proteins

A

First, the binding of one hormone molecule to one receptor catalytically activates several Gs molecules. Next, by activating a molecule of adenylyl cyclase, each active Gs? molecule stimulates the catalytic synthesis of many molecules of cAMP. The second messenger cAMP now activates PKA, each molecule of which catalyzes the phosphorylation of many molecules of the target protein

123
Q

Define adaptor protein

A

non-catalytic proteins that hold together other protein molecules that function together

124
Q

What is phospholipase C specific for?

A

PIP2

125
Q

What is the long name for IP3

A

Inositol 1,4,5-triphosphate

126
Q

What are Raf-1, MEK and ERK

A

Protein kinases

127
Q

Ion fluxes are __ in contrast to _ transport by the Na+K+ ATPase

A

Ion fluxes are passive in contrast to active transport by the Na+K+ ATPase

BC 2- (19 decks)

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