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Flashcards in BIOL 360: Molecules Deck (388):
1

What enzyme keeps phosphatidylserine positioned on the cytosolic face of the plasma membrane of a living cell?

Flippase.

2

What is sphingosine?

A molecule with a 3-C backbone, linked to a fatty chain on one end, a hydroxyl group at either end, and an amine group at the central C; forms the basis of sphingolipids and glycolipids.

3

What is a lamellipodium?

A 2-dimensional cell protrusion, created by a 2-D network of actin filaments spreading outward from the cell.

4

Which actin homologues in bacterial cells help to determine cell shape?

MreB and Mbl.

5

What is YFP (yellow fluorescent protein)?

A fluorescent protein used to transgenically label specific proteins for visualization by fluorescence microscopy (emits yellow light).

6

What is the G0 phase of the cell cycle?

A prolonged interphase in a cell that stays in G1 for a very long time (or forever).

7

How do the S4 helices in voltage-gated Na+ channels trigger the conformational change that opens the channel?

When the membrane depolarizes, the extracellular side of the membrane becomes negatively charged relative to the cytosolic side, so the positively charged amino acids on the S4 helices experience an electrostatic pulling force as they are attracted to the opposite side of the membrane.

8

What happens in S phase of the cell cycle?

Genetic material is replicated (S = synthesis of genetic material).

9

What is a triacylglycerol?

A class of esters derived from glycerol and 3 fatty acids, stored in lipid droplets where they arrange in monolayers; the main form in which fat is stored.

10

What is a low-density lipoprotein (LDL)?

A spherical particle containing about 1,500 cholesterol molecules esterified to fatty acid tails, used to tranport cholesterol in the blood.

11

What are Cdc6 and Cdt1?

Proteins that collaborate with the ORC in late M/early G1 to help load inactive DNA helicases onto the DNA next to the origin of replication.

12

What is the main structural difference between cytoplasmic and axonemal (ciliary) dyneins?

Cytoplasmic dyneins are homodimers; axonemal dyneins are heterodimers or heterotrimers.

13

What is ParM?

An actin homologue in bacterial cells that helps to segregate plasmids during plasmid replication.

14

What is p21?

A Cdk inhibitor protein (CKI) in mammalian cells that suppresses G1/S- and S-Cdk activity following DNA damage.

15

What is an APC/C?

An anaphase-promoting complex (cyclosome): a complex present in anaphase that catalyzes the destruction of M- and S-cyclins and securin. 

16

What adaptor protein functions as a coincidence detector during clathrin coat assembly?

AP2.

17

Why is yeast an especially good model for studying genes involved in the cell cycle?

It can proliferate in a haploid state, so any mutant genes introduced will have their full effect (no backup wild-type gene to compensate).

18

What is the first interaction that occurs between a vesicle and its target membrane?

Binding between the vesicle's Rab-GTP and the target membrane's Rab effector.

19

What is a farnesyl anchor?

A lipid anchor that irreversibly attaches a protein to the cytosolic side of the plasma membrane with a thioether linkage between a prenyl group and a Cys residue in the protein.

20

What is a morphogen?

An extracellular signal that stimulates uncommitted stem cells to differentiate.

21

What is fimbrin?

A protein that packs actin filaments tightly together in tight parallel bundles, allowing no room for other proteins between the filaments.

22

What is Cas9?

An engineered Cas mutant that does not cleave double-stranded DNA but instead inhibits it (allowing researchers to turn off specific genes).

23

What is condensin?

A protein complex made up of 2 Smc molecules and 3 CAP proteins with a hinge domain and an ATPase domain, which forms a ring around DNA to help condense chromosomes during mitosis.

24

What is Cdh1?

A protein that maintains APC/C activity after anaphase and throughout G1 until inhibited by Cdk activity.

25

What happens to a nuclear export receptor once it reaches the cytosolic side of a nuclear pore complex?

Ran-GAP in the cytosol causes receptor-bound Ran-GTP to hydrolyze its GTP to GDP, which causes the receptor to release both Ran-GDP and its cargo protein (as Ran-GTP is no longer present to promote its binding to either). 

26

What is an Arp2/3 complex?

A complex of two actin-related proteins (ARPs) that nucleates actin filament growth from the minus end to create branching actin filaments.

27

What is Cas? How does it work?

A protein involved in the bacterial CRISPR system:

  • RNA transcribed from CRISPR locus binds a Cas protein
  • New virus injects double-stranded DNA 
  • If complementary, RNA mediates binding between Cas and foreign DNA
  • Cas cleaves foreign DNA

28

What is Cdc25 phosphatase?

A phosphatase that removes an inhibitory phosphate group (added by Wee1 kinase) from a Cdk-cyclin complex to activate it. 

29

What is a GDI (Rab-GDP dissociation inhibitor)?

A protein that binds inactive Rab-GDP and keeps it soluble in the cytosol until Rab is activated.

30

Why is it important to use conditional mutants when studying genes involved in the cell cycle?

The cell cycle needs to function correctly to generate enough cells to work with, so conditional mutants allow researchers to turn genes on long enough to get a good culture, then off to study the effects of the mutations.

31

How are intermediate filaments assembled?

  • 2 α-helical monomers form a parallel coiled-coil dimer
  • 2 dimers form a staggered, antiparallel tetramer
  • 8 tetramers associate laterally into bundles
  • Bundles link end-to-end to form filaments

32

How long does S phase take in E. coli cells?

About 20 minutes.

33

What type of linkages are formed between membrane-bound proteins and myristoyl, palmitoyl, and farnesyl anchors? 

  • Myristoyl: amide (irreversible)
  • Palmitoyl: thioester (reversible)
  • Farnesyl: thioether (irreversible)

34

How do aquaporins prevent protons from travelling through their channels?

Protons usually travel by hopping between water molecules (briefly converting them to H3O+), but strategically placed Asn residues interact with H2O within the channel so that the O has no free electrons to participate in proton relay (and the proton has no choice but to bounce back to where it came from).

35

Which kinase is needed to fully activate a Cdk-cyclin complex?

CAK (Cdk-activating kinase).

36

True or false: All linkages between lipid anchors and their associated membrane-bound proteins are post-translational.

True.

37

What are the 3 main protrusive structures in cells used for whole-cell locomotion?

  • Filopodia
  • Lamellipodia
  • Pseudopodia

38

What is treadmilling?

Movement of actin filaments by simultaneous polymerization at the plus end and depolymerization at the minus end.

39

How does the inactivation gate work in voltage-gated Na+ channels?

As soon as membrane depolarization triggers the opening of the channel, the inactivation gate automatically swings shut to keep the channel from transporting more Na+ even while the membrane is still depolarized, ensuring that membrane depolarization is propagated in one direction only.

40

What is p27?

A Cdk inhibitor protein (CKI) in mammalian cells that suppresses G1/S- and S-Cdk in G1 and helps cells withdraw from the cell cycle when they terminally differentiate.

41

How do lysosomes protect themselves from degradation by their own enzymes?

Lysosomal membrane proteins are very highly glycosylated on the inner face of the membrane, so they protect the membrane from damage.

42

What are kinesins?

A group of motor proteins that move along microtubules toward the plus end. 

43

What are the 2 functional phases of mitosis?

Cdk activity (early) and APC/C activity (late).

44

What is unique about COPI coat assembly (vs. COPII & clathrin)?

The components of their inner and outer coat layers are recruited as a preassembled complex (coatomer).

45

What is a γ-tubulin ring complex (γ-TuRC)?

A complex of 7 γ-TuSC subunits in an overlapping spiral structure that acts as a template for microtubule nucleation.

46

What is SCAP (SREBP cleavage activation protein)?

A protein normally associated with SREBP in the ER membrane: at high [cholesterol], it has cholesterol bound, but at low [cholesterol], its lack of cholesterol triggers a conformational change that causes SCAP and SREBP to be transported to the Golgi, where SREBP is processed so that it can act as a transcription regulator for cholesterol synthesis. 

47

Where does a nuclear pore complex get the energy to drive active transport of proteins into the nucleus?

