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BME 501 > Section 5 - Intracellular Traffic and Energy Conversion > Flashcards

Section 5 - Intracellular Traffic and Energy Conversion Flashcards

1
Q

How much total membrane does the ER take up?

A

50%

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2
Q

True or false: the ER is connected to the nuclear membrane

A

True: it extends from the nucleus into the cytosol

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3
Q

What are the functions of the ER?

A

Production of transmembrane proteins, secreted proteins, lipids, and calcium storage

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4
Q

What is the ER composed of?

A

Tubules and membranous sacs

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5
Q

Where is the ER the densest?

A

Near the nucleus

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6
Q

Where is the ER the least dense?

A

In the cytosol (away from the nucleus)

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7
Q

True or false: the ER in mammalian cells is the same as the ER in plant cells

A

False: they have very different structures

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8
Q

True or false: the entirety of the ER has the same function

A

False: different regions of the ER can be specialized for different functions

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9
Q

What is an example of a specific region of ER having a specialized function?

A

Rough ER

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10
Q

What is rough ER?

A

ER with attached ribosomes

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11
Q

What is smooth ER?

A

ER without ribosomes

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12
Q

What is co-translation?

A

When proteins are transported to the ER during translation

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13
Q

Is the rough ER constantly rough?

A

No. The ribosomes associate and dissociate from the ER, thus changing it to rough or smooth

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14
Q

True or false: ribosomes sit on the ER, waiting for mRNA to come

A

False: they are assembled in the cytosol and translocated to the ER

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15
Q

How does the rough ER become rough?

A

By the ribosome assembling in the cytosol, and then moving towards the ER

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16
Q

What is the function of smooth ER?

A

Transporting synthesized proteins / lipids to other regions of the cell (golgi)

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17
Q

Where is rough ER most likely to be found?

A

Closer to the nucleus

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18
Q

Why is rough ER found more commonly closer to the nucleus?

A

That is where mRNA is most likely to be found

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19
Q

What is the function of calcium in the cell?

A

Act as initiators for many biological functions

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20
Q

Why is calcium kept in the ER?

A

Keep cytosolic concentration low for proper function (proper cell signaling)

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21
Q

What is the specialized ER in muscle cells important for?

A

Contraction

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22
Q

How does the ER sequester calcium?

A

Through calcium binding proteins and calcium channels

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23
Q

What is needed on a polypeptide to direct it to the ER?

A

A signal sequence

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24
Q

Where are transmembrane proteins made?

A

Embedded in the ER

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25
Q

Where are water-soluble (secreted) proteins made?

A

In the ER lumen

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26
Q

What cleaves the signal sequence?

A

Signal peptidase

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27
Q

What does signal peptidase do?

A

Cleave the signal sequence off of a polypeptide

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28
Q

What is a translocater?

A

Where the growing protein in the ER is held

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29
Q

What does SRP stand for?

A

Signal recognition particle

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30
Q

What does the SRP do?

A

Move the ribosome from the cytosol to the ER

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31
Q

How does the SRP move a ribosome from the cytosol to the ER?

A

It binds to the signal sequence and an SRP receptor found on the ER membrane

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32
Q

What is the structure of SRP?

A

Proteins and RNA

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33
Q

True or false: the protein continues translating as it is moved from the cytosol to the ER

A

False: translation is halted by the SRP

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34
Q

Why does the SRP halt translation?

A

To ensure that it reaches the ER first so it can be processed correctly before continuing

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35
Q

What would happen if the SRP did not halt translation?

A

The protein would be misfolded (cassette tape)

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36
Q

What does an SRP do once it is bound to an SRP receptor?

A

It moves the polypeptide into a translocator

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37
Q

What are the parts of an SRP molecule?

A

Signal sequence binding pocket, hinge, and translational pause domain

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38
Q

Where is SRP most likely to be found?

