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Biology Exam 2 > Sorting > Flashcards

Sorting Flashcards

1
Q

plasma membrane

A

outer boundary of cells
phospholipid bilayer
protection, transporters, cell signaling

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2
Q

nucleus

A

houses genome

RNA and DNA synthesis

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3
Q

cytoplasm

A

cytosol + cytoplasmic organelles

intermediary metabolism

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4
Q

endoplasmic reticulum

A

with ribosomes = rough
w/o = smooth

protein/lipid synthesis, protein folding, quality control, Ca storage, signaling

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5
Q

golgi apparatus

A

stacks of disc-like compartments

post-translational changes to proteins/lipids
trafficking

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6
Q

mitochondria

A

outer and inner membrane matrix
powerhouse of cell
signaling
cell differentiation and death

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7
Q

what happens when a mitochondria is leaky?

A

apoptosis

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8
Q

lysosomes

A

contain digestive enzymes to degrade organelles and biomolecules

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9
Q

peroxisomes

A

small vesicular compartments that contain enzymes used in oxidative rxns

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10
Q

topological compartments

A
  1. nucleus and cytosol
  2. secretory and endocytic organelles
  3. mitochondria
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11
Q

3 types of transport for trafficking

A
  1. gated transportation
  2. TM transportation
  3. vesicular trafficking
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12
Q

gated transportation

A

between nucleus and cytosol
thru nuclear pores
bidirectional

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13
Q

TM transportation

A

cytosol to peroxisomes, plastids, mito, ER
monodirectional
membrane transporters directly transport proteins from cytosol to target

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14
Q

vesicular trafficking

A

ER —-> elsewhere

use of membrane bound vesicles to transport molecules

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15
Q

what guides protein sorting?

A

protein sorting signals

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16
Q

protein sorting signals

A

sequence of AAs on protein
can be anywhere or multiple places in protein

but when folded they come together to form a signal patch

necessary and sufficient

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17
Q

signal peptidase

A

after a protein has reached it’s final destination

peptidase can cleave the signal sequence off because it is no longer needed

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18
Q

what is more important in a signal sequence?

A

physical properties are more important than the actual sequence

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19
Q

_____ receptors recognize and read signal sequences.

A

complimentary receptors

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20
Q

import into nucleus

A

lys and Arg rich

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21
Q

import into mitochondria

A

combination of + charged and hydrophobic AAs

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22
Q

import into ER

A

bunch of hydrophobic AAs

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23
Q

export from ER

A

KDEL

Lys-Asp-Glu-Leu-COO-

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24
Q

what molecules are exported from the nucleus?

A

mRNA and tRNA

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25
Q

NPC

A

nuclear pore complexes

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26
Q

NPC characteristics

A

composed of nucleoporins
octagonal
extending fibrils facilitate mvt
3000-4000 NPC per nucleus

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27
Q

NPC components

A 
cytosolic fibers
scaffold nucleoporins
membrane ring proteins
channel nucleoporins
disordered region of C nucleoporins
nuclear basket
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28
Q

NLS

A

nuclear localization signals

direct mvt of protein into nucleus
rich in + AAs (lys Arg)

located in loops or patches on surface of cargo

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29
Q

NIR

A

nuclear import receptors
cytosolic proteins that:
recognize NLS and bind to it and NPC proteins

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30
Q

types of NIR binding

A

direct binding

indirect binding
via adaptor protein

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31
Q

NPC binding sites for NIR

A

FG repeats

phenylalanine glycine repeats

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32
Q

after NIR delivers protein to destination where does it go?

A

delivers protein to nucleus and returns to cytosol

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33
Q

NES

A

nuclear export signals

same as import just signal opposite direction

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34
Q

NER

A

nuclear export receptors

complimentary to NES, bind to it and NPC proteins to move out of the nucleus

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35
Q

monomeric G protein

A

Ran

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36
Q

cytosolic Ran vs. nuclear Ran

A

GDP cytosol

GTP nucleus

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37
Q

Ran cytosol

A

GAP
GAPase activating protein

cleaves phosphate bond to keep Ran as GDP

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38
Q

Ran nucleus

A

GEF
guanine exchange factor

exchanges guanine with a GTP guanine
does not add Pi group

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39
Q

driving factor for gated transportation

A

Ran-location type gradient

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40
Q

Ran-GTP binding……

A 
binds to (NIR + cargo)
cargo is released
NIR--Ran exit nucleus
GAP cleaves
Ran-GDP now ready for another cycle
41
Q

proteins that contain both NLS and NES sequences

A

shuttling proteins

42
Q

relative rate of gated transportation controls….

