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BIO 344 > exam 4 > Flashcards

exam 4 Flashcards

1
Q

Cell surface receptors do not enter the what?

A

*cytosol or the nucleus

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2
Q

Intracellular signal receptors are what?

A

*small hydrophobic signal molecules

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3
Q

What acts as signal transducers?

A

*cell surface receptors

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4
Q

What is a signal transducer?

A

*convert extracellular signals into intracellular ones

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5
Q

What are the three large classes of cell surface receptor proteins?

A
  • ion-channel coupled
  • G-coupled
  • enzyme-coupled
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6
Q

What is G-coupled seen?

A

*NPC

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7
Q

What are also known as transmitter-gated ion channels or ioniotropic receptors?

A

*ion-channel coupled receptors

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8
Q

What is involved in rapid synaptic signaling between nerve cells and other electrically excitable target cells such as nerve and muscle cells?

A

*ion-channel coupled receptors

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9
Q

What Signal is mediated by a few neurotransmitters that transiently open or close an ion channel?

A

*ion-channel coupled receptors

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10
Q

What Briefly changes permeability of postsynaptic target cell?

A

*ion-channel coupled receptors

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11
Q

What do most ion-channel coupled receptors belong to?

A

*a large family of homologous, multipass transmembrane proetiens

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12
Q

Ion channel coupled receptors can’t get in until what?

A

*the signal molecule binds

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13
Q

Once the ion channel lets the signal molecule in what happens?

A

*it changes the permeability of membrane to ions

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14
Q

What Act by indirectly regulating the activity of a separate plasma-membrane-bound target protein?

A

*G-protein coupled receptors

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15
Q

What are the general things G-proteins regulate?

A

*enzyme or an ion channel

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16
Q

What mediates the interaction between the activated receptor and this target protein?

A

*a trimeric GTP binding protein (G protein)

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17
Q

The activation of the target protein can change what?

A
  • the concentration of one or more small intracellular mediators
  • the ion permeability of the plasma membrane
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18
Q

IF the target is an enzyme what is changed?

A

*the concentration of one or more small intracellular mediators

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19
Q

IF the target if an ion channel what is changed?

A

*ion permeability of the plasma membrane

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20
Q

WHat do the small intracellular mediators act in turn to alter?

A

*the behavior of yet other signaling proteins in the cell

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21
Q

Once the active sites are exposed and the signal molecule binds what happens?

A

*the G protein will dissociate and bind to inactive enzyme (activating it)

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22
Q

WHat Functions directly as enzymes or associate directly with enzymes that they activate?

A

*enzyme coupled receptors

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23
Q

What are enzyme coupled receptors usually?

A

*ingle pass transmembrane proteins

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24
Q

What is outside the cell and inside the cell in enzyme coupled receptors?

A

*ligand binding site outside, and catalytic or enzyme binding site inside

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25
Q

Enzyme coupled receptors are what in their structure?

A

*heterogeneous

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26
Q

What are the majority of enzyme coupled receptors?

A

*majority, however, are either protein kinases or associate with protein kinases, which phosphorylate specific sets of proteins in the target cell when activated.

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27
Q

Enzyme coupled receptors pass how many times?

A

*once (so they have huge variation in structure, very different)

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28
Q

WHat belongs to a large family of homologous, multipass transmembrane proteins (conserved)?

A

*G protein coupled receptors

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29
Q

What is induced proximity?

A

*when the dimer binds it brings the inactive domain closer together to become active

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30
Q

What else can activate an enzyme coupled receptor?

A

*receptor activates an enzyme

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31
Q

What are small intracellular signaling molecules also called?

A

*small intracellular mediators or second messengers

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32
Q

What are first messengers?

A

*the extracellular molecules

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33
Q

Second messengers are generated in?

A

*large numbers in response to the receptor activation

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34
Q

What do second messengers do?

A

*diffuse away from their source spreading their signal to other parts of the cell

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35
Q

What are some second messengers?

A
  • cAMP and Ca2+ (water soluble, diffuse in cytosol)

* diacylglycerol (lipid soluble and diffuse in the plane of the plasma membrane)

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36
Q

How do second messengers work?

