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Flashcards in Midterm 2 Deck (146):
1

Are GLUT uniporters reversible?

Yes

2

What is faster, protein mediated transport or simple diffusion

protein mediated transport

3

What is transport rate limited by

number of transporters (Vmax) and transporter affinity (Km) for the ion

4

How many conformational states to uniporters have

Two

5

What do ATP Powered pumps do

use energy from hydrolysis of the terminal phosphoanhydride bond of ATP

6

What are the 4 classes of ATP powered pumps

P-class, V-class, F-class and ABC

7

What are P-class pumps

contain 2 identical catalytic alpha subunits that each have an ATP binding site, also contain 2 smaller beta subunits with regulatory functions. Often involved in generating ion gradients across membranes

8

What are V class pumps

function to generate the low pH of plant vacuoles and of lysosomes and other acidic vesicles by pumping protons from cytosolic to exoplasmic face of membrane against concentration gradient

9

What are F class pumps

are reverse proton pumps, also called ATP synthase

10

T or F: V and F class pumps have a similar structure

T

11

What are ABC Superfamily pumps

pump a variety of substrates, ex.multidrug resistance proteins
4 core domains: 2 T domains, form passageway for cargo. 2 ATP binding A domains, bind and hydrolyze ATP. 4 independant proteins in bacteria

12

what are some characteristics of the cytosol

have a pH of around 7.2, have a high K+, low NA+ and Ca2+

13

protein synthesis requires a high concentration of __ ions

K+

14

release of __ ions causes muscle relaxation, and pumped by what

Ca2+, pumped by P-class ATPase

15

What are some characteristics of P-class Ca2+ ATPase

2 binding sites of Ca2+, E1 states have binding sites facing CYTOSOL, E2 binding sites facing EXOPLASMIC face

16

E1 has __ affinity state, __ oxygen atons surround Ca2+ ions in 2 high affinity states

high, 7

17

E2 state has __ affinity state, has different orientations and releases __ ions

low, Ca2+

18

How can ATPase be converted from E1 to E2

by movements of spinning alpha helices

19

P class pumps are phosphorylated on an ____ residue

Asp

20

If Km ___ than free concentration, ions will bind

less than

21

__ Na+ out, __ K+ in

3, 2

22

Which class ATPases usually only pump H+ ions

V and F class

23

How do V class H+ ATPases generate electric potential

H+ ions are transported in, counter ion (OH-/Cl-) moves left of the cytoplasmic face to create an electric potential. As charge builds, the harder it is to pump H+

24

How do cells address positive charge build up

Let in equal number of anions, or move an equal number of different cation out of the lumen

25

What are some ABC Protein Flippases

ABCB1- multidrug export
ABCB4- flips phosphatidylcholine from cytosolic to exoplasmic leaflet

26

Is ABC CTFR a pump?

No, it is a Cl- channel

27

T or F: there is an electric potential across the membrane in all cells

T

28

What is the average charge of the membrane

-60 -> -70mV

29

Transmembrane potential depends on ?

ion movement

30

In reality, membranes are permeable to what ions?

Na, K , Ca and Cl

31

Animal resting membrane potential depends largely on outward flow of __ ions

K+

32

what are nongated channels

opening and closing of chaneels not afected by membrane potential or signaling molecules

33

how is the K+ gradient maintained

by the Na/K ATPase

34

bacterial, plant and fungal cells are inside- ______ (positive or negative) due to pumping __ out of the cell and leaving behind ____

negative, H+, anions

35

structure and chemical nature of a pore _____ (lowers or raises) the activation energy

lowers

36

what are the two forces that constitue an electrochemical gradient across a membrane

electric potential and ion concentration gradient

37

what type of transport is cotransport

secondary active transport

38

what are cotransporters

use energy released by ion movement down tis electrochemical gradient to power transport of another molecule or different ion up its concentration gradient

39

why in Na+ a good ion to power the uphill movement of other molecules

Na gradient is established by Na/K ATPase, Na reentry down concentration gradient movement goverened by sun of ion concentration gradient and membrane electric potential

