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Flashcards in Chapter 15 Deck (127):
1

What is the most common way to transmit messages between cells

Extracellular messenger molecules

2

What is autocrine signaling?

Cell signaling - cell uses receptors on its surface to respond to messages (from itself)

3

What is paracrine signaling?

Messenger molecules travel short distance through intracellular space (ex. hunger is triggered)

4

What is endocrine signaling. The molecules involved in this are otherwise known as?

Messenger molecules reach target cells through blood stream (ex. smell food, become hungry). Molecules known as hormones.

5

______ refers to any process by which a cell converts one kind of signal/stimulus into another

Signal transduction

6

Signal transduction involves _______ of biochemical reactions inside the cell, which are carried out by ____, activated by ______

ordered sequences,
enzymes,
second messengers

7

How are many enzymes switched on or off?

Phosphoryation/dephosphorylation

8

_____ add a phosphate group whereas _____ remove a phosphate group

Kinases, phosphatases

9

What are the two types of signalling kinases?

Tyrosine kinases and serine threonine kinase

10

What are the two types of tyrosine kinases?

Receptor (on membrane) tyrosine kinase and non-receptor tyrosine kinase

11

Protein kinases (such as signalling kinases) phosphorylate _____, _____, or _____ residue protein

Serine, Thrionine, Tyrosine

12

What is a "second messenger"?

Intracellular substance that can activate (or inactivate) certain proteins - produced by receptor through an effector (enzyme)

13

If a surface receptor receives a signal but does not utilize a second messenger, what does it do?

Recruit proteins to their intracellular domains at the plasma membrane, so that proteins interact with one another by means of specific interaction domains.

14

What occurs in a signalling pathway?

Each protein in the pathway alters the conformation of the next (usually by phosphorylation). Target proteins receive the message to alter cell activity.

15

_____ add phosphate groups whereas ____ remove them

Kinases, phosphatases

16

What is another term for a signalling pathway?

Signal transduction

17

What does protein phosphorylation result in?

Can activate/inactivate enzymes.
Can increase/decrease protein-protein interactions.
It can change the subcellular location of the protein.
Can trigger protein degradation.

18

How do receptors differ on different breast cancer cells

In breast cancer cells, different receptors are present: estrogen, progesterone, and her2. If none are present, it is triple negative breast cancer (deadliest kind). Figuring this out allows for proper treatment (ex. ERPR positive patients are given a drug that inhibits estrogen and progesterone receptors).

19

What is a cell line?

A cultured group of cells coming from a single cell (usually cancerous tumour cells)

20

Describe how phosphorylation patterns can differ between cell types using an example?

It is possible to construct a figure of phosphorylation of specific proteins in varying cell lines, comparing them to each other. For example, triple negative breast cancer cells have completely different receptor tyrosine kinase rates

21

List varying types of extracellular messengers

Small molecules such as amino acids and their derivatives (ex. acetylcholine)
Gases such as NO and CO
Steroids (for sex differentiation, pregnancy, etc.)
Eicosanoids (lipids derived from fatty acids)
Peptides + proteins

22

What are different types of receptors?

G-protein coupled receptors (GPCRs)
Receptor protein-tyrosine kinases (RTKs)
Ligand gated channels
Steroid hormone receptors
Specific receptors such as B and T cell receptors

23

Describe the structure of function of GPCRs

Largest superfamily of proteins. Have seven alpha-helical transmembrane domains and interact with G proteins. Their amino-terminus is on the outside of the cell and the carboxyl terminus is on the inside of the cell. Three loops outside the cell form the ligand binding site, and three sites inside the cytoplasm provide binding sites for intracellular signalling.

24

G proteins have three parts, referred to as.....
How are they arranged

G-alpha, G-beta-, G-gamma.
When G-alpha is in bound form with GDP it will form a stable complex with the G-beta and G-gamma segment. When GDP becomes GTP (caused by change in conformation of GPCRs), the G-alpha is activated and will bind to and activate effector molecule.

25

What are some examples of stimuli that attach to GPCRs?