Ran (Ras-related nuclear GTPase). 

48

What fluorescent dye is used to stain DNA for visualization by fluorescence microscopy?

DAPI.

49

What is a t-SNARE?

A protein complex of 2 or 3 proteins found on a vesicle or target membrane that binds to a specific v-SNARE on a complementary target membrane or vesicle to form a trans-SNARE complex.

50

Why can the same cyclin-Cdk complex induce different effects at different times in the cell cycle?

The accessibility of some Cdk substrates changes during the cell cycle, so some targets are only available for phosphorylation at certain times.

51

What happens in M phase of the cell cycle?

Mitosis and cytokinesis.

52

In a nuclear pore complex, how do the fibrils attached to channel nucleoporins help with transport?

  • Form a tangled mesh that makes it difficult for unwanted molecules to diffuse through
  • Contain FG repeats as binding sites for nuclear receptors, which let them "hop" through the channel

53

What is monitored at the first cell-cycle checkpoint (start transition)?

Whether the environment is favourable for division.

54

What is a V-type proton pump?

An ATP pump activated by a single phosphorylation event to drive active transport of protons; used to regulate pH.

55

How does acetylcholine interact with GPCRs to reduce the rate and strength of heart muscle cell contraction?

  • Acetylcholine binds GPCR
  • GPCR activates Gi protein
  • Gi-α inhibits adenylyl cyclase, reducing [cAMP]
  • Gi-βγ opens K+ channels, making it more difficult for the cell to depolarize

56

When in the cell cycle is G1/S-cyclin active?

G1: the cyclin is made just after the start point and degraded at the beginning of S-phase.

57

What is a major difference between myosins (actin-associated motor proteins) and kinesins (microtubule-associated motor proteins)?

  • Myosins: 
    • No ATP: tightly bound to filament
    • ATP: released from filament
  • Kinesins:
    • No ATP: released from filament
    • ATP: tightly bound to filament

58

Which two major classes of binding proteins regulate actin filament behaviours?

  • Proteins that bind along the side of a filament
  • Proteins that bind to the ends of a filament

59

How does M-Cdk participate in a positive feedback loop to promote activation of more M-Cdk?

M-Cdk activates CAK (Cdk-activating kinase) and inhibits Wee1 (a Cdk inhibitor). 

60

What is DNA catenation?

The interlocking of DNA strands between sister chromatids to make them inseparable until cleaved and re-sealed by topoisomerase II. 

61

True or false: Transporters can be involved in either active or passive transport.

True.

62

What happens to Rab-GTP once it has bound to its corresponding Rab effector on its vesicle's target membrane?

It is hydrolyzed to Rab-GDP and becomes soluble in the cytosol.

63

What is the difference between homotypic and heterotypic fusion?

  • Homotypic: membranes are from the same compartment, and SNARE interaction is symmetrical (v-SNAREs and t-SNAREs contributed by both membranes)
  • Heterotypic: membranes are from different compartments, and SNARE interaction is asymmetrical (v-SNAREs on 1 membrane, t-SNAREs on the other)

64

How long does the S phase take in human cells?

About 12 hours (to fully replicate the human genome).

65

What happens to PI(4,5)P2 when it is cleaved by PLCβ?

It splits into diacylglycerol and inositol 1,4,5-trisphosphate (IP3); diacylglycerol stays bound to the plasma membrane, and IP3 becomes soluble in the cytosol, and both recruit further signalling molecules.

66

What is the key difference between FITC (fluorescent dye) and GFP/CFP/RFP/YFP (fluorescent proteins)?

FITC is added to a sample to stain all proteins non-selectively; fluorescent proteins must be added transgenically to proteins and can be used to tag specific proteins of interest for visualization.

67

What is clathrin?

A vesicular coat protein found on vesicles budding toward the cytosol from the plasma membrane or from the trans-Golgi membrane.

68

What is DAPI?

A fluorescent dye used to stain DNA for visualization by fluorescence microscopy.

69

What is a Na+-driven glucose symport?

A transporter that couples the active transport of glucose with the passive transport of Na+ into the cell

70

What is the role of PIP phosphatases in vesicle formation?

They remove a phosphate group from the PIP to which the coat assembly adaptor protein is bound, causing the adaptor protein and therefore the coat protein to dissociate from the completed vesicle.

71

What is the role of kinetochore microtubules in the mitotic spindle?

They attach to the chromatids at 1 end (plus) and to the centrosomes at the other (minus), and they pull the chromatids apart to either end of the cell during anaphase.

72

Which two transport proteins create and maintain the membrane potential in animal cells?

  • Na+-K+ pump (P-type pump/transporter)
  • K+ leak channel (ion channel)

73

What is p16?

A Cdk inhibitory protein (CKI) in mammalian cells that suppresses G1-Cdk activity in G1 (frequently inactivated in cancer).

74

Which actin homologue in bacterial cells helps during plasmid segregation?

ParM.

75

Which forms of Ran are found inside and outside of the nucleus?

  • In the nucleus: Ran-GTP
  • In the cytosol: Ran-GDP

76

What is Rab?

A monomeric GTPase that labels vesicles according to their membrane domain or organelle of origin and that helps vesicles tether and dock to their target membrane.

77

What is the simplest mechanism for intercellular communication in multicellular organisms?

Gap junctions.

78

What are Sec23/24 and Sec13/31?

2 sets of proteins that function as GAPs for Sar1-GTP in COPII-coated vesicles, promoting hydrolysis of Sar1-GTP to Sar1-GDP to trigger shedding of the protein coat once the vesicle is complete.

79

What is the role of interpolar microtubules in the mitotic spindle?

The minus ends are attached to the centrosomes at either end of the cell, and the plus ends of opposite MTs interact via kinesins to push and pull on the centrosomes until the entire apparatus is positioned correctly for anaphase.

80

What happens to transport vesicles once they have budded off from the ER?

They shed their COPII coats and fuse with one another to form vesicular tubular clusters, which then bud off transport vesicles of their own that have COPI coats.

81

Is [K+] higher inside or outside a cell? How is this maintained?

Inside (as maintained by Na+-K+ pumps and K+ leak channels).

82

What are the 3 main types of ATP pumps?

  • P-type pumps
  • ABC transporters
  • V-type proton pumps

83

What triggers the opening of a mechanically gated ion channel?

High osmotic pressure causes the surrounding membrane to stretch and pull the channel pore open.

84

How does activation of two different G proteins by GPCRs result in the localized activation of Rac and Rho pathways at the front and back, respectively, of a moving lamellipodium?

  • Rac: G protein activates PI 3-kinase to create membrane-bound PI(3,4,5)P3, which activates the Rac pathway at the front of the cell
  • Rho: G protein dissociates into Gα & Gβγ, which can diffuse further down the cell to activate the Rho pathway at the back 

(Rac inhibits Rho, so any Rho components activated at the front are immediately inactivated by Rac activity.)

85

What is a glycolipid?

A membrane lipid based on sphingosine, containing a single fatty acid tail (in addition to the fatty chain of sphingosine) and one or more sugars (where sphingolipids would have a phosphate group attached instead).

86

How does the use of COPII in ER vesicles and COPI in vesicular tubular cluster vesicles reduce the number of ER resident proteins accidentally leaving the ER?

ER resident proteins have a higher affinity for COPI than for COPII, so they are less likely to end up in vesicle budding from the ER and more likely to end up in retrograde transport vesicles from the clusters.

87

How do mechanically gated ion channels protect cells from rupturing due to osmotic pressure?

Osmotic pressure increases when cells take up water in response to increased ion concentration, so the opening of mechanically gated channels to move ions out of the cell results in water also leaving the cell to maintain the concentration gradient.

88

Which protein complexes are responsible for inserting proteins into the inner membrane of the mitochondria?

TIM22, TIM23, and OXA.

89

What fluorescent dye is used to stain proteins (non-selectively) for visualization by fluorescence microscopy?

FITC.

90

What does cohesin interact with in order to form a ring around sister chromatids to keep them together until anaphase?