A

*they pass the signal by binding and altering the confirmation and the behavior of selected signaling proteins or effector proteins

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37
Q

What do intracellular signaling proteins help do?

A

*relay signal into the cell

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38
Q

What do intracellular signaling protein form?

A

*functional network (each protein helps to process the signal in one or more of the following ways as it spreads the signal’s influence through the cell)

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39
Q

How are intracellular signaling spread?

A
  1. protein may relay the signal to the next signaling component
  2. May act as a scaffold to bring 2 or more signaling proteins together to enhance interaction
  3. May transform or transduce the signal into a different form to pass signal or stimulate a response
  4. Amplify the signal it receives via a signaling cascade
  5. Integrate signals from two or more signaling pathways as it moves it forward
  6. Spread the signal from one signaling pathway to another
  7. May anchor one or more signaling proteins in a pathway to a particular structure n the cell where the signal is needed
  8. Can modulate the activity of other signaling proteins and regulate the strength of the signal (amplify or silence them)
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40
Q

The spread of intracellular signaling is in what direction?

A

*multiple directions, while relay is going down the same path

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41
Q

Many signaling proteins act as?

A

*molecular switches

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42
Q

What are these molecular switches activated by?

A

*phosphorylation or GTP binding

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43
Q

WHat is the largest class of molecular switches activated or inactivated by and regulated by?

A
  • phosphorylation

* regulated by protein kinase and protein phosphatase

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44
Q

What does protein kinase do?

A

*adds one or more phosphate group

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45
Q

WHat does protein phosphatase do?

A

*removes phosphate group

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46
Q

What is another class of molecular switches?

A

*GTP binding proteins

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47
Q

What is bound when the molecular switch is in the off state?

A

*GDP is bound

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48
Q

How do molecular switches shut themselves off?

A

*hydrolyzing their bound GTP to GDP

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49
Q

What are the two major types of GTP binding proteins?

A
  • large trimeric GTP binding protein (G proteins)

* small monomeric GTPases (monomeric GTP binding protein)

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50
Q

What do large trimeric GTP binding proteins help do?

A

*relay signals from G-protein-coupled receptors that activate them

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51
Q

What do small monomeric GTPases help do?

A

*help relay signals from many classes of cell-surface receptors.

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52
Q

What are some regulatory proteins?

A
  • GTPase activating proteins (GAP)

* guanine nucleotide exchange factors (GEF)

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53
Q

What do GAP proteins do?

A

*Drive proteins into an “off” state by increasing the rate of hydrolysis of bound GTP

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54
Q

What do GEF proteins do?

A

*activate monomeric GTPases, by promoting the release of bound GDP in exchange for binding of GTP.

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55
Q

What must cells do to respond appropriately?

A

*Cells must integrate information coming from multiple signals to respond appropriately

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56
Q

Integration depends on what?

A

*intracellular coincidence detectors

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57
Q

When do intracellular coincidence detectors activate?

A

*Only activated if they receive multiple converging signals

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58
Q

Intracellular signaling enhances what?

A

*the speed, and efficiency and specificity of the response

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59
Q

How is it possible to achieve specificity and avoid cross talk?

A

*scaffold proteins

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60
Q

What Bind together groups of interacting signaling proteins into signaling complexes, often before a signal has been received?

A

*scaffold proteins

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61
Q

What do scaffold proteins do?

A
  • holds the signaling proteins in close proximity
  • components can interact at high local concentrations and be sequentially
  • activated speedily, efficiently, and selectively in response to an appropriate extracellular signal
  • avoiding unwanted cross-talk with other signaling path-ways
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62
Q

What is another way to prevent cross talk?

A
  • Signaling complexes form only transiently in response to an extracellular signal
  • Receptor activation leads to the production of modified phospholipid molecules (called phosphoinositides)
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63
Q

What is commonly used to relay signals from protein to protein along a signaling pathway?

A

*induced proximity where a signal triggers assembly of a signaling complex

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64
Q

What are interaction domains?

A
  • compact protein molecules
  • help induced proximity work
  • enable signaling proteins to bind to one another in multiple specific combinations.
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65
Q

Intracellular signaling networks usually make use of what?