Epinephrine, serotonin, IgE-antigen complexes, neurotransmitters such as acetylcholine

26

Describe the sequence of events, step by step, that occurs when a ligand binds to a GPCR

1. GPCR changes conformation, resulting in a greater affinity for G protein.
2. G-alpha of a G protein binds to the GPCR receptor.
3. This triggers GDP on the G protein to be replaced by GTP.
4. The activated G-alpha binds to the effector molecule and ATP is converted into cAMP (second messenger).
5. The GTPase of G-alpha kicks in and converts GTP to GDP
6. G-alpha joins G-beta and G-gamma once more
7. The original GPCR is phosphoryated and arrestin binds the receptor, preventing further activation of G proteins

27

Once G-alpha is bound to an effector molecule, it will keep converting ATP to cAMP until what is triggered?

G-alpha has slow-acting GTP phosphatase activity, and over time the GTP is eventually broken down into GDP. The inactivated G-alpha goes back to G-beta and G-gamma to once again form the heterotrimatic G-protein complex

28

What molecule exchanges GDP for GTP

GEF (guanine nucleotide exchange factor)

29

_____ bind to A GPCR to block G-alpha from attaching to it again in a process called _____. What else occurs during this process?

Arrestins, called desensitization. During desensitization, GPCR is also phosphorylated by GRK (g-coupled receptor kinase)

30

What are well known organisms that produce toxins that target G proteins?

Cholera toxin, pertussis virulence factors

31

Describe the function of secondary messengers such as cAMP

Released into the cytoplasm after binding of a ligand, amplifying the response of a single extracellular ligand (basically bring message from membrane to cytoplasm)

32

Some phospholipids of cell membranes are converted into second messengers by activated _______

Phospholipases

33

Phosphoinositides are derivatives of _______, which produces the most well-studied lipid second messengers

Phosphatidylinositol

34

If a phospholipid is cleaved by phospholipase C right in the middle, what happens?

Head and neck groups (inositol tri-phosphate) enter the cytoplasm and body and tail (including diacylglycerol) stay in the plasma membrane

35

Cleaving phosphatidylinositol is related to muscle contraction how?

Opens calcium ion channels - creating a second messenger that results in a muscle contraction.

36

DAG extracted by cleaving phospholipids serves what purpose?

DAG activates protein kinase C, which phosphorylates serine and theronine residues on target proteins.

37

Phosphorylated phosphoinositides form lipid-binding domains called _____

PH domains

38

When Lowell and Mabel Hokin discovered phosphorylation of phosphatidylinositol, what were they trying to accomplish and why were the results a surprise?

They tagged [32P]orthophosphate to stdy the effect of acetylcholine on RNA synthesis in pancreatic cells. They noticed that the tagged orthophosphate was incorporated into PI and rapidly converted to phosphoinositides.

39

What are the four "flavours" of G-alpha?

G-alpha s, G-alpha q (phospholipase C), G-alpha I (inhibitory), G-alpha 12/13 (important role in carcinogenesis)

40

Glucagon and epinephrine both stimulate glycogen breakdown into _____, inhibiting the enzyme _____, which stimulates further glycogen production

glucose-1-phosphate, inhibiting glycogen synthase

41

What is glycogen?

Polymer of glucose (long chain of glucose) created to store excess glucose

42

cAMP is synthesized by _____. Where does it go once formed?

Adenylyl cyclase. Go into cytoplasm and bind with a cAMP-dependent protein kinase (PKA) to initiate a signalling cascade that leads to glucose mobilization

43

Briefly lay out the steps of intracellular signalling cascades

1. Transfer the signal
2. Transform the signal
3. Amplify the signal
4. Distribute the signal
5. Can be modulated to vary the response

44

If Glycogen synthase is phosphorylated, it is _____.
What about Glycogen synthase kinase is phosphorylated, what happens?

inactive.
GSK also becomes inactive

45

What is the purpose of phosphorylating glycogen synthase in a liver cell

To inactivate it, so glycogen can be broken down into glucose without immediately being reassembled

46

What does cAMP cause in liver cells, fat cells, and smooth muscle cells?

Liver cells - glycogen breakdown
Fat cells - triacylglycerol breakdown
Muscle cells - Causes muscle relaxation

47

Why is it that cAMP causes so many different effects in different cells?

It is thought that cAMP activates PKAs, which display varying AKAPs (PKA-anchoring proteins) which act as signalling hubs with different functions in different cells

48

What purpose do AKAPs serve?