2 Smc molecules.

91

What is a phosphoglyceride?

A type of membrane phospholipid based on a glycerol backbone, with 2 fatty acid tails, a phosphate group, and one of several possible head groups. 

92

What is an inositol phospholipid?

A minor class of phospholipids that are phosphorylated to form phosphoinositides during cell signalling events.

93

What does TIC stand for?

Translocator of the inner chloroplast membrane.

94

What is separase?

An enzyme that cleaves cohesin so that sister chromatids can be separated into daughter cells during cell division.

95

What is an SRP receptor?

A receptor bound to the cytosolic face of the ER membrane that binds incoming SRPs, allowing protein translocators to bind to the SRP-bound protein's signal sequence, which causes the associated ribosome to resume translation and the SRP to be released back into the cytosol.

96

What is a BAR domain protein?

A positively charged, crescent-shaped protein that helps to deform the plasma membrane via electrostatic interactions during clathrin coat assembly in vesicle formation.

97

Which vesicles are assembled with COPI or COPII protein coats?

Vesicles transported between the Golgi and the ER.

98

Where are centrosomes (MTOCs) usually located in the cell?

At the centre, with microtubules radiating outward (astral configuration).

99

How is cholesterol transported to cells?

Cholesterol aggregates within LDLs, which travel through the bloodstream and are bound by LDL receptors on the outer surface of cell membranes, which then trigger the assembly of clathrin-coated vesicles for import from the plasma membrane.

100

What are glutaraldehyde and osmium tetroxide used for in cell work?

To fix samples for electron microscopy.

101

What is the basic structure of a voltage-gated Na+ channel?

  • 1 polypeptide made up of 4 similar domains, meeting in a ring to form a central channel
  • Selectivity filter between α-helices 
  • Inactivation gate between domains 3 and 4 
  • Lateral portals connecting the central cavity to the hydrophobic portion of the membrane

102

Which proteins act as chaperones for precursor proteins destined for import into the mitochondria?

Cytosolic hsp70.

103

What sugar groups are found in the core region of the precursor oligosaccharide added to glycosylated proteins in the ER?

2 GlcNAc and 3 mannose.

104

What are the different responses to acetylcholine in skeletal muscle cells, heart pacemaker cells, and salivary gland cells?

  • Skeletal muscle: muscle contraction
  • Heart pacemaker: decreased firing rate
  • Salivary gland: secretion

105

What is a K+ leak channel?

A channel protein that allows the diffusion of K+ across the plasma membrane to maintain the membrane potential of the cell by regulating cytosolic [K+].

106

How does the hsp70 chaperone protein interact with clathrin-coated vesicles?

It functions as an uncoating ATPase to help strip off the clathrin coat once the vesicle has detached from its donor membrane.

107

What happens to a nuclear import receptor once it has entered the nucleus through a nuclear pore complex?

Ran-GTP in the nucleus binds to the receptor, causing the receptor to dissociate from its cargo protein.

108

What is a sphingolipid?

A membrane lipid based on sphingosine, which incorporates a fatty chain tail capped by a hydroxyl group, with one additional fatty acid tail, a phosphate group, and one of several possible head groups.

109

Which 3 kinesins interact with microtubules to position the mitotic spindle?

  • Kinesin-5 (where antiparallel microtubules meet; pushes poles outward)
  • Kinesin-14 (pulls poles inward)
  • Kinesin-4,10 (pulls DNA toward the centre of the spindle)

110

In the context of voltage-gated Na+ channels, what is the refractory period?

The time necessary for enough Na+ channels to recover from inactivation to support a new action potential.

111

What is galactocerebroside?

A glycolipid with a galactose residue at its head, found most commonly in myelin sheaths.

112

Which type of filament's rapid assembly and disassembly drives the rapid movement of neutrophils?

Actin filaments.

113

What is FITC?

A fluorescent dye used to stain proteins non-selectively for visualization by fluorescence microscopy.

114

What are the 2 main signalling pathways that can follow from phosphorylation of PI(4,5)P2 by PI 3-kinase to PI(3,4,5)P3?

  • PI(3,4,5)P3 can act as a docking site for intracellular signalling proteins
  • PI(3,4,5)P3 can be cleaved by phospholipase C, with diacylglycerol remaining in the membrane and the rest of the molecule (IP3) diffusing into the cytosol, so each portion participates in different signalling activities

115

Which protein coat is found on vesicles transported from the ER to the Golgi?

COPII.

116

What two proteins form a complex to nucleate actin filaments in branching actin filament assemblies?

Arp2 and Arp3.

117

What is an ion channel?

A channel protein used to passively transport ions across a membrane.

118

What molecule activates condensin to trigger chromosome condensation during mitosis?

M-Cdk (by phosphorylation).

119

What does TOC stand for?

Translocator of the outer chloroplast membrane.

120

What is rhodamine B?

A fluorescently labelled antibody used to visualize specific proteins by fluorescence microscopy (emits red light).

121

What molecules are exchanged by the Ca2+ pumps found in the sarcoplasmic reticulum?

2H+ for 2Ca2+.

122

What is synaptotagmin?

A protein jutting out of a primed synaptic t-SNARE/v-SNARE-complexin complex that contains Ca2+ binding sites, responsible for activating the complex to allow release of neurotransmitters when a signal is received.

123

Which motor proteins are associated with actin filaments?

Myosins.

124

What is a kinetochore?

A protein that creates a binding area at the centromere of each chromatid for attachment of kinetochore microtubules during anaphase.

125

What is a polyprotein?

A single large protein that yields many copies of the same (smaller) protein when cleaved into fragments.

126

When does K+ stop diffusing out of a cell through a K+ leak channel?

When the electrical gradient opposes further K+ diffusion (even when the chemical gradient favours it).

127

How do CKIs inactivate cyclin-Cdk complexes?

By stimulating a large rearrangement in the structure of the Cdk active site, making it completely unable to bind its protein substrates.

128

Why is it important during mitosis that kinesin-14 walks in the opposite direction to all the other kinesins?

Kinesin-14 and kinesin-5 both interact with microtubules to position the mitotic spindle, and coordinated pushing and pulling allows more precise positioning of the centrosomes and DNA.

129

What is a protein signal sequence?

A sequence of amino acids in a protein that is recognized by sorting receptors and determines where in the cell the protein will be localized.

130

What is Rac-GTPase?

A monomeric GTPase that activates PAK and WASp family proteins, resulting in increased formation of branched actin webs and decreased formation of stress fibres in lamellipodia.

131

What is Smc?

A protein that binds in pairs via cohesin to form rings around sister chromatids, keeping them together until anaphase.

132

What is the basic structure of an individual clathrin protein?

A triskelion, with 3 heavy chains and 3 light chains.

133

What are axonemal (ciliary) dyneins?

Dyneins involved in beating of cilia and flagella. 

134

What is Wee1 kinase?

A kinase that adds an inhibitory phosphate group to inactivate Cdk-cyclin complexes.

135

What does TIM stand for?

Translocator of the inner mitochondrial membrane.

136

How do morphogens determine the differentiation pathway of undifferentiated cells?

A morphogen concentration gradient: cells closer to the source have more receptors activated than cells further away, so cells at different positions along the gradient will react differently depending on how many receptors are activated in each.

137

What two layers of specificity are conferred by glyosyl transferases in the synthesis of glycosylated proteins?

  • Different sugars require different transferases (each enzyme is specific to one sugar)
  • Different cell types contain different transferases

138

True or false: Once a cell has reached its start point (restriction point) in the cell cycle, it is irreversibly committed to repeating the entire cycle (from G1 to S).

True (even if conditions become unfavourable for division).

139

What 3 domains are characteristic of a nuclear receptor protein?

  • Ligand-binding domain
  • DNA-binding domain
  • Transcription-activating domain

140

What are WASp family proteins?

Proteins activated by Rac-GTP that activate Arp2 & Arp3 to stimulate nucleation of branched actin filaments, resulting in the formation of a branched actin web in lamellipodia. 

141

What is a filapodium? 