A

*feedback loops (positive and negative feedback)

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66
Q

Feedback loops operate over what kind of time range?

A

*enormous range or time scales (from milliseconds to hours)

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67
Q

Cells can adjust their sensitivity to a signal by?

A

*reversible process of adaptation or desensitization

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68
Q

What does adaptation and desensitization allow cells to do?

A

*Enables cells to respond to changes in the concentration of an extracellular signal molecule

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69
Q

What are some ways cells can adjust their sensitivity to a signal?

A
  • receptor sequestration
  • receptor down regulation
  • receptor inactivation
  • inactivation of signaling protein
  • production of inhibitory protein
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70
Q

What is receptor sequestration?

A

*put receptor in an endosome

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71
Q

What is the cytoskeleton necessary for?

A
  • shape, internal structure

* movement, intracellular transport, cell division

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72
Q

What is the behavior of the cytoskeleton?

A
  • depends on 3 families of protein molecules
  • each of the 3 types of filaments
  • all 3 share certain fundamental principles
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73
Q

What are the 3 types of filaments?

A
  • intermediate
  • microtubules
  • actin filaments
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74
Q

What provides mechanical strength, and flexibility?

A

*intermediate filaments

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75
Q

What determines the positions of organelles and directs intracellular transport?

A

*microtubules

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76
Q

What determines the shape of the cell’s surface and necessary for whole cell locomotion?

A

*actin filaments

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77
Q

All 3 types of filaments would be useless without what?

A

*accessory proteins

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78
Q

What do accessory proteins do?

A
  • link the filaments to other cell components and each other
  • includes motor proteins
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79
Q

What is the plus end?

A

*the actively growing end (has directionality)

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80
Q

What is much more rigid than actin?

A

*microtubules

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81
Q

What has alpha and beta structures which has GTP bound?

A

*microtubules

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82
Q

Actin and microtubules are made or what?

A

*globular proteins, while intermediate filaments are rope like fibers

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83
Q

What has high tensile strength and less structured arrangement in the cell?

A

*intermediate filaments

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84
Q

Cytoskeletal filaments are?

A
  • dynamic and adaptable

* rearranges rapidly, requires little extra energy

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85
Q

What are the phases of cell division?

A
  • IPMATC

* interphase, prophase, metaphase, anaphase, telophase, cytokinesis

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86
Q

What are some crawling fibroblast?

A
  • actin cytoskeleton
  • microtubules
  • chromosomes
  • actin contractile ring
87
Q

What do microtubules form?

A

*form mitotic spindle

88
Q

What direction do actin cytoskeleton crawl?

A

*to the right

89
Q

How long do crawling fibroblast take?

A

*only takes about an hour

90
Q

What can cytoskeleton also form?

A
  • stable structures

* also form stable large scale structure for cell organization (microvilli)

91
Q

What maintains a constant location, length, and diameter over a lifetime?

A

*microvilli

92
Q

HOw is cell polarity achieved?

A

*through the cytoskeleton (allowing the cell to maintain a top and bottom and front to back and proper contact with each other)

93
Q

What are cytoskeletal filaments constructed from?

A

*smaller subunits (filaments 10-100 micrometers, individual molecules)

94
Q

What Diffuse rapidly in cytoplasm due to small size and Allows cells to undergo rapid structural rearrangements?

A

*individual molecules

95
Q

WHat are intermediate filaments made up of?

A

*of smaller subunits that are themselves elongated and fibrous

96
Q

What are actin and microtubules made up of?

A

*made of subunits that are compact and globular

97
Q

What subunits are for actin filaments?

A

*actin subunits

98
Q

What subunits are for microtubules?

A

*tubulin subunits

99
Q

All 3 types of cytoskeletal filaments form what?

A

*form as helical assemblies of subunits

self-associate

100
Q

What types of forces hold together filaments?

A
  • hydrogen bonds, van der wals, and ionic bonds (weak associations)
101
Q

What does these forces permit?

A

*use to form and break apart (rearrange)

102
Q

What do accessory proteinsn bind to?

A

*filaments or their subunits (determine the sites of assembly of new filaments)

103
Q

What are cytoskeletal polymers?

A

*Combine strength with adaptability

built out of multiple protofilaments

104
Q

WHat are protofilaments?