Couple PKA with potential substrates and other ptoeins in signalling pathway. They localize signalling proteins and can do so in the cytoplasm or in organelles. Basically they cause an accumulation of PKA

49

Which GPCRs are involved in sensory perception

Rhodopsin - photosensitive protein for black and white vision
Several colour receptors in the retina
Distal tips of neurons located in the nasal epithelium contain odorant receptors, GPCRs that bind various chemicals.
Many taste receptors include GPCRs (perception of bitterness, sweetness, or savory is dependent on the compound interacting with GPCRs on the tongue)

50

GPCRs are also known as _____

G protein-coupled receptors

51

What eye-related disease is a result of GPCR mutation

Retinitis pigmentosa (progressive retinal degeneration) can be caused by mutations in rhodopsin's (A GPCR) ability to activate G proteins

52

How can mutations in thyroid GPCRs result in benign tumours?

Receptors do not need to be stimulated by the pituitary hormone TSH to secrete thyroid hormone, and instead constitutively secrete it. The mutation results in constant G protein attachment to GPCR and subsequent cell proliferation (which leads to cancer)

53

What are protein tyrosine kinases? Name and describe the two types

Enzymes that phosphorylate specific tyrosine resiudes on protein substrates.
1. Receptor protein-tyrosine kinases (RTKs) - integral membrane proteins that contain a single transmembrane helix and an extracellular ligand binding domain
2. Non-receptor protein-tyrosine kinases

54

Receptor protein-tyrosine kinases do what?

Exist in the membrane (trans-membrane) and phosphorylate target protein: tyrosine residues

55

What is dimerization?

The process of bringing to monomer molecules together

56

How is receptor tyrosine kinase related to dimerization? Describe using the terms "ligand-mediated dimerization" and "Receptor-mediated dimerization"

Either a specific ligand binds to a receptor, which brings the receptors together (ligand-mediated dimerization) or the ligand induces change in conformation of the monomers, which results in them binding together (receptor-mediated dimerization).
Once bound together, tyrosine kinases "trans-autophosphorylate", that is, give phosphate groups to each other. These phosphotyrosine residues serve as binding sites for SH2 or PTB domains

57

Phosphorylated tyrosine is otherwise known as _____

Phosphotyrosine

58

Phosphotyrosine residue is the binding motif for all proteins that have ___ domain or ____ domain

SH2 or PTB

59

PTB means

Phosphotyrosine binding domain (phosphorylated tyrosine)

60

SH2 stands for

Src homology 2

61

SH2 and PTB domains include?

Adapter proteins that bind other proteins
Docking proteins that supply receptors with other tyrosine phosphorylation sites
Signaling enzymes (kinases) that lead to changes in the cell
or
transcription factors

62

SOS protein is referred to as...? What type of protein is this?

Son of 7-less. GEF protein.

63

GEF proteins are referred to as?

Guanine-nucleotide exchange factor

64

When IRS (insulin receptor substrate) attaches to Receptor tyrosine kinase, it has a ____ domain and functions as a ______

PTB domain and functions as a docking station for more tyrosine residues, which will be phosphorylated and can then bind to even more SH2 or PTB domains

65

When a transcription factor in the STAT family attaches to receptor tyrosine kinase what happens?

It activates STAT monomer to cause it to create a dimer with another one, sending it to the nucleus for transcription.

66

If you cleave phospholipids you get...

DAG and inositol triphosphate (IP3)

67

describe the G-protein "Ras"

Active when bound to GTP and inactive when bound to GDP. Is a small G-protein (in comparison to heterotrimeric G-protein complex). Acts as its own GTP-ase, over time automatically hydrolyzing its bound GTP to GDP.

68

How do GTP-ase activating proteins (GAPs) affect the function of "Ras" protein

Shorten the active time of Ras (bring about faster GTP hydrolysis)

69

How do Guanine nucleotide-exchange factors (GEFs) affect the function of "Ras" protein

Stimulate exchange of GDP for GTP, activating more Ras

70

How do guanine nucleotide-dissociation inhibitors (GDIs) affect the function of "Ras" protein

Inhibits the release of GDP, leaving more Ras inactive

71

The general feature of Ras-MAP kinase pathway is that it ....