A 1-dimensional cell protrusion, created by a single actin filament extending from the cell.

142

How do motor proteins generate the energy needed to move along cytoskeletal filaments?

From repeated cycles of ATP hydrolysis. 

143

What enhances the hydrolysis of GTP to GDP to inactivate G proteins?

RGS (regulator of G-protein signalling).

144

What is geminin?

A protein that inhibits Cdt1 in late G1 to prevent the formation of new preRCs.

145

What is PAK?

A kinase activated by Rac-GTP that inhibits MHC & MLCK, resulting in decreased myosin activity (and thus decreased stress fibre formation), and activates filamin, resulting in increased formation of branched actin webs in lamellipodia.

146

What is RFP (red fluorescent protein)?

A fluorescent protein used to transgenically label specific proteins for visualization by fluorescence microscopy (emits red light).

147

What is the difference between a voltage-gated Na+ channel in its closed state and in its inactive state?

An inactive channel is unable to reopen until after the membrane potential has returned to its initial negative value, while a closed channel is free to be reopened as soon as another action potential is initiated.

148

What does TOM stand for?

Translocator of the outer mitochondrial membrane.

149

Where are all transmembrane proteins made?

In the ER (except for transmembrane mitochondrial/chloroplast proteins).

150

Why do glycerols and cholesterol esters arrange themselves in monolayers rather than bilayers?

They have no hydrophilic portion.

151

What is a signal recognition particle (SRP)?

A protein-RNA complex that recognizes and binds emerging ER-import signal sequences of proteins being synthesized, pauses translation, and delivers the ribosome and protein to the ER membrane.

152

What is a transmitter-gated ion channel?

A type of ion channel found in cells on either side of a chemical synapse for highly selective transport of specific neurotransmitters.

153

What molecule is required for a nuclear import receptor to successfully deliver its protein cargo to the nucleus?

Ran-GTP.

154

What is the main functional difference between myosin II and myosin V?

Myosin V has a longer lever arm domain, so it can swing further with each "step".

155

What is an inhibitory neurotransmitter?

A neurotransmitter that prevents membrane depolarization by causing Cl- or K+ channels to open, which makes it harder for Na+ channels to create an overall positive charge inside the cell.

156

Which 3 processes in early mitosis are regulated entirely by M-Cdk?

  • Mitotic spindle assembly (and chromatid attachment)
  • Chromosome condensation
  • Nuclear envelope disassembly

157

Which phosphoglyceride is found only on the cytosolic face of plasma membranes?

Phosphatidylserine.

158

What is the key property of signal sequences labelling proteins destined for the mitochondria?

Positive charge.

159

What is cofilin?

A protein that binds actin filaments and adds mechanical stress to induce disassembly at the lagging end of a net array during whole-cell movement by lamellipodia.

160

How are α- and β-tubulin oriented in tubulin dimers?

  • β-tubulin toward the plus end 
  • α-tubulin toward the minus end

161

What is a v-SNARE?

A single protein extending from a vesicle or target membrane that fuses with its corresponding t-SNARE complex on the complementary target membrane or vesicle to form a trans-SNARE complex.

162

What are the three main types of gated ion channels?

  • Voltage-gated ion channels
  • Ligand-gated ion channels
  • Mechanically gated ion channels

163

What is flippase?

An enzyme that keeps phosphatidylserine positioned on the cytosolic face of the plasma membrane until apoptosis is triggered, when it flips phosphatidylserine to the outer face of the membrane to flag the cell for phagocytosis.

164

What are dyneins?

A group of motor proteins that move along microtubules toward the minus end. 

165

What is a complex oligosaccharide?

An oligosaccharide that has been extensively modified in the Golgi, with sugar groups removed and new ones added (where binding sites are readily accessible).

166

Is the membrane potential of animal cells typically positive or negative?

Negative.

167

What is Sic1?

A Cdk-inhibitor protein (CKI) in budding yeast cells that suppresses Cdk1 activity in G1.

168

When do cells usually use CKIs to inhibit cyclin-Cdk complexes?

Early in the cell cycle (to regulate G1/S- and S-Cdks).

169

Which is the most important class of enzyme-coupled cell-surface receptors?

Receptor tyrosine kinases (RTKs).

170

How does tetanus cause muscles to lock up?

The toxin blocks synaptic transmissions by cleaving SNARE proteins in the nerve terminal so that vesicles containing neurotransmitters can no longer fuse with synaptic membranes.

171

How do the pore helices of K+ channels contribute to the selectivity of the channel for K+?

The helices are amphiphilic, with carbonyl Os on the selectivity loop (on the hydrophilic side of each helix) that jut out into the narrow selectivity filter, where they form transient bonds with K+ to strip its hydrate shell (Na+ is too small to form enough bonds to overcome the energy barrier to dehydration).

172

What happens to centrosomes/MTOCs during cell division?

The centrosomes duplicate as well, and they move apart from the centre of the cell to form the mitotic spindle.

173

What is calcineurin?

A phosphatase that dephosphorylates inactive NF-AT in the cytosol of a resting T-cell, blocking nuclear export signals and exposing nuclear import signals on NF-AT so that it can enter the nucleus and activate transcription of genes needed for T-cell activation.

174

When measuring voltage across membranes with voltage-gated ion channels, why does the patch current show individual, identical peaks, while the aggregate current shows a steady incline or decline?

The current is always the same at each individual channel (open current or closed current), but the combined activity of all channels in a region of membrane results in a steady slope according to the direction of signal propagation.

175

What happens to microtubules during catastrophe in dynamic instability?

The T-cap at the plus end is lost, and the remaining D-form subunits begin to peel apart, depolymerizing the microtubule. 

176

What is a centrosome/MTOC (microtubule organizing centre)?

A spherical structure in animal cells composed of a centrosome matrix, which is studded with 50 or more γ-TuRCs (nucleation sites for microtubules) and has microtubules growing radially outward from them, and which in animal cells contains a pair of centrioles.

177

What is the difference between MAPs (cytoskeletal) and MAP kinases (signalling)?

  • Cytosketal: MAP = microtubule-associated protein
  • Signalling: MAP = mitogen-associated protein 

178

What are the two sources of energy for active transport of proteins into the mitochondria?

  • ATP hydrolysis
  • Membrane potential

179

What is cholesterol?

A sterol found within membranes that increases membrane fluidity and decreases membrane permeability; contains a polar head group, a rigid steroid ring structure, and a nonpolar hydrocarbon tail.

180

What happens to a partly active Cdk-cyclin complex when it is activated by a CAK?

The CAK phosphorylates an amino acid near the entrance of the Cdk active site, causing a small conformational change that improves the ability of Cdk to bind its protein substrates.

181

True or false: About 1/3 of a cell's energy goes toward driving Na+-K+ pumps.

True.

182

What is dynamin?

A protein that helps to cleave a budding vesicle from its donor membrane once its protein coat is fully assembled.

183

What two gates are present in ER protein translocators?

  • Lateral gate: allows hydrophobic portions of proteins to diffuse into the ER membrane
  • Pore gate: allows hydrophilic portions of proteins to diffuse into the ER lumen

184

Which motor proteins are associated with microtubules?

Dyneins and kinesins.

185

What is the difference between a homomeric connexon and a heteromeric connexon?

  • Homomeric: all connexin subunits are of the same type
  • Heteromeric: contains different types of connexin subunits

186

In what direction do most myosins travel along actin filaments?

Toward the plus end.

187

What is the difference between interphase and mitosis with respect to microtubule configuration in the cell?

  • Interphase: a few long microtubules in astral configuration (radiating from the centrosome)
  • Mitosis: many shorter, more dynamic microtubules between 2 poles of the mitotic spindle

188

What is Sar1?

A coat-recruitment GTPase involved in COPII coat assembly during vesicle formation.

189

What is Cy3?

A fluorescently labelled antibody used to visualize specific proteins by fluorescence microscopy (emits yellow light).

190

How is nuclear envelope assembly and disassembly regulated?