A

Close to the nucleus

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39
Q

What happens to the SRP and SRP receptor after the polypeptide is in a translocator?

A

It gets recycled (it can be used again)

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40
Q

What is the structure of a ribosome in the cytosol (before translation)?

A

Dissociated subunits

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41
Q

What is the structure of the translocator?

A

A pore type structure

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42
Q

What is needed for the translocator to function properly?

A

A plug

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43
Q

What is the significance of the plug in the translocator?

A

Prevents the mixing of cytosol and ER lumen contents

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44
Q

What displaces the plug in the translocator?

A

The signal sequence

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45
Q

What happens when the plug is displaced in the translocator?

A

The growing polypeptide can be fed into the translocator into the ER lumen

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46
Q

What is the structure of the translocator in the closed position?

A

Hinge is closed, with a plug

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47
Q

What is the structure of the translocator in the open position?

A

The signal peptide is holding the hinge open, the plug is displaced, and the polypeptide can be fed through the pore

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48
Q

If a polypeptide sequence only has a start sequence at the end, what can you say about the protein?

A

It is a soluble (secreted) protein

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49
Q

For a soluble (secreted) protein, what sequence(s) does it have?

A

A start transfer sequence

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50
Q

For a multipass transmembrane protein, what sequence(s) does it have?

A

A start transfer sequence and a stop transfer sequence

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51
Q

What does a stop transfer sequence do?

A

Moves the polypeptide out of the translocator, and continues translation in the cytosol

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52
Q

True or false: the start transfer sequence can be cleaved

A

True: if it is at the end of a polypeptide, it can be cleaved

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53
Q

True or false: the stop transfer sequence can be cleaved

A

False: it must remain embedded in the membrane

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54
Q

What is the phobicity of the stop transfer sequence?

A

Hydrophobic

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55
Q

Why must the stop transfer sequence be hydrophobic?

A

It stays embedded within the membrane

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56
Q

True or false: a start transfer sequence can be found at the start or middle of the polypeptide

A

True: it can be in either location

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57
Q

True or false: a stop transfer sequence can be found at the start or middle of the polypeptide

A

False: it can only be in the middle of the polypeptide

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58
Q

True or false: the N-terminal of a polypeptide is always in the ER

A

False: this direction can be changed depending on the specific protein

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59
Q

What determines the direction of the start transfer sequence if it is in the middle of the polypeptide?

A

The positive and negative ends of the start transfer sequence must line up with the membrane

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60
Q

What side of the membrane does the positive side of the start transfer sequence line up with?

A

The positive side

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61
Q

How come the positives of the membrane and the start transfer sequence are together?

A

It is similar to a capacitor (like charges line up at opposite sides of the membrane)

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62
Q

Which leaflet of the cell membrane is more positive?

A

The external leaflet (compared to the internal leaflet)

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63
Q

For a single pass protein, where is the start sequence found?

A

At the beginning of the polypeptide

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64
Q

For a multi pass protein, where is the start sequence found?

A

In the middle of the polypeptide

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65
Q

What sequences are needed to create multi pass proteins?

A

Pairs of start and stop sequences

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66
Q

Which sequences will signal peptidase cleave?

A

Start signal sequences at the beginning of the polypeptide

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67
Q

Which sequences will signal peptidase not cleave?

A

Start and stop signal sequences in the middle of the polypeptide

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68
Q

True or false: a start sequence can be unpaired to a stop

A

True: it does not need a stop

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69
Q

True or false: a stop sequence can be unpaired to a start

A

False: every stop requires a start

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70
Q

What must the charge be between a start and stop sequence?

A

Negative

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71
Q

Why must the charge between a start and stop sequence be negative?

A

It needs to align with the cell membrane charge gradient

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72
Q

True or false: one translocator is used per polypeptide

A

False: multiple translocators can be used

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73
Q

True or false: proteins that come off of the ribosome are functional

A

False: they need to be processed post-translation to be functional

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74
Q

Where are most proteins processed after translation?