Map kinase kinase kinase phosphorylates map kinase kinase and that phosphorylates map kinase

72

In insulin receptor is a _____

Protein-tyrosine kinase

73

Once insulin receptors autophosphorylate it associates with ____? This binds with ___ domains to activate downstream signal molecules.

insulin receptor substrate (IRSs).
IRSs bind with SH2 domains

74

Describe in steps what happens when insulin receptors are activated by insulin.

They autophosphrylate (leads to phosphorylation of tyrosine residues - allowing binding to SH2 or PTB domains) and associate with insulin receptor substrate proteins (IRSs - docking proteins that increase docking sites).
IRSs binds to SH2 domains to activate signal molecules.

75

SH2 domain-containing proteins are kinases that phosphorylate the lipid: _________

PI 3-kinase (PI3K)

76

PI3K catalyzes the reaction of ____ into ____

PIP2 into PIP3

77

activated IRS proteins can activate the major signalling pathways of ___ and ___

PI3K and Ras

78

How does PI3K trigger activation of the downstream proteins PDK1 and Akt

PIP3 embeds in the plasma membrane (it is a phospholipid) and provides a binding site for Akt or PDK1 (which have PH domains). PDK1 activates Akt, which regulates protein synthesis, glucose uptake, and glycogen synthesis

79

If the activation of Akt by PDK1 affects things like protein and glycogen synthesis, glucose uptake, does that mean it is related to disease?

It is related to diabetes and also to cancer tumours.

80

Glycogen synthase kinase (GSK) is ______ regulated by phosphorylation of AKT. What does this mean?

Negatively. Means that activation of PI3-kinase-PKB pathway in response to insulin results in a decrease in GSK activity, which causes an increase in glycogen synthase activity.

81

For their signalling pathways, plants lack _____ nucleotides and ____

Cyclic, RTKs

82

What is diabetes mellitus and how is it influenced by insulin?

Type 1 diabetes - Caused by an inability to produce insulin
Type 2 diabetes - Caused by chronic insulin secretion, which overstimulates target cells in the body and causes desensitization of receptors in a condition called "insulin resistance". Most health risks that result from Type 2 diabetes are thought to be because of damage to blood vessels.

83

Describe cytoplasmic calcium and how levels are determined

Calcium levels are low in the cytosol because it is pumped into extracellular space and membrane is highly impermeable to it. Calcium is often sequestered in the smooth ER or the vacuole (in plant cells). Calcium channels can be opened by action potential (Voltage) or by calcium (ligand) itself. Calcium binds to calcium-binding proteins, affecting other proteins

84

What is Store-operated calcium entry?

When levels of Ca2+ in the smooth ER are extremely low, STIM 1 calcium ion channels move close to cell membrane's Orai1 calcium channels, to direct Ca+ ions from outside the cell almost directly into the smooth ER

85

Where is calcium stored in the cell?

Calcium is stored in smooth ER

86

Cytosolic calcium changes in the plants can be induced by...? What cellular response does it cause?

light, pressure, gravity, hormones. Aids in decreasing turgor pressure in guard cells

87

Both GPCR and receptor tyrosine kinase can activate phospholipase C (PLC). This is referred to as ___ (describe this process)

Convergence: meaning that the same pathway is started 2 different ways

88

Receptor tyrosine kinase can activate 3 different processes. What is this referred to as?

Divergence

89

Describe what is referred to as a crosstalk in signalling pathways and give an example?

Crosstalk occurs when two things influence each other in one signalling pathway. Ex. Ca2+ and cAMP influencing each other's signalling pathways

90

How does nitric oxide (NO) function as an intracellular pathway?

Calcium ion channel activated by Acetylcholine binding. Nitric oxide synthase produces NO and NO stimulates guanylyl cyclase to make cGMP (from GTP). cGMP decreases cytosolic calcium to relax smooth muscle.

91

What does viagra do?

Inhibits phosphodisterase so cGMP cannot be destroyed, resulting in constant muscle relaxation around capillaries

92

What is apoptosis?

Programmed cell death involving cell shrinkage, loss of adhesion to other cells, dissection of chromatin, and engulfment by phagocytosis

93

What is the hallmark feature of apoptosis?