By phosphorylation: 

  • Disassembly: phosphorylation by M-Cdk
  • Assembly: dephosphorylation by APC/C

191

How do positive feedback and inactivation contribute to the propagation of action potentials by voltage-gated Na+ channels?

  • Channels open when membrane potential becomes positive
  • Na+ import makes m.p. even more positive: opens  surrounding channels
  • Opened channels immediately inactivated: only the ones they have triggered are open
  • Inactive channels can't reopen: signal can only go forward

192

What is GFP (green fluorescent protein)?

A fluorescent protein used to transgenically label specific proteins for visualization by fluorescence microscopy (emits green light).

193

What is Mia40?

A protein that helps to pull proteins through the TOM complex into the mitochondrial intermembrane space with formation of disulfide bonds. 

194

What must be true of the cargo receptors in the plasma membrane before adaptor proteins can bind to them to initiate clathrin coat assembly for vesicle formation?

The cargo receptors must be displaying endocytosis signals on their cytosolic domains (indicating that they have bound cargo).

195

What are the 3 classes of microtubules involved in the mitotic spindle apparatus?

  • Astral microtubules
  • Kinetochore microtubules
  • Interpolar microtubules

196

What is the difference between proteoglycans and glycoproteins?

Proteoglycans typically have longer sugars that are attached differently than in glycoproteins.

197

What is SCF?

A protein complex that catalyzes the ubiquitylation of regulatory proteins involved in G1 control, including CKIs, to allow activation of Cdks at the start of the cell cycle.

198

What is phospholipase C-β (PLCβ)?

A plasma-membrane-bound enzyme activated by GPCR-associated Gq that cleaves PI(4,5)P2 to generate IP3 and diacylglycerol, splitting the signalling pathway into two branches (plasma membrane and cytosol).

199

Which cytoskeletal filament subunits also function as enzymes?

Actin (ATP hydrolysis) and tubulin (GTP hydrolysis).

200

What is taxol?

A cancer drug (derived from yew cells) that binds and stabilizes microtubules to keep cells from growing and dividing aggressively.

201

When are Ca2+ pumps activated in the sarcoplasmic reticulum?

As soon as there is any Ca2+ in the cytosol (e.g. following a signalling event): the pumps maintain a low cytosolic [Ca2+] so that only a small increase in [Ca2+] is enough to trigger a signalling event.

202

What is an aquaporin?

A special type of channel protein that allows the transport of pure water only (no ion transport).

203

What is colchicine?

A toxin found in autumn crocus that binds free tubulin subunits to prevent microtubule polymerization.

204

In what 2 ways can chromosomes be attached to microtubules in the mitotic spindle?

  • Directly, via kinetochores
  • Indirectly, via motor proteins

205

What type of enzyme is APC/C?

Ubiquitin ligase.

206

What is the active form of Rab, found on vesicle membranes?

Rab-GTP.

207

What does the ABC in ABC transporter stand for?

ATP-binding cassette.

208

What is phalloidin? 

A toxin made by Amanita mushrooms that inhibits actin filament depolymerization, preventing actin filaments from rearranging and thus cells from moving.

209

What is securin?

A protein that inhibits separase to keep sister chromatids from separating until the cell is ready to divide. 

210

Which protein complexes are responsible for inserting proteins into the outer membrane of the mitochondria?

TOM and SAM.

211

What is an excitatory neurotransmitter?

A neurotransmitter that stimulates membrane depolarization by causing Na+ channels to open.

212

What is a γ-tubulin small complex (γ-TuSC)?

A complex made up of two γ-tubulins and accessory proteins that forms a subunit of a γ-tubulin ring complex (γ-TuRC), which acts as a template for microtubule nucleation.

213

How is GTP associated with the subunits of α-/β-tubulin dimers?

  • α: GTP is trapped and never hydrolyzed
  • β: GTP is accessible and can be hydrolyzed

214

What is phosphatidylethanolamine?

A common membrane phosphoglyceride incorporating ethanolamine into its head group. 

215

What is a palmitoyl anchor?

A lipid anchor that reversibly attaches a protein to the cytosolic side of the plasma membrane with a thioester linkage between a palmitic group and a Cys residue on the protein.

216

What is CapZ?

A protein that caps actin filaments at the plus end.

217

How are escaped soluble ER resident proteins returned to the ER?

They bind to KDEL receptors in the Golgi, which recognize the KDEL sequence (labelling them as ER residents) and packages them into COPI-coated vesicles for transport back to the ER.

218

What is a connexin?

A monomeric subunit of a connexon; 6 connexins join to form a connexon, which is one half of a gap junction.

219

True or false: Intrachain disulfide bonds within transmembrane proteins can be found on either side of the plasma membrane.

False: Intrachain disulfide bonds are only found on the extracellular side of the plasma membrane.

220

What is arrestin?

A protein that binds to phosphorylated GPCRs to prevent them from interacting with their associated G proteins, desensitizing the receptor.

221

How is calcineurin activated in resting T-cells?

By an increase in [Ca2+] resulting from a signal cascade.

222

What is Cy5?

A fluorescently labelled antibody used to visualize specific proteins by fluorescence microscopy (emits red light).

223

What main structural difference makes ion channels faster than transporters?

Ion channels don't bind their substrates, so once they are open, ions can flow freely through without taking time to bind anywhere (at millions of ions per second).

224

What triggers the opening of a voltage-gated ion channel?

A change in membrane potential (difference in charge on either side of the membrane).

225

What is the difference between kinesin-14 and all other kinesins?

All other kinesins walk along microtubules toward the plus end, but kinesin-14 walks toward the minus end.

226

What 4 features do myosins, kinesins, and dyneins have in common?

  • All use ATP hydrolysis 
  • All are unidirectional
  • All have a head region containing the motor, which recognizes the right "track" and determines direction of travel
  • All have a tail region that determines the cargo and biological function of the motor protein

227

What is the difference between a phosphoinositol (PI) and a phosphoinositide (PIP)?

A PIP is a PI that has been phosphorylated at position 3, 4, and/or 5 of its inositol head group.

228

What is an origin recognition complex (ORC)?

A large protein complex that binds to replication origins on DNA throughout the cell cycle, eventually collaborating with Cdc6 and Cdt1 to form the preRC.

229

What is a connexon?

A cylindrical structure made up of 6 connexin subunits, forming one half of a gap junction.

230

Why do chloroplasts have more protein import signals and transport pathways than mitochondria?

Chloroplasts have thylakoids, so they have an extra set of membranes and compartments to regulate.

231

Why do chloroplasts need additional energy sources (compared to mitochondria) to drive active transport of proteins?

Chloroplasts have no electrochemical gradient across their internal membranes, so they can only rely on energy from ATP or GTP. 

232

What is phosphatidylserine?

A common membrane phosphoglyceride, incorporating serine into its head group, with an overall negative charge; found only on the cytosolic face of plasma membranes.

233

What is glycosylphosphatidylinositol (GPI anchor)?

A glycolipid that attaches to the C-terminus of a protein to anchor it on the extracellular face of the plasma membrane. 

234

What is cohesin?

A protein that holds sister chromatids together during cell division until they are ready to be separated into daughter cells.

235

What is a P-type pump?

An ATP pump activated by a single phosphorylation event to actively transport ions.

236

What are the 3 functional domains of the Ca2+ pump found in the sarcoplasmic reticulum? What do they do?

  • Nucleotide-binding domain (binds ATP)
  • Phosphorylation domain (contains Asp to be phosphorylated)
  • Activator domain (changes conformation on activation to allow phosphorylation of Asp by bound ATP)

237

What is CFP (cyan fluorescent protein)?

A fluorescent protein used to transgenically label specific proteins for visualization by fluorescence microscopy (emits blue light).

238

What are the 4 main functions of glycosylation?

  • Promotes protein folding
  • Makes proteins more resistant to digestion
  • Has regulatory roles (recognition, communication, etc.)
  • Protects cells against pathogens and other damage

239

Why is it important that the trans-SNARE complex needs to be actively disassembled after vesicle-membrane fusion?