A

The ER

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75
Q

What does disulfide isomerase do?

A

Catalyzes the formation of the disulfide bond

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76
Q

Where is disulfide isomerase found?

A

In the ER lumen

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77
Q

For most loops in a transmembrane protein, are they small or large?

A

Small

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78
Q

For most tails in a transmembrane protein, are they small or large?

A

Large

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79
Q

If the loops of a transmembrane protein are large, what can you say about the loops?

A

They are in an organized structure (alpha helix, beta sheet, etc.)

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80
Q

What does oligosaccharyl transferase do?

A

Adds sugars to the growing polypeptide

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81
Q

What is the function of sugars on proteins?

A

Help with folding by assisting chaperone proteins

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82
Q

How do chaperone proteins use sugars?

A

If the sugar looks a certain way, then the protein should be folded correctly (on-folding pathway)

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83
Q

True or false: chaperones physically fold the polypeptide into the correct shape

A

False: they only check if it is folded correctly

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84
Q

What drives protein folding?

A

Thermodynamics

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85
Q

What happens if the chaperone / sugar pathway starts a perpetual loop?

A

It will get signaled for degradation

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86
Q

What pathway is used to degrade a protein?

A

The ubiquitin pathway

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87
Q

What is the purpose of the ubiquitin pathway?

A

It is a proteolytic pathway (break down misfolded proteins)

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88
Q

How can a misfolded protein signal for its own degradation?

A

The misfolded protein can activate a receptor to make a transcription factor, which creates more chaperones to help folding

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89
Q

What is the “lie” in having a misfolded protein signal for its own degradation?

A

Non-process mRNA was found in the cytosol (not the nucleus)

90
Q

True or false: the ER synthesizes many phospholipids

A

True: many phospholipids are made in the ER

91
Q

Where is phosphatidylcholine made?

A

In the ER

92
Q

Where can the phospholipids in the ER be transferred to?

A

The cell membrane

93
Q

In the ER, how are the phospholipids arranged?

A

Almost perfectly segregated (PC on outside, PS on inside)

94
Q

Is the portion of membrane added to the cell membrane from the ER largely symmetrical or largely asymmetrical?

A

Largely asymmetrical

95
Q

Which enzyme fixes phospholipids in the cell membrane?

A

Flippase

96
Q

Which enzyme fixes phospholipids in the ER?

A

Scramblase

97
Q

What is vesicular transport?

A

The transport of one vesicle from one compartment to another

98
Q

True or false: vesicular transport can also include material

A

True: vesicles can deliver both membrane and material

99
Q

True or false: vesicular transport is a symmetric process

A

False: the donor loses membrane, and the target gains membrane

100
Q

What is the significance of vesicular transport being an asymmetric process?

A

There needs to be vesicular transport in both directions to prevent one side from losing all of its membrane

101
Q

What are the functions of the golgi?

A

Carbohydrate synthesis, sorting and dispatching products from the ER

102
Q

If a vesicle leaves the ER, what is it coated with?

A

COPII

103
Q

If a vesicle leaves the golgi, what is it coated with?

A

COPI

104
Q

True or false: every protein from the ER goes into the golgi

A

False: some proteins are ER resident and stay with the ER

105
Q

True or false: only folded proteins can leave the ER

A

True: a chaperone signal prevents the exit of misfolded proteins

106
Q

How does the ER ensure that only folded proteins can leave in vesicles?

A

Chaperones block the exit signal until it is properly folded and can leave the ER

107
Q

What are the functions of SNARE proteins?

A

Allow for vesicles to fuse together

108
Q

If a vesicle is coated with COPII, where is it going?

A

To the golgi

109
Q

If a vesicle is coated with COPI, where is it going?

A

To the ER

110
Q

What is the structure of a SNARE protein?