A
  • Long linear strings of subunits joined end to end
  • Associate with one another laterally
  • Typically twist around one another in a helical lattice
105
Q

HOw are intermediate filaments assembled?

A

*assemble by forming strong lateral contacts between alpha-helical coiled coils

106
Q

What does the staggered intermediate filaments allow?

A
  • intermediate filaments tolerate stretching and bending, forming strong rope-like structures
107
Q

What are built from globular subunits?

A

*microtubules

108
Q

What are held together primarily by longitudinal bonds, and the lateral bonds holding the 13 protofilaments together are comparatively weak?

A

*microtubules

109
Q

Microtubules do what much more when they are bent?

A

*break

110
Q

What change the kinetics of filament assembly and disassembly (rate at which new filaments are made or broken down)?

A

*accessory proteins

111
Q

What is the rate limiting step in the formation of a cytoskeletal polymer?

A

*nucleation

112
Q

What can assemble spontaneously are unstable, and disassemble readily?

A

*short oligomers composed of a few sub units

113
Q

What must happen for a new large filament to form?

A

*subunits must assemble into an initial aggregate, or nucleus

114
Q

What has low affinity for each other and are loosely bonded?

A

*monomers

115
Q

What is nucleation?

A

*aggregate of monomers

116
Q

What is filament nucleation?

A

*the initial process of nucleus assembly

117
Q

How long does filament nucleation take?

A

*can take quite a long time (depending on how many subunits must come together to form the nucleus)

118
Q

What creates a kinetic barrier to nucleation?

A

*instability if smaller aggregates

119
Q

What is the critical concentration?

A
  • the rate of monomer addition equals rate of monomer subtraction
  • Cc=Koff/kon
120
Q

HOw is the lag phase in filament growth eliminated?

A

*if preexisting seeds (such as filament fragments that have been chemically cross-linked) are added to the solution at the beginning of the polymerization reaction

121
Q

Why don’t we want large ones to be made?

A

*they would be hard to transport (more static, hard to rapidly diffuse)

122
Q

Are tubulin and actin filaments nonpolar or polar?

A

*polar

123
Q

What are microtubules made of?

A

*tubulin (heterodimer)

124
Q

How are microtubules bounded?

A

*non covalently bounded

125
Q

What type of site is on the heterodimer?

A

*GTP binding site

126
Q

What tubulin is never hydrolyzed, and why is this important?

A
  • alpha tubulin

* important for structural stability

127
Q

What tubulin can by hydrolyzed, and why is this important?

A
  • beta tubulin

* plays an important role WRT microtubule synthesis

128
Q

Microtubules are composed of what?

A

*13 parallel protofilaments

129
Q

What are the two types of protein protein contacts in microtubules?

A
  • longitude (beta-alpha)

* lateral (alpha-alpha, beta-beta)

130
Q

What forms a regular helical lattice?

A

*microtubules

131
Q

What is the persistence length of a microtubule, and why is this important?

A

*several millimeters (makes microtubules the stiffest and straightest structural elements found in most animal cells)

132
Q

How can the stiffness of a filament be characterized?

A

*by its persistence length

133
Q

What is composed of a single globular polypeptide chain (monomer)?

A

*actin

134
Q

What do each monomer have?

A

*ATP (or ADP) binding site

135
Q

How do actin filaments assemble?

A

*head-tail polar filaments

136
Q

What are actin filaments composed of?

A

*two parallel protofilaments

137
Q

What is the persistence length of actin filaments?

A

*few tens of micrometers

138
Q

What are actin filaments polar?

A

*the end with the beta subunit exposed is called the positive end, and the one with the alpha subunit exposed is called the minus end

139
Q

What ends are exposed in actin molecules?

A

*amino terminus and carboxy terminus (at the plus end)

140
Q

What end is the ATP binding cleft at in actin filaments?

A

*minus end

141
Q

Do the plus ends and minus ends grow at the same rate?

A

*no they grow at different rates

142
Q

What is the plus end?

A

*the more dynamic of the two ends of a filament, where both growth and shrinkage are fast

143
Q

Which end is more stable?

A

*minus end

144
Q

In microtubules what subunits are exposed at the minus and plus end?