40

What is the role of GLUT

transports glucose down its concentration gradient

41

when [glucose] in cytosol is greater than in extracellular lumen, how does glucose move

up concentration gradient via active transport, facilitated transport when opposite

42

what are the three antiporters that regulate the cytosolic pH and when are they active

Na+HCO3-/ Cl- , active at low pH only
Na+/H+, active at low pH only
Cl-/HCO3- , active at high pH only

43

synthesis of secreted proteins begins with ____ _____

cytosolic ribosomes

44

what sequence targets proteins to the ER

N-terminal signal sequence

45

what are the two key components of targeting a ribsome

signal recognition particle (SRP) and its receptor

46

what is the role of SRP

a cytolsoic ribonucleoprotein that binds to ER signal sequence forming a large complex. it targets nascant protein ribosome complex to ER by binding to receptor

47

what does the mammalian translocon consist of

3 proteins,and Sec61 complex

48

what is the hydrophobic hourglass

an hourglass shaped channel that has a helical plug that seals the translocon

49

what is signal peptidase

transmembrane ER protein that recognizes a sequence of the C-terminal end of the hydrophobic core of the signal peptide and cleaves the chain specifically

50

In most eukaryotes, most secreatory proteins enter the ER by ________ ________

cotranslational translocation

51

in yeast, how does post-translational translation occur

no SRP or receptor, Sec63 in ER near translocon. molecular chaperone BiP has peptide binding domain and ATPase domain

52

T or F: Intergral membrane contain one or more hydrophobic membrane-spanning domains

T

53

Where and how are periphrial proteins bound

to the side of the membrane by interactions with anchored membrane proteins

54

can membrane proteins flip flop across the membrane?

No

55

what is the proteins topology

the spatial orientation of proteins

56

how can membrane protein topology be determined

by computer programs that identify hydrophobic topogenic segments within the primary amino acid sequence

57

what are the 5 topological classes of intergral membrane proteins

Type I, II, III, IV, and tail-anchored proteins

58

which type of intergral membrane proteins have N-terminus of EXOPLASMIC and C-terminus on CYTOPLASMIC FACE

Type I and Type III

59

which type of intergral membrane proteins have N-terminus of CYTOPLASMIC face and C-terminus on EXOPLASMIC

Type II

60

how are tail-anchored proteins inserted

post-translational instertion

61

What are some characteristics of Type I membrane proteins

N-terminal signal sequence bound by SRP
stop-transfer anchor squence anchroed in phosphoipid bilayer

62

what are some characteristics of Type II and III membrane proteins

Internal signal-anchor equence bound by SRP, positive charged region stays on cytoplasmic face

63

Tail-anchored proteins have a __ - terminal hydroophobic tail

C-terminal

64

Type IV-A proteins have N terminus in the ______, while Type IV-B have N terminus in the _______.

cyotsol, ER-lumen

65

what are GPI anchored proteins

protein portion is synthesized and inserted to the ER membrane, like Type I protein

66

What is GPI transamidase

cleaves the precursor protein within the exoplasmic facing domain, covalentaly linked new C-terminus

67

What are the four main modifications in the ER

1. Covalent addition and processing of carbohydrates (glycosylation) in the ER and Golgi
2. Formation of disulfide bonds in ER
3. Proper folding of polypeptide chains in ER
4. Specific proteolytic cleavages in the ER, Golgi and secretory vesicles

68

What is the role of oligosaccharide attachment

required for some protein folding, confer stability in some glycoprotiens, play a role in cell to cell adhesion

69

what do disulfide bonds to to many proteins

help stabilize the tertirary and quaternary structure of many proteins, form oxidative linkage of sulfhydryl groups

70

what does the prescence of unfolded proteins in the rough ER do

increases transcription of genes that encode ER chaperones

71

Modificationso f N-linked oligosaccharides are used to monitor what?

folding and quality control

72

what proteins are targeted for transport from ER back to cytosol

dislocation-misfolded proteins

73

What is the role of the ERAD complex

enables dislocation of misfolded proteins through the membrane

74

what ensures proper forlding or translport in the ER

ER chaperones

75

Proteins require oligosaccharides and disulfide bonds via ?