A

Has a v-SNARE and t-SNARE strands

111
Q

What breaks the two SNARE strands apart?

A

NSF

112
Q

What does NSF do?

A

Separates the two strands of the SNARE

113
Q

When the SNARE proteins are separated by NSF, how can they reform?

A

By binding to SNARE strands on another vesicle

114
Q

What prevents the v and t SNARES on the same vesicle from coming back together?

A

The NSF molecule

115
Q

What are the purposes of the retrieval pathway?

A

To give more membrane to the ER, and to return any ER resident proteins that accidentally made it to the golgi

116
Q

What must soluble proteins do to go back from the golgi to the ER?

A

Bind to a KDEL receptor

117
Q

What is the purpose of a KDEL receptor?

A

Bind to soluble ER resident proteins, and bring them back into the ER through the retrieval pathway

118
Q

When are the attractions between the KDEL receptor and the ER resident proteins the highest?

A

When they are both outside of the ER

119
Q

In the ER, is the KDEL receptor bound to the ER resident protein?

A

No: the binding kinetics are not favorable

120
Q

In the golgi, is the KDEL receptor bound to the ER resident protein?

A

Yes: this signals the retrieval pathway

121
Q

Where does the retrieval pathway start from?

A

Either the golgi or vesicular tubular clusters

122
Q

How is the golgi organized?

A

In a collection of flattened membranes

123
Q

What are the flattened membranes of the golgi called?

A

Cisternae

124
Q

What are cisternae?

A

Flattened membranes (pancakes) found in the golgi

125
Q

True or false: the golgi is a symmetrical structure

A

False: it has a distinct direction

126
Q

What is the cis face of the golgi?

A

Entry from the ER

127
Q

What is the trans face of the golgi?

A

Exit to various location

128
Q

Which face of the golgi is the entry from the ER?

A

The cis face

129
Q

Which face of the golgi is the exit to other locations?

A

The trans face

130
Q

What are the functions of the cisternae?

A

Finalize the functional form of the proteins, and get similar proteins in the same packaging

131
Q

True or false: each cisternae in the golgi has a unique function

A

True: they each function to finalize the final protein

132
Q

What are some examples of modifications done by the golgi?

A

Adding and removing carbohydrates, adding sulfur groups, etc.

133
Q

What is the purpose of glycosylation of proteins?

A

Helps with folding, solubility, and the state of the protein (secreted, self molecule, etc.)

134
Q

What are the two theories about transport within the golgi?

A

Vesicular transport, and cisternal maturation

135
Q

What is vesicular transport (in terms of transport within the golgi)?

A

Each cisternae can bud into the next cisternae, with a retrieval pathway

136
Q

What is the challenge of verifying the vesicular transport theory in golgi?

A

Hard to determine directional movement of vesicles

137
Q

What is cisternal maturation?

A

The cisternae transform along the chain to perform a different function

138
Q

True or false: cisternal maturation and vesicular transport are mutually exclusive

A

False: cisternal maturation theory needs some vesicular transport

139
Q

What vesicular transport is needed in the cisternal maturation theory?

A

The retrieval pathway

140
Q

What do the two theories about the golgi describe?

A

How materials move through the golgi

141
Q

Why is a retrieval pathway needed for transport within the golgi?

A

Need to be able to move specific enzymes back into the specific cisternae to carry out their function

142
Q

What are some challenges with the vesicular transport theory (in terms of transport within the golgi)?

A

Need a complicated mechanism (many receptors), and vesicles can skip a cisternae, thus skipping the function

143
Q

What is the challenge with the cisternal maturation theory?

A

The enzymes must mature with the cisternae, and that vesicle transport is there

144
Q

True or false: cisternal maturation can be the only mechanism of golgi transport

A

False: vesicles have been observed, so it can only be a part of the mechanisms

145
Q

True or false: vesicular transport can be the only mechanism of golgi transport

A

True: however, this has not been proven yet

146
Q

What is the function of the mitochondria?