A
  • minus: alpha subunits

* plus: beta subunits

145
Q

How does elongation proceed?

A
  • proceeds spontaneously when the free energy change (ΔG ) for addition of the soluble subunit is less than zero.
  • This is the case when the concentration of subunits in solution exceeds the critical concentration.
146
Q

HOw does depolymerization proceed?

A

*proceeds spontaneously when this free energy change is greater than zero.

147
Q

What is depolymerization?

A

*when microtubules can rip apart the chromosomes

148
Q

What can cells do?

A

*couple processes (can use free energy released during spontaneous filament polymerization or depolymerization to do mechanical work)

149
Q

What does elongating microtubules help with?

A

*can help push out membranes, and shrinking microtubules can help pull mitotic

150
Q

What does elongating actin filaments help with?

A
  • help protrude the leading edge of motile cells
151
Q

The actin and tubulin subunits are both what?

A

*enzymes (can catalyze the hydrolysis of a nucleoside triphosphate, ATP or GTP, respectively)

152
Q

GTP is on what?

A

*tubulin

153
Q

ATP is on what?

A

*actin

154
Q

For the free subunits the hydrolysis proceeds?

A

*very slowly

155
Q

ON tubulin the nucleotide binding site lies where?

A

*at the interface between two neighboring subunits

156
Q

On actin the nucleotide is where?

A

*deep in a cleft near the center of the subunit

157
Q

What are the two different types of filaments structures that can exist?

A
  • one with the “T form” of the nucleotide bound (ATP for actin, GTP for tubulin)
  • one with the “D form” bound (ADP for actin, GDP for tubulin).
158
Q

In living cells, most of the free subunits are in what form?

A

*T form

159
Q

The longer the time that subunits have been in the polymer lattice the more likely what will happen?

A

*more likely they are to have hydrolyzed their bound nucleotide (controls if we are building or tearing down the cytoskeletal segments)

160
Q

Whether the subunit is in the T or the D form depends on what?

A

*the rate of this hydrolysis compared with the rate of subunit addition

161
Q

As long as addition is happening faster than hydrolysis what will continue to happen?

A

*growth, if not the microtubules will fall apart

162
Q

The rate or subunit addition is?

A

*high

163
Q

If the filament is growing rapidly then what is likely?

A
  • it is likely that a new subunit will add on to the polymer before the nucleotide in the previously added subunit has been hydrolyzed,
  • so that the tip of the polymer remains in the T form, forming an ATP cap or GTP cap.
164
Q

If the rate of subunit addition is low what may occur?

A
  • hydrolysis may occur before the next subunit is added,

* and the tip of the filament will then be in the D form

165
Q

Subunits are recruited at the plus end in what form?

A

*T form

166
Q

Subunits are shed from the minus end in what form?

A

*D form

167
Q

What is treadmilling and what does steady state treadmilling require?

A
  • At a particular intermediate subunit the filament growth and shrinkage is balanced (length unchanged)
  • requires constant consumption of energy
168
Q

What is dynamic instability?

A

*This rapid interconversion between a growing and shrinking state, at a uniform free subunit concentration

169
Q

What is catastrophe?

A

*the change from growth to rapid shrinkage

170
Q

What is rescue?

A

*the change to growth

171
Q

Why do microtubules break apart?

A

*when GTP is bound it changes the conformation but when it is hydrolysis to GDP it is slightly bent (making it unstable)

172
Q

Why do microtubules peel back once they fall apart?

A

*alpha beta have greater associations then the lateral ones

173
Q

Where is treadmiling predominate?

A

*actin filaments

174
Q

Where is dynamic instability predominate?

A

*in most eukaryotic cells in microtubules

175
Q

What aid rapid cytoskeletal rearrangement?

A

*treadmilling and dynamic instability

176
Q

What do dynamic instability and treadmilling allow?

A
  • the cell to maintain the same overall filament content

* individual subunits constantly recycle between the filaments and the cytosol

177
Q

What does a typically micrtobules switch between?

A

*growth and shrinkage every few minutes

178
Q

What is the advantage of dynamic behavior of filaments?