Breakdown of DNA

94

What causes apoptotic changes?

Proteolytic enzymes called "caspases"

95

The proteolytic enzymes called caspases target several things in the process of apoptosis. What are they?

Protein kinases, Lamins (nuclear envelope), proteins of the cytoskeleton, caspase activated DNase (CAD)

96

Why is apoptosis so important during embryonic development?

Very precise cell death is needed to form structures such as organs, tissues, and most importantly spaces between digits (removing unnecessary nerve connections)

97

Why is apoptosis so important to adults?

Reduced apoptosis can lead to alzheimers or cancer

98

What is the major difference between apoptosis and necrosis?

Necrosis is unplanned and usually caused by external factors such as toxins.

99

Describe, step by step and in detail, the extrinsic pathway of apoptosis

1. Tumour necrosis factor (TNF) is detected by TNFR1 cell surface receptor.
2. Binding of TNF to TNFR1 produces conformational changes in the "Death domain" on the cytosolic side of the receptor. This recruits various proteins
3. These proteins include the adapter proteins FADD and TRADD along with procaspases
4. Procaspases convert other procaspases to caspases.
5. The caspases activate "executionar caspases", leading to apoptosis.

100

what are proenzymes?

Enzymes that will be activated when a portion is cleave

101

Describe, step by step and in detail, the intrinsic pathway of apoptosis.

1. Proapoptotic proteins (Bax or Bak) stimulate mitochondria to leak proteins (mostly cytochrome c).
2. Once in the cytosol, cytochrome c forms part of a multiprotein complex called the apoptosome, including several molecules of procaspase-9.
3. Procaspase-9 activates caspase-9 (eventually leading to activation of downstream executioner caspases)

102

The downstream target of both the extrinsic and intrinsic pathways of apoptosis is...

Caspase 3

103

Balance between the pro-survival protein _____ and the anti-survival protein ______ of the CL family of proteins determines whether cell dies

BCLXL, Bad and Bax

104

What does Bax protein do when activated?

Bind to mitochondria and forms a protein lined channel to allow cytochrome c to be released to trigger cell death

105

The release of cytochrome c from the mitochondria results in the production of a _______, which is the point of no return for cell death

Apoptosome

106

______ is the protein used to repair DNA

PARP

107

What function does CAD serve in breaking down DNA?

It cleaves PARP apart so it cannot fix DNA

108

How is signalling terminated after a ligand binds to a cell surface receptor?

Either by destroying the extracellular messenger with extracellular enzymes or by phagocytizing the whole receptor and breaking it down

109

What are arrestins and how do they relate to clathrin-coated vesicles?

Protein hubs that are capable of binding to many different proteins, including AP2 adapters of clathrin-coated pits. The interaction between these two results in phosphorylated GPCRs entering the cell via endocytosis. Sometimes, arrestin-bound GPCRs in endosomes can serve as a scaffold for other signalling pathways, but other times they are returned to the plasma membrane or degraded in lysosomes

110

If an inactivated GPCR is brought into the cell via and endosome, then recycled back to the plasma membrane it is referred to as _____

RE-sensitized

111

What does stimulation of cAMP cause?

Glucose mobilization by activating a protein kinase that adds a phosphate group onto a specific serine residue of the glycogen phosphorylase polypeptide.

112

Describe, step by step and in excruciating detail, the pathway in which phosphatidylinositol triggers second messengers that cause Ca2+ release in muscle cells in response to acetylcholine

1. PI is converted by a kinase into PIP
2. PIP is converted by another kinase into PIP2
3. Acetylcholine binds to the GPCR, and the G-alpha that attaches activates the effector PLC-beta
4. PLC-beta converts PIP2 into DAG (which stays in the membrane), and IP3 (which enters the cytosol)
5. DAG recruits PKC, which regulates cell growth
6. IP3 binds to the IP3 receptor on the smooth ER, which acts as a calcium channel and causes Ca2+ to be released into the cytoplasm
7. Muscle contracts

113

The hormone _____ is produced by alpha cells of the pancreas in response to low blood glucose levels

Glucagon

114

Compare insulin, glucagon, and epinephrine

Insulin - secreted by the beat cells of pancreas in response to excess blood glucose, causes storage of glucose as glycogen
Glucagon - secreted by alpha cells of pancreas and stimulates breakdown of glycogen in response to low blood glucose levels, and release of glucose into the blood stream
Epinephrine - Secreted by adrenal gland in response to fight or flight situations to provide a quick increase in blood glucose levels to deal with stressful situations

115

If epinephrine and glucagon produce the same effects in the cell, do they use the same receptor?