A

Harvest energy

147
Q

Why do mitochondria have large internal membrane space?

A

More surface area for energy creating proteins

148
Q

How do mitochondria generate energy?

A

By using chemiosmotic coupling

149
Q

What is chemiosmotic coupling?

A

Protons moving down their concentration gradient is coupled to the creation of ATP

150
Q

Where do protons move down in their concentration gradient (in the mitochondria)?

A

Through ATP synthase

151
Q

What are the two steps of ATP formation?

A
  1. ETC pumps protons against the concentration gradient

2. Protons move down their concentration gradient through ATP synthase to generate ATP

152
Q

What energy do the pumps in chemiosmosis use?

A

Electrons from activated carriers

153
Q

What does ETC stand for?

A

Electron transport chain

154
Q

What does the ETC do?

A

Create a chain that uses electrons to pump protons across the membrane

155
Q

What molecules are involved in the ETC?

A

Proteins and small transport molecules (NADH)

156
Q

What is the input of the citric acid cycle?

A

Fats and carbohydrates

157
Q

What is the output of the citric acid cycle?

A

CO2 and activated carriers

158
Q

What is the purpose of the citric acid cycle?

A

Convert fats and carbohydrates into CO2 and activated carriers

159
Q

Where does the citric acid cycle occur?

A

In the mitochondrial matrix

160
Q

True or false: a pump in the ETC uses all the energy of the electron

A

False: it uses some of that energy to pump, and then passes it on

161
Q

What is the final electron acceptor of the ETC?

A

O2

162
Q

What is the product of the ETC?

A

H2O

163
Q

Where does water come from in the ETC?

A

Protons and O2 being reduced

164
Q

How many membranes does the mitochondria have?

A

2 (an inner and outer membrane)

165
Q

True or false: the internal spaces of the mitochondria are the same

A

False: they differ in compositions and proteins

166
Q

Where is the matrix located?

A

Within the inner mitochondrial membrane

167
Q

Where is the intermembrane space located?

A

Between the outer and inner mitochondrial membranes

168
Q

Which mitochondrial membrane is more permeable?

A

The outer membrane

169
Q

Which mitochondrial membrane is more impermeable?

A

The inner membrane

170
Q

Where are the protons pumped to during the ETC?

A

Into the intermembrane space

171
Q

Where in the mitochondria is ATP made?

A

In the matrix

172
Q

Which membrane in the mitochondria has a lot of surface area (folds)?

A

The inner membrane

173
Q

Which proteins are found in the inner mitochondrial membrane?

A

The ETC proteins, and ATP synthase

174
Q

True or false: the mitochondria was thought to be its own cell

A

True: it is thought to have originated from a symbiotic relationship with another cell

175
Q

What supports the idea that mitochondria was its own cell in the past?

A

They have their own DNA, and the citric acid cycle is not seen anywhere else

176
Q

True or false: mitochondria have their own DNA

A

True: this DNA is maternal

177
Q

True or false: the citric acid cycle is seen in many areas of life

A

False: it is only seen in the mitochondria

178
Q

What is the inner mitochondrial membrane composed of?

A

Cardiolipin

179
Q

What is the structure of cardiolipin?

A

A double phospholipid (two phospholipids connected by isopropyl alcohol)

180
Q

True or false: the cell membrane and the inner mitochondrial membrane have similar compositions

A

False: the cell membrane does not contain cardiolipin

181
Q

True or false: activated carriers can skip pumps in the ETC (ex: go from pump 1 to pump 3)

A

False: they are linked in such a way so that they must go through all of the pumps

182
Q

Which reaction in the ETC is associated with a lot of energy?

A

H2 + 1/2O2 –> H2O

183
Q

How is the energy from the creation of water in the ETC used?

A

In a series of steps

184
Q

Why is the energy from creating water broken down into a series of steps?