It provides an extra level of regulation: SNAREs are only active when needed, so membranes and vesicles can only fuse when they need to, not just when they happen to come in contact.

240

What is GPCR kinase (GRK)?

A kinase that phosphorylates activated GPCRs at multiple sites to create a binding site for arrestin, which desensitizes the receptor.

241

Why are SCF complexes inactive whenever APC/C is active?

SCF complexes can only recognize target CKIs that have been phosphorylated by Cdks, and Cdks are inactivated by APC/C activity. 

242

How do we know that chromosomes have some active role in mitotic spindle formation and activity?

If 1 chromosome is artificially severed from the microtubules and moved elsewhere in the cell, new microtubules form and assemble next to the chromosome.

243

What is monitored at the third cell-cycle checkpoint (metaphase/anaphase transition)?

Whether all chromosomes are attached properly to the mitotic spindle.

244

How does signalling via the IP3-gated Ca2+-release channel work?

  • PLCβ cleaves PI(4,5)P3 to IP3 and diacylglycerol
  • IP3 diffuses as an intracellular signalling molecule to trigger release of Ca2+ from the ER
  • Ca2+ activates PKC, which travels to the membrane to phosphorylate target proteins
  • Diacylglycerol acts as a second messenger to help with activation of PKC and amplify the signal

245

What is complexin?

A protein that holds partially assembled (primed) v-SNARE/t-SNARE complexes in place at synaptic membranes until triggered by an incoming signal (via [Ca2+] increase), at which point complexin is released and the trans-SNARE complex forms completely, allowing fusion of synaptic vesicles.

246

What is dynamic instability?

Movement of microtubules by alternating polymerization (rescue) and depolymerization (catastrophe) at the GTP-capped plus end. 

247

What triggers the opening of a ligand-gated ion channel?

The binding of some specific ligand to a ligand binding site on the outside of the channel (which may be on either side of the membrane).

248

What is a high-mannose oligosaccharide?

An oligosaccharide that has had sugars cut off but no new sugars added in the Golgi (where no binding sites were accessible for additional sugars).

249

What are (cytoskeletal) MAPs?

Microtubule-associated proteins.

250

What are formins?

Dimeric proteins that nucleate the growth of straight, unbranched actin filaments.

251

What is a glycoprotein?

A transmembrane protein that has been glycosylated, with sugar residues extending into extracellular space, involved in cell protection and cell-cell recognition.

252

What is thymosin?

A protein that binds free actin monomers to keep them from being added to actin filaments.

253

What is a CRE-binding protein (CREB)?

A transcription regulator activated by PKA that recognizes the CRE sequence within cAMP-regulated genes and recruits a transcriptional coactivator (CBP) to stimulate transcription of target genes.

254

Which type of protein nucleates actin filaments for formation of straight, unbranched filaments?

Formins.

255

What is a myristoyl anchor?

A lipid anchor that attaches proteins irreversibly to the cytosolid side of the plasma membrane by an amide linkage between myristic acid and the N-terminus of the protein.

256

What is a gap junction?

A narrow water-filled channel that directly connects adjacent cells to allow symmetric exchange of inorganic ions and small, water-soluble molecules.

257

What are cytoplasmic dyneins?

Dyneins involved in vesicular transport and in localizing the Golgi in all eukaryotic cells.

258

How does APC/C activation at the end of mitosis lead to the formation of new preRCs for the next cell cycle?

APC/C activation leads to inactivation of Cdks and destruction of geminin, resulting in the reactivation of ORC, Cdc6, and Cdt1, which are free again to form preRCs.

259

Which component of the preRC stays attached to DNA after the rest of the complex has dissociated in S phase?

Mcm helicase (to help during elongation).

260

What is a Na+-K+ pump?

A transporter that actively transports K+ into the cell and Na+ out of the cell to maintain the resting potential across the membrane and the concentration of Na+ inside the cell for Na+-driven transport.

261

What is Arf1?

A coat-recruitment GTPase involved in COPI and clathrin coat assembly during vesicle formation.

262

What is a Rab effector?

A long protein chain extending from target membranes into the cytosol that recognizes and binds specific Rab-GTP units on incoming vesicles to help tether and dock vesicles to their target membrane.

263

Why are voltage-gated Na+ channels wider than K+ channels?

The Na+ channels transport Na+ with a partial or complete hydrate shell, which is wider than a dehydrated K+ ion (which fits through the K+ channel) but smaller than a hydrated K+ ion (which is too big for the Na+ channel).

264

What are acid hydrolases?

Enzymes found in lysosomes that function only at low pH to degrade specific types of macromolecules.

265

Where is proteoglycan assembly completed?

In the Golgi.

266

What is a trans-SNARE complex?

A complex formed by the binding of complementary t-SNAREs and v-SNAREs on a vesicle and its target membrane, which excludes water to bring the two membranes close enough for fusion and delivery of the vesicle's contents.

267

What is XMAP215?

A protein that stabilizes microtubules and enhances growth rate at the plus end to prevent catastrophe (depolymerization). 

268

What is filamin?

A protein that binds at overlapping actin filaments to stabilize net-like actin assemblies.

269

Which cytoskeletal filaments are necessary for whole-cell locomotion via filopodia, lamellipodia, or pseudopodia?

Actin filaments.

270

What molecules are exchanged by a Na+-K+ pump?

2K+ for 3Na+.

271

What is the role of topoisomerase II in cell division?

To cleave catenated DNA between sister chromatids so that the chromatids can be separated in anaphase.

272

For which 3 proteins does APC/C catalyze ubiquitylation and degradation?

  • Securin
  • S-cyclins
  • M-cyclins

273

What is sphingomyelin?

A common membrane sphingolipid with a choline head group.

274

How do aquaporins exclude ions and allow only water molecules through?

The channel portion is so narrow that water molecules, which are much smaller than any ions, can only go through single-file (ions don't fit at all).

275

Which form of Rab is soluble in the cytosol?

Rab-GDP.

276

What is the role of astral microtubules in the mitotic spindle?

They are anchored to the plasma membrane at one end (plus) and to the centrosomes at the other (minus), and they pull the duplicated centrosomes apart to either end of the cell. 

277

What is the main functional difference between bacterial and eukaryotic ABC transporters?

Eukaryotic ABC transporters usually only function in export, while bacterial ABC transporters function in both export and import.

278

How does the K+ channel prevent the passage of negatively charged ions?

Many negatively charged groups on either side of the channel repel negatively charged ions while attracting the positively charged K+.

279

Which subunit of a SCF complex is responsible for recognizing phosphorylated target proteins?

The F-box protein.

280

What type of ATP pump is the Na+-K+ pump?

A P-type ATPase.

281

What are Cdc genes?

Genes that encode proteins involved in the cell cycle (cell division cycle).

282

Which motor proteins associate with astral microtubules in the mitotic spindle to shorten the microtubules and push the poles toward the plasma membrane?

Dyneins.

283

Why is it important that the Rho and Rac pathways inhibit each other during movement of lamellipodia?

  • Rac pathway: formation of branched actin web at the front 
  • Rho pathway: formation of stress fibres and focal adhesion at the back
  • For forward motion, lamellipodia must be forming actin webs only at the front and adhering only at the back

284

True or false: Channels can be involved in either active or passive transport.

False: Channels are only involved in passive transport.

285

Which is the most important Ca2+-binding protein?

Calmodulin.

286

What is PI 3-kinase?

An enzyme that phosphorylates membrane phosphoinositols (PIs) to PI(3,4,5)P3, which is then active for intracellular signalling.

287

Which two complexes often work together in transporting proteins from the cytosol into the mitochondria?

TOM and TIM23.

288

How does intermediate filament assembly make intermediate filaments more tolerant of stretching and bending than actin filaments or microtubules?

Intermediate filaments make strong lateral contacts between α-helices, with individual subunits staggered in the filament to form a strong, rope-like filament.

289

Which tubulin homologue in bacterial cells forms the dividing ring during cell division?

FtsZ.

290

When is the SCF complex active?

In late G1 (after the start-transition point).

291

What is Cdc20?