No! They bind to different GPCRs

116

Describe, in excruciating detail, the pathway that leads from glucagon/epinephrine reception to the release of glucose

1. Glucagon or epinephrine bind to the GPCR in the plasma membrane
2. A G-protein binds to the GPCR, and the G-alpa binds to the effector adenyl cyclase
3. Adenyl cyclase catalyzes the conversion of ATP to cAMP
4. cAMP molecules diffuse into the cytoplasm and bind to cAMP-dependent protein kinase A (PKA)
5a. PKA triggers phosphorylation of Glycogen synthase, preventing further conversion of glucose to glycogen
5b. PKA triggers phosphorylation of phosphorylase kinase, which catalyzes the transfer of phosphate groups to glycogen phosphorylase molecules
6. Glycogen phosphorylase is activated, and stimulates breakdown of glycogen
7. Glycogen is broken down into glucose-1-phosphate, then glucose-6-phosphate, then glucose before being distributed in the bloodstream

117

A fraction of activated PKA molecules translate into the nucleus where they cause what?

Phosphorylation of key nuclear proteins such as CREB.

118

The adapter protein Grb2 has an SH2 domain and can attach to phosphorylated tyrosine residues. What protein activator can attach to Grb2 and activate my favourite downstream protein

SOS activates the protein Ras

119

How does the docking protein IRS attach to phosphorylated tyrosine residues? What purpose does it serve?

Attaches with PTB domain, serves as a multi-port containing more tyrosine residues (which become phosphorylated upon docking).

120

Describe, in excruciating detail, the Ras-MAP kinase cascade

1. A growth factor binds to the extracellular domain of RTK
2. Grb2 binds to the activated RTK. SOS binds to Grb2
3. SOS is a GEF (activator) for Ras, and the close proximity of SOS to Ras activates it.
4. Conversion of Ras-GDP to RAs-GTP results in activation of Raf (a MAP kinase kinase kinase).
5. A series of reactions activate MEK (a MAP kinase kinase) and the MAP kinases ERK1 and ERK2
6. MAP kinases move into the nucleus and activate transcription factors involved in cell proliferation/growth
7. MPK-1 is produced, which removes phosphate groups from MAPK and inactivates the pathway

121

The PH domain on the N-terminus of IRS polypeptides allow them to bind to what? What does the PTB domain allow?

Phosphoinositides of the membrane. PTB domain allows them to bind to specific phosphorylated tyrosine residues on activated insulin receptors

122

Is activation of AKT by PDK1 enough to stimulate glucose production?

No, another kinase called mTOR is needed to phosphorylate AKT again

123

AKT is otherwise known as _____

PKB

124

How is insulin thought to be related to life span?

It's been shown that life span may be increased by decreasing the level of insulin. Long-lived humans often show increase insulin sensitivity, and laboratory studies have shown that calorie restriction leads to decreased insulin levels and increased sensitivity

125

Plants have a signalling pathway that is very similar to our MAP kinase cascade. Briefly describe this

The products of the Ert1 gene code for a receptor for ethylene gas, which regulates processes like germination and fruit ripening. Binding of this receptor leads to a long cascade similar to the MAP kinase cascade, resulting in downstream transcription factors

126

How does calcium-induced calcium release occur in a cardiac muscle cell?

1. Membrane potential causes voltage-gated Ca2+ channels in the plasma membrane to open
2. Influx of calcium ions bind to Ryanodine receptors on the smooth ER membrane
3. Ca2+ from ER is released into cytosol
4. Cell contracts
5. Ca2+ ions pumped back into SER
6. Secondary transport Na+/Ca2+ system in plasma membrane pumps out Ca2+ ions after heart beat, returning cell to relaxation

127

The best known calcium binding protein is _____, which can activate a number of signalling pathways

Calmodulin