ER enzymes

76

What class ATPase used to synthesize ATP?

F-class

77

Proteins on mitochrondrial and chloroplast are synthesized in ______

ribosomes

78

how many targeting sequences and translocation systems are required for protein import

two of each

79

where are precursor proteins synthesized

cytosolic ribosomes

80

What are the three energy imports required for protein import to mitochondrial matrix

1. Cytosolic Hsp70
2. Matrix Hsp70 achored to Tim44 protein
3. H+ electrochemical gradient

81

many mitochondrial outer membrane proteins have a __ -barrel structure

beta

82

Antiparallel strands for _______ transmembrane segments surrounding a central channel

hydrophobic

83

How are chloroplast stromal proteins imported

rubisco is encoded by chloroplast DNA and transported to chloroplasts from the cytosol. stromal Hsp70 chaperone required to hydrolyze ATP

84

what are thykaloids

membranous sacks that contain enzymes for photosynthesis

85

what are the four pathways for transporting proteins from thykaloid to stroma

SecA-like
Oxa1-like
SRP-dependant
pH-dependant

86

what are some similarities between the SRP and pH depenadant pathways

First imported in an unfolded state, N-terminal cleaved off

87

What happens in SRP-dependant pathway

Unfolded protein translocated into thykaloid lumen, chaperones keep protein unfolded, thylakoid targeting sequence removed, then protein folds in thylakoid lumen

88

What happnens in pH- dependant pathway

folded protein transfered to thylakoid lumen, has two Arg residues, powered electrochemical gradient across thylakoid membrane, thylakoid targeting sequence cleaved off

89

how are targeting sequences directed in post translational transport

through translocons

90

what are peroxisomes

small organelles in plants and animals that contain enzymes that oxidize amino and fatty aids, breaking them down for biosynthetic pathways

91

do peroxisomes contain DNA and ribosomes?

No

92

How are Peroxisomal proteins targeted

requires C-terminal PTS1 sequence, binds to Rex5 receptor and imports folded proteins

93

Are peroxisomal membrane proteins targeted by PTS1

no

94

what are luminal peroxisomal proteins

synthesized on cytosolic ribosomes, contain c-terminal targeting sequence

95

what is the role of nuclear pores

allow movement of mRNAs, tRNAs, and ribosomal subunits out of the nucleus

96

what does the import of nuclear proteins require

nuclear localization signals

97

What is a nuclear pore complex

many copies of 30 distinct nucleoporins, contains nuclear basket, ions can diffuse passively but not large proteins

98

what are the three types of nucleoporins

Structural, membrane and F-G nucleoporins

99

What are structural nucleoporins

form scaffold of nuclear pore, 16 copies of Y complex

100

What are membrane nuceleoporins

form outer curvature of the nuclear pore

101

what are F-G nucleoporins

rich in hydrophobic Phe and Gly residues

102

How are nuclear proteins targeted

by Nuclear localization signal (NLS) nad also requires Ran and Nuclear transport receptor (Binds to NLS)

103

nuclear import of proteins- what happens in the cytoplasm

importin binds NLS of a cargo protein to form importin-cargo complex and diffuses thorugh NPC by interacting wtih FG nucleoporin

104

nuclear import of proteins- what happens in the nucleoplasm

Ran-GDP activated by GF. Releases GDP, binds GTP.
Ran-GTP bidning to importin conformational change that relases NLS-cargo protein

105

nuclear import of proteins- what happens in system recycling

Importin-Ran-GTP complex transported back to cytoplasm with filaments of the NPC stimulates Ran hydrolysis of bound GTP

106

How are proteins larger than 40kDa transported into/out of the nucleus?