A protein that is stimulated by M-Cdk to activate APC/C at the metaphase/anaphase transition point in the cell cycle.

292

Where does nucleation of microtubules begin?

At centrosomes/MTOCs (microtubule organizing centres).

293

What is Rho-GTPase?

A monomeric GTPase that activates Rock (Rho-dependent kinase) and formins, resulting in increased myosin activity and actin bundle growth leading to stress fibre formation, integrin clustering, and focal adhesion formation.

294

What is an inhibitory G protein (Gi)?

A G protein that inhibits adenylyl cyclase, resulting in decreased levels of cAMP (as any existing cAMP quickly degrades to 5'-AMP).

295

What is a pre-initiation complex?

A protein complex formed by initiator proteins activated by S-Cdk at the onset of S phase that activates DNA helicases and recruits DNA synthesis machinery for genome replication.

296

What is Alexa 568?

A fluorescently labelled antibody used to visualize specific proteins by fluorescence microscopy (emits yellow light).

297

Which vesicles are assembled with clathrin protein coats?

Vesicles for import from the plasma membrane or from the trans-Golgi membrane.

298

What is the main purpose of aquaporins?

To speed up the diffusion of water into cells or compartments when rapid diffusion is needed to quickly balance ion concentrations.

299

What is the simplest type of transmembrane cell-surface receptor?

Ion-channel-coupled receptors.

300

What type of enzyme is SCF?

Ubiquitin ligase.

301

When microtubules are arranged in astral configuration, how are they oriented?

Minus ends in (attached to the centrosome), plus ends out (in the cytosol).

302

Where are the 3 checkpoints in the cell cycle?

  1. Start transition (G1/S)
  2. G2/M transition
  3. Metaphase/anaphase transition

303

How are multipass transmembrane proteins translocated into the ER membrane?

Alternating stop- and start-transfer signal sequences in the protein trigger the translocator to alternately release the intervening portions of the protein into the ER membrane or into the ER lumen.

304

How is protein transport between the nucleus and the cytosol regulated?

By activating or deactivating nuclear import & export signals, usually by phosphorylation/dephosphorylation.

305

How does the amphiphilic nature of aquaporins prevent the transport of ions?

Dehydrated ions that might otherwise be small enough to fit through the channel are repelled by the hydrophobic part of the channel and attracted to the hydrophilic part, which is where water molecules interact, so the ions can't just go around past the water.

306

What is SREBP (sterol response element binding protein)?

A protein anchored in the ER membrane when [cholesterol] is high, and transported to the Golgi when [cholesterol] is low, where it is cleaved so that its cytosolic domain can act as a transcription factor to direct synthesis of more cholesterol.

307

What is the main function of PIPs in vesicular transport?

PIPs act as organelle and membrane domain markers and are recognized by specific enzymes to ensure that vesicles are transported between the correct compartments.

308

What is an ABC transporter?

A dimeric ATP pump activated by phosphorylation at two ATPase domains to transport small molecules. 

309

How is ArfGAP1 triggered to begin disassembly of COPI or clathrin coats on finished vesicles?

ArfGAP1 is pressure-sensitive and senses membrane curvature, and it becomes active when membrane curvature is great enough to indicate that the vesicle has budded completely from the membrane.

310

What structure forms the voltage sensor in voltage-gated Na+ channels?

A transmembrane S4 helix in each domain that contains many positively charged amino acids, which cause the conformational change that opens the channel in response to a change in membrane potential.

311

Which cAMP-dependent signalling process in the brain is thought to play an important part in learning and memory?

Gene transcription initiated by CREB (converting a short cAMP signal into a long-term change in the cell).

312

How does Ran-GTP function in both nuclear import and nuclear export?

  • Import: Ran-GTP binds to incoming nuclear import receptors and causes them to release their cargo
  • Export: Ran-GTP binds to nuclear export receptors and promotes binding of cargo to receptors

313

What is Gq?

A G protein that activates phospholipase C-β (when its associated GPCR is activated).

314

What is profilin?

A protein that binds free actin monomers to enhance their addition to actin filaments.

315

What is α-actinin?

A protein that stabilizes contractile bundles (actin) by acting as a spacer between filaments (making room for myosin between filaments).

316

What is the basic structure of an Smc molecule?

  • 2 antiparallel α-helices in coiled-coil formation
  • An ATPase domain at 1 end
  • A hinge domain at the other end

317

What is the basic structure of a monomeric intermediate filament protein?

An α-helix with an N-terminus and a C-terminus.

318

What is a stimulatory G protein (Gs)?

A G protein that activates adenylyl cyclase, resulting in increased levels of cAMP. 

319

What is a protein sorting receptor?

A protein that recognizes protein signal sequences based on certain structural motifs (e.g. charged regions, hydrophobicity, etc.) and is involved in localizing proteins to the correct part of the cell.

320

What affinity properties must a KDEL receptor have for efficient retrieval of ER resident proteins?

  • High affinity for resident proteins in the Golgi or in vesicular tubular clusters (where their concentration is low)
  • Low affinity for resident proteins in the ER (where their concentration is high)

321

What is a GM1 ganglioside?

A glycolipid containing a negatively charged sialic acid (NANA) residue in its head group.

322

What are the 4 phases of the cell cycle?

  • G1
  • M
  • G2
  • S

323

How do lysosomes maintain a low internal pH?

V-type ATPases actively pump protons into the lysosome to increase [H+].

324

What is the role of NSF (and its accessory proteins) during vesicle transport?

It uses ATP hydrolysis to promote the dissociation of trans-SNARE complexes into their component v- and t-SNAREs, reactivating the individual SNAREs for new fusion events.

325

What is a pseudopodium?

A 3-dimensional cell protrusion created by a 3-D network of actin filaments spreading outward from the cell.

326

What is 14-oligosaccharide?

The precursor oligosaccharide attached to glycosylated proteins in the ER and modified in the Golgi to complete protein synthesis.

327

What is phosphatidylcholine?

A common membrane phosphoglyceride with a choline head group.

328

What are the 3 possible states of a voltage-gated Na+ channel?

  • Open
  • Inactive
  • Closed

329

What are the two main roles of cyclins in the cell cycle?

  • Bind and activate specific Cdks (at specific points in the cell cycle)
  • Direct Cdks to specific targets to perform specific functions

330

What is the difference between transport of proteins and transport of RNAs between the nucleus and the cytosol with respect to energy source?

Protein transport involves GTP; RNA transport involves ATP.

331

What is a cyclic AMP response element (CRE)?

A short cis-regulatory sequence within the regulatory sequence of a gene whose expression is activated by cAMP.

332

True or false: Motor proteins can be found in both eukaryotes and prokaryotes. 

False: no motor proteins have been found yet in prokaryotes.

333

What is Cdk-activating kinase (CAK)?

A kinase that phosphorylates the T-loop of a partly active Cdk-cyclin complex to fully activate it. 

334

What are the 3 subunits of the SCF complex?

  • Cullin
  • Skp1
  • F-box protein

335

True or false: Cdks are only present in the cell when their corresponding cyclins are active.

False: Cdks are always present in the cell, but they are inactive until they bind their corresponding cyclins (which are not always present).

336

What is a glycosyl transferase?

An enzyme that adds a specific sugar to a glycosylated protein.

337

What is an ATP pump?

A type of transporter that uses energy from ATP hydrolysis to power active transport across a membrane.

338

What are the three most common phosphoglycerides found in cell membranes?

  • Phosphatidylcholine
  • Phosphatidylethanolamine
  • Phosphatidylserine

339

Which monomeric GTPase is bound in the α subunit of G proteins?

Ras.

340

What is kinesin-13 (catastrophe factor)?

A kinesin that interacts with the plus end of microtubules and destabilizes it, increasing the frequency of catastrophe (depolymerization) for dynamic instability.

341

What is the difference between a homotypic gap junction and a heterotypic gap junction?

  • Homotypic: the two connexons are identical in composition of connexin subunits
  • Heterotypic: the two connexons are composed of different combinations of connexin subunits

342

What is γ-tubulin?