A

More useful work can be gained from this energy (can extract more energy in stages)

185
Q

What is the reaction of producing electrons from activated carriers?

A

NADH –> NAD+ + H-; H- –> H+ + 2e-

186
Q

How are activated carriers made?

A

Through the citric acid cycle

187
Q

What is combustion?

A

The explosive release of energy

188
Q

What is biological oxidation?

A

Harvesting energy through a series of redox reactions

189
Q

What is the disadvantage of combustion?

A

Much of the energy is lost as heat and cannot be harvested

190
Q

How is energy stored from the electrons in the ETC?

A

Pumping protons against their concentration gradient

191
Q

What reaction is powered by protons moving down their concentration gradient (in the mitochondria)?

A

ADP + Pi –> ATP

192
Q

True or false: the pumps in the ETC are all the same

A

False: they are all different

193
Q

How many pumps are usually found within the ETC?

A

3

194
Q

What is the structure of ATP synthase?

A

A stator, a rotor, and a globular head

195
Q

How does ATP synthase work?

A

It uses a chemical gradient to drive mechanical motion

196
Q

What motion does the stator go through in ATP synthase?

A

None (stationary)

197
Q

What motion does the rotor go through in ATP synthase?

A

Rotation

198
Q

What motion does the globular head go through in ATP synthase?

A

Rotation (coupled to rotor)

199
Q

Where do the protons go through in ATP synthase?

A

Between the stator and the rotor

200
Q

Where do the protons bind in ATP synthase?

A

The rotor section

201
Q

How does the rotor of ATP synthase move?

A

Through the bumping of protons (due to the high gradient)

202
Q

What are the subunits of the globular head in ATP synthase?

A

Alpha and beta

203
Q

What does the rotor rotate in ATP synthase?

A

The globular head

204
Q

What is the significance of the subunits of the globular head?

A

One subunit binds to ADP, and the other subunit binds to Pi

205
Q

How is the bond between ADP and Pi formed in ATP synthase?

A

They are physically brought together due to the rotation of the rotor

206
Q

True or false: ATP synthase is reversible

A

True: it can work in either direction

207
Q

What determines the direction of ATP synthase?

A

The ATP:ADP ratio

208
Q

What happens if ATP synthase runs in the opposite direction?

A

It uses ATP to pump protons across the membrane

209
Q

When does ATP synthase pump protons?

A

When the amount of ATP in the cell is high

210
Q

How is pyruvate moved into the intermembrane space?

A

Through the various pores

211
Q

How is pyruvate moved into the matrix?

A

Through a coupled proton symport

212
Q

How does the coupled proton / pyruvate symport work?

A

Protons move down their concentration gradient, which helps move pyruvate into the matrix for the citric acid cycle

213
Q

True or false: the proton gradient in the mitochondria is only used for ATP synthesis

A

False: it is also used to transport pyruvate into the matrix

214
Q

How is Pi moved into the matrix?

A

Through a coupled proton symport

215
Q

How does the coupled proton / Pi symport work?

A

Protons move down their concentration gradient, which helps move Pi into the matrix for ATP synthesis

216
Q

True or false: pyruvate and Pi both move into the matrix of the mitochondria through similar mechanisms

A

True: both use protons moving down their concentration gradients to get transported into the matrix

217
Q

What is ADP influx coupled to in the mitochondria?

A

ATP efflux

218
Q

What is ATP efflux coupled to in the mitochondria?

A

ADP influx

219
Q

What antiport is present in the mitochondria?

A

The ATP/ADP antiport

220
Q

True or false: transporters are found in the outer membrane of the mitochondria

A

False: the outer membrane is very permeable

221
Q

True or false: transporters are found in the inner membrane of the mitochondria

A

True: they are commonly coupled to proton gradients

222
Q

How come the outer membrane of the mitochondria has no transporters?

A

It is a fairly permeable membrane

BME 501 (5 decks)

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