Unidirectional transport though large complex nuclear pore that requires nuclear localization or export signal

107

What is the seceretory pathway of protein sorting

distribution of solubule and membrane protein synthesized by rough ER to final destinations at cell surface

108

what is the endocytic pathway of protein sorting

vesicles budding from plasma membrane take up soluble extracellular proteins and deliver them to lysosomes via endosomes

109

what are some techniques for studying the secretory pathway

SDS-PAGE, temperature sensitive sec mutants, cell-fre assays, can be visualized by flurescence microscopy porducing GFP tagged protein

110

What is the Bradford Assay

to determine protein concentration in biological samples

111

what are some pros and cons of the bradford assay

adv - accurate and simple, widely used in all biological fields
disadv. - requires irreversable dye binding, linear over a short range, inhibited by some detergents (SDS) , modestly time consuming

112

what is a good model organism for vesicular transport

yeast, as secretory pathways are similar in all eukaryotes

113

How does vesicle budding occur

initiated by recuritment of GTP-binding
Driven by polymerization of soluble protein
Intergral membrane domains interact with vesicle coat and cargo proteins
coat proteins shed after vesicle released

114

how does vesicle targeting occur

by V and t-SNAREs

115

Wht are V-SNAREs

incorporated into vesicle membrane during assembly of coat. are accessible after release

116

What are t-SNAREs

embedded in target membrane and can interact with conjugate v-SNAREs

117

T or F: all transport vesicles use t and v-SNAREs to fuse

T

118

How des vesicle fusion occur

provided by interactions of specific v-SNAREs with specific target t-SNAREs, fusion brings bilayers together and releases cargo proteins

119

What are Rab proteins

small GTP-bidning proteins that regulate vesicle trafficking and fusion

120

what are the two steps in Rab protein association with a vesicle

1- cytosolic Rab-GDP rageted to vesicle membrane-held in place by anchor
2. GEF in membrane converts Rab-GDP to Rab-GTP, which is enabled to bind Rab effectors. GTP hydrolysis releases Rab GDP

121

what must first be removed after it buds off parent membrane in order to expose Rab + v-SNAREs

the vesicle coat

122

how are SNAREs inserted into membranes

via C-terminal transmembrane chains

123

complexes of v and t-SNAREs are capable of reversable, tight ___-helix bundles

four

124

how are SNARE complexes stabilized

by arrangement of hydrophobic and charged amino acid residues in heptad residues

125

What are the three types of coated vesicles

COP II, COP I and Clathrin

126

What do COPII vesicles do

transport proteins form ER to Golgi

127

What do COP I vesicles do

transport proteins from Golgi eisternae and cis-Golgi back to ER

128

what do Clathrin coated vesicles do

transport proteins from plasma membrane and trans-Golgi to late endosomes

129

What vesicles contain ARF protein

COPI and Clathrin

130

What vesicles contain Sar1 protein

COPII

131

ARF, SAR1, Ran and Rab are all ______ switch proteins

GTPase

132

What is the other function of small GTPases

pinching off completed vesicle from parent membrane

133

what do luminal domains do that are on some cargo proteins

identify and bring soluble cargo proteins into the vesicle

134

Newly synthesized proteins travel in ____- vesicles from ER to the __-Golgi

COPII, Cis-golgi

135

retrograde transport recycles v-SNAREs in ____ vesciles from cis-Golgi to __

COPI, ER

136

Yeast cells with mutations in genes for COPII proteins are class __ sec mutants

B

137

Sar1-GTP binds to ER memnrane and recruits ____ and _____

Sec23 and Sec24

138

Cytosolic domains of COPII contain____

di-acidic sorting signal

139

Certain intergral ER membrane proteins also bind cargo proteins in the lumen via _____ ____

exoplasmic domain

140

All signal domains interact with ____ in COPII

Sec24

141

How do vesicles move?

Many move by diffusion in the cytoplasm, microtubules act as railroad tracks to transport vesicles

142

what is retrograde transport

COPI vesicles transport between Gogli cisternae and from cis-golgi to rough ER

143

What are some characteristics of ER-resident proteins

many soluble proteins that assist in folding and modification of newly synthesized proteins, most carry KDEL sorting sequence

144

what is the role of KDEL receptor

acts mainly to retrieve soluble proteins containing KDEL sorting signal at end of C-terminal segment

145

what is cisternal maturation

responsbile for anterograde transport thorough the Golgi (cis to trans)

146

What fusion can demonstrate cisternal maturation

Fluorescence-tagged fusion