A form of tubulin that organizes into complexes for nucleation of microtubules (which are made of α- and β-tubulin).

343

What is tropomodulin?

A protein that caps actin filaments at the minus end (longer-lived than Arp2/3).

344

What is an F-type ATP synthase?

A transporter that uses the passive transport of protons to make ATP from ADP; essentially the reverse of a V-type proton pump.

345

How does S-Cdk prevent new preRCs from forming during S-phase?

It inhibits (by phosphorylation) ORC and Cdc6 proteins, which are required for preRC formation.

346

What is monitored at the second cell-cycle checkpoint (G2/M transition)?

Whether the environment is favourable for division and whether all DNA has been successfully replicated.

347

What is calmodulin-dependent kinase II (CaM-kinase II)?

A protein complex that acts as a molecular memory device: 

  • Calmodulin + Ca2+ bind phosphorylation sites on CaM-kinase to trigger autophosphorylation
  • CaM-kinase fully active when all domains phosphorylated
  • If [Ca2+] drops, calmodulin dissociates, but CaM-kinase stays partially active until dephosphorylated by protein phosphatases

348

How do adaptor proteins act as coincidence detectors during assembly of clathrin-coated vesicles?

The adaptor protein must bind to the head group of PI(4,5)P2 (the membrane marker) and to a cargo protein before it can bind clathrin (so the coat can't form unless it is the right membrane and there is cargo ready to go).

349

How is SCF complex activity regulated?

The complex is always active, but it can only detect phosphorylated targets (i.e. CKIs that have been phosphorylated by an active Cdk).

350

What are the 2 main differences between intermediate filament proteins and actin & tubulin?

  • Intermediate filament proteins are symmetrical, so they don't form polarized filaments
  • Intermediate filaments have no inherent enzymatic activity

351

Why is the vestibule so much wider than the selectivity filter in K+ channels?

To accommodate ions that still have their hydrate shell (which is stripped in the selectivity filter).

352

What is the most likely mechanism for the affinity properties of KDEL receptors that allow them to bind their target proteins at low [protein] and release them at high [protein]?

pH regulation: the pH is lower in the Golgi than in the ER, so it is likely that KDEL receptors are more active at low pH and less active at higher pH.

353

What type of ATP pump is the Ca2+ pump found in the sarcoplasmic reticulum?

A P-type ATPase.

354

Why does nuclear import require active transport?

Proteins quickly accumulate in the nucleus, resulting higher protein concentration inside than out.

355

What are myosins?

A large class of motor proteins that interact with actin filaments.

356

What is mitochondrial hsp60?

A protein complex that binds incorrectly or incompletely folded proteins in the mitochondria and helps them to fold correctly before they are released into the mitochondria again.

357

How are escaped resident ER membrane proteins returned to the ER?

They bind directly to the COPI coat of ER transport vesicles and are sent back to the ER in COPI-coated vesicles.

358

What is a CREB-binding protein (CBP)?

A transcriptional coactivator recruited by PKA-activated CREB to stimulate transcription of cAMP-regulated target genes.

359

What are the 3 modes of desensitization of GPCRs?

  • Receptor inactivation
  • Receptor sequestration
  • Receptor downregulation

360

What happens during transautophosphorylation of a receptor tyrosine kinase (RTK)?

Two inactive RTKs dimerized by an extracellular signal protein phosphorylate each other, activating their kinase domains, which then undergo further transautophosphorylation to generate binding sites for intracellular signalling proteins.

361

What makes epidermal growth factor (EGF) receptors different from other receptor tyrosine kinases (RTKs)?

It is the only RTK that doesn't undergo transautophosphorylation: 1 unit of the activated dimer phosphorylates itself and the other unit. 

362

Which monomeric GTPase mediates signalling by most receptor tyrosine kinases (RTKs)?

Ras.

363

What makes insulin receptors different from other receptor tyrosine kinases (RTKs)?

They exist as tetramers in active or inactive form, so they don't need to be dimerized by extracellular signals; signal binding induces a conformational change in tetramer, which activates the receptor with a single phosphorylation event.

364

What is the main role of SH2 & SH3 domains in cell signalling?

Intracellular signalling proteins with SH2 and/or SH3 domains use those domains to recognize and bind to docking sites on receptor proteins.

365

How do intracellular signalling proteins without SH2 or SH3 domains attach to docking sites on receptor proteins?

They interact with adaptor proteins that recognize docking sites on the receptor and binding sites on the signalling protein.

366

What is insulin receptor substrate-1 (IRS1)?

A docking protein that is the first protein to bind to an activated insulin receptor; once it binds to the receptor, IRS1 is phosphorylated to provide more docking sites for additional proteins (more than would be accommodated by the receptor's tail alone).

367

Which monomeric GTPase activates MAP kinase cascades?

Ras.

368

True or false: A MAP kinase cascade both relays and amplifies a signal.

False: MAP kinase cascades only relay a signal (no amplification).

369

True or false: GPCRs and RTKs can both activate MAP kinase cascades.

True.

370

What are Raf, Mek, and Erk?

Kinases in mammals that are involved in MAP kinase cascades:

  • Raf: MAP kinase kinase kinase
  • Mek: MAP kinase kinase
  • Erk: MAP kinase

371

What is a MAP kinase module?

A scaffold protein with bound MAP kinases and/or containing kinase domains that are all part of the same MAP kinase cascade. 

372

Which phosphoinositide is an especially important docking site for intracellular signalling proteins?

PI(3,4,5)P3.

373

What happens when PI 3-kinase is activated?

It phosphorylates a target PI(4,5)P2 to PI(3,4,5)P3, which can then function as a binding site for intracellular signalling proteins.

374

What is PDK1?

An intracellular signalling protein that activates Akt, leading to inhibition of apoptosis in response to a survival signal.

375

What is Akt?

An intracellular signalling protein phosphorylated & activated by PDK1 and mTOR that phosphorylates Bad, resulting in inhibition of apoptosis in response to a survival signal.

376

What is Bad?

A protein that binds and inactivates an apoptosis-inhibitory protein until phosphorylated by Akt, resulting in release of the inhibitory protein and inhibition of apoptosis in response to a survival signal.

377

What type of signalling cascade is triggered by mating factors in yeast cells?

A MAP kinase cascade.

378

What type of signalling cascade is triggered by a change in osmolarity, resulting in glycerol synthesis?

A MAP kinase cascade.

379

How can parallel MAP kinase cascades result in different responses?

  • Different protein scaffolds
  • Different combinations of kinases

380

What is the main difference between a receptor tyrosine kinase (RTK) and a tyrosine-kinase-associated receptor? 

In tyrosine-kinase-associated receptors, the kinase and receptor are 2 separate proteins encoded by 2 different genes; in RTKs, the kinase and the receptor are 2 parts of the same protein.

381

What class of receptor do cytokine receptors belong to?

Tyrosine-kinase-associated receptors.

382

What is a Janus kinase (JAK)?

A kinase associated with cytokine receptors (a type of tyrosine-kinase-associated receptor); once 2 receptors have been dimerized by a cytokine, the JAKs on each receptor phosphorylate each other, then their associated receptor subunits, to activate the entire complex.

383

What are STAT1 and STAT2?

Intracellular signalling molecules that dock to JAK-associated receptors and are phosphorylated by JAK, which causes them to dissociate from the receptor and dimerize with each other; the resulting STAT dimer then acts as a transcription factor for cytokine-responsive gene transcription.

384

Why do we have so many different protein tyrosine phosphatases?

High specificity: tyrosine phosphatases target specific phosphate groups on specific Tyr residues. 

385

Which proteolytic signalling pathway is especially important in cell differentiation?

Notch signalling.

386

Is the activation of a Notch receptor reversible or irreversible?

Irreversible (involves proteolysis).

387

What is the general role of Notch signalling in animal cells?

Controlling cell fate choices and regulating pattern formation in cell differentiation during development and renewal of tissues.

388

What are the 2 types of caspases involved in apoptosis?

Initiator and executioner caspases.