A

*advantage to the cell seems to be the spatial and temporal flexibility that is inherent in a structural system with constant turnover. (allows the cell to test what the best microtubules arrangement is)

179
Q

What is the rate limiting step in dynamic instability?

A

*in the formation of a new filament is nucleation

180
Q

The new filaments are what?

A

*highly dynamic (have a fleeting existence)

181
Q

Why dynamic instability?

A
  • cell can control which filaments are growing (if not favorable it will tear it down and rearrange it)
  • preserving favorable ones
182
Q

When external conditions change, or when internal signals arise what does dynamic instability allow?

A

*the cell is poised to change its structure rapidly

183
Q

All eukaryotic cells contain?

A

*actin and tubulin

184
Q

What forms a cytoplasmic filaments in only some metazoans?

A

*intermediate filaments

185
Q

What type of organisms have intermediate filaments?

A

*vertebrates, nematodes, and mollusks

186
Q

what is prominent in the cytoplasm of cells that are subject to mechanical stress?

A

*intermediate filaments

187
Q

What do intermediate filaments play an important role in imparting?

A

*mechanical strength to tissues for the squishier animals

188
Q

Unlike the actin or tubulin, intermediate filament subunits do not have what?

A

*binding site for a nucleoside triphosphate (no hydrolysis)

189
Q

The monomer of intermediate filaments is what compared to the tetramer?

A

*monomer is polar, tetramer is not

190
Q

What lacks overall structural polarity?

A

*intermediate filaments

191
Q

Intermediate filaments have what type of interactions and why is that important?

A
  • strong lateral hydrophobic interactions typical of coiled coil proteins
  • gives them a rope like character
192
Q

Are intermediate filaments easily bent and difficult to break?

A

*yes

193
Q

What is the persistence length of intermediate filaments?

A

*less than one micrometer (compared to several millimeters for microtubules and about ten micrometers for actin)

194
Q

What is the most diverse intermediate filament family?

A

*keratins

195
Q

Where is keratin found?

A
  • human epithelial cells

* hair and nails

196
Q

About how many distinct keratins are there?

A

*50

197
Q

What are disulfide bonds and why are they important?

A
  • really strong bounds

* they survive after the cell dies (forms tough coverings for animals)

198
Q

Mutation in keratin genes can cause?

A

*genetic diseases (skin blisters)

199
Q

What happens when intermediate filaments are not nicely anchored?

A

*skin blisters in response to even slight mechanical stress, which ruptures the basal cells

200
Q

What can alter filament polymerization?

A

*drugs (filaments are frequent targets for natural toxins)

201
Q

What can drugs prevent from happening?

A

*monomers from coming together, or it can not let the filaments disassemble

202
Q

HOw can drugs help plants, fungi or sponges?

A

*produced in self defenses so they will not be eaten from predators

203
Q

Drugs can affect changes in actin filaments what are some examples?

A
  • latrunculin
  • phalloidin
  • all cause cell death
204
Q

Drugs can affect changes in tubulin what are some examples?

A
  • colchicine
  • taxol
  • cause cell death
205
Q

Synthesis has now been achieved and used for cancer treatment, how does this work?

A

*stops replication

206
Q

Nearly all bacteria and many Achaea contain what?

A

*homolog of tubulin

207
Q

What does the z ring do?

A
  • the site where the septum forms during cell division

* constricts during eukaryotic division and cleaves it into two

208
Q

What is FtsZ?

A
  • 3D folded protein

* similar to the structure of alpha or beta tubulin

209
Q

As the bacterium divides what happens to the Z ring?

A

*becomes smaller until it completely disassembles

210
Q

What serves as a site for localization of specialized cell wall synthesis enzymes required for building the septum between the two daughter cells?

A

*the z ring

211
Q

What does the disassembled FtsZ later do?

A

*reassemble at the new sites of septum formation in the daughter cells

212
Q

Many bacteria also contain homologs of?

A

*actin

213
Q

What do MreB and Mbl filaments assemble in?

A

*vivo to form large scale spiral (contribute to cell shape determination)

214
Q

As with FtsZ, the filaments within the MreB and Mbl?

A
  • spirals

* highly dynamic, with half lives of a few minutes

BIO 344 (3 decks)

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