A

homeostasis = importing = exporting

import greater = nuclear
export greater = cytosolic

43
Q

what controls transportation?

A

genes

keep proteins out of nucleus until they are needed

44
Q

how is transportation controlled?

A

by turning NLS/NES on or off

45
Q

mechanisms for transportation control?

A

phosphorylation
proteolysis
binding to inhibitory proteins

46
Q

two examples given in this lecture: gated transportation

A

T-Cell activation

low cholesterol

47
Q

mitochondria structures

A

outer memb.
intermemb. space
inner memb.
inner matrix

cristae of inner memb.

48
Q

significance of cristae

A 
folds in inner membrane
function to increase surface area
49
Q

source of mitochondria protein

A

most are encoded by nuclear DNA

but some are made in the mito itself, has it’s own translation machinery

50
Q

translocation

A

mvt of proteins of membrane

51
Q

what directs proteins to a specific organelle or compartment?

A

signal sequences

52
Q

mitochondria signal sequences

A

located at N terminus or in middle

amphiphilic alpha helix shape

53
Q

describe amphiphilic alpha helix

A

shape of proteins destined for mitochondria

created by positive residues on one end and hydrophobic ones on other end

54
Q

nonpolar residues are ?

A

hydrophobic

55
Q

how do receptor proteins recognize precursor proteins bound for mitochondria?

A

by the alpha helix configuration not the signal sequence itself

56
Q

where are protein translocators located?

A

on the membrane of organelle protein is imported to

57
Q

protein translocators of mitochondria

A

multi-subunit protein complexes that mediate translocation

58
Q

list the mitochondrial translocators

A

cytosol to inter space
TOM
SAM

inter space to matrix
TIM 22
TIM 23
OXA

59
Q

translocator that transfers or inserts all proteins from cytosol to outer membrane

A

TOM

60
Q

sorting and assembly machinery

A

SAM

Translocates and inserts or folds beta barrel proteins

61
Q

mediates insertion of specific subclass proteins

A

TIM22

ATP, ADP, Pi transporter

62
Q

transport of soluble proteins and insertion of proteins into inner membrane

A

TIM23

63
Q

insertion of proteins synthesized in the mitochondria

A

OXA

a few exceptions recently found

64
Q

TOM and TIM have 2 components

A

receptors for precursor protein

translocation channel

65
Q

describe a precursor protein

A

unfolded proteins in cytosol

maintained by chaperone hsp70

66
Q

describe protein import through TOM

A

TOM binds to signal seq.
chaperones are stripped off –ATP
protein fed thru channel into space
peptidase cleaves signal

67
Q

when is energy required in TM transport?

A

to remove hsp70

to remove mito hsp70 in matrix

for hsp60 to fold/refold protein in matrix

68
Q

what drives protein mvt through TOM?

A

ATP hydrolysis drives removal of hsp70

free unfolded peptide is then pulled thru TOM

69
Q

what drives protein mvt through TIM?

A

the electrochemical membrane potential gradient, drives the positive protein by electrophoresis

protein wants to get to the negatively charged matrix

70
Q

mitochondrial hsp70

A

binds to protein in matrix and helps pull it thru TIM23

ATP is required for hsp70 to release

71
Q

hsp60

A

binds to protein in mito matrix and helps fold the imported protein
requires ATP to do so

72
Q

integration within the outer mitochondrial membrane

A

pass thru TOM
chaperones bind
protein binds to SAM
SAM - inserts and folds protein into memb.

73
Q

example of TM proteins on outer mitochondrial membrane

A

porins

74
Q

ER structure

A

network of branching tubules and sacs

membrane is continuous with nuclear memb.

internal space = ER lumen

75
Q

types of ER translocation

A

co-translational

post-translational

76
Q

co-translational translocation

A

mvt into ER
ribosome still attached
translation still in process

77
Q

post-translational translocation

A

mvt into ER

translation finished

78
Q

ER signal sequence

A

AA specific order varies

8 or more nonpolar/hydrophobic AA’s in center or protein

79
Q

signal sequence guidance to ER—2 factors

A

SRP

SRP receptor

80
Q

what does SRP stand for?

A

signal receptor particle

81
Q

SRP structure

A

6 proteins bound to a small RNA backbone
rod shaped
large hydrophobic pocket

82
Q

describe the hydrophobic pocket of SRPs

A

lined by methionines

accommodates hydrophobic signal seq. of varying size, shape, sequence

83
Q

SRPs cycle back and forth between ?

A

cytosol and surface of ER membrane

84
Q

what do SRPs bind to?

A

ER signal sequence on protein

SRP receptor of ER membrane

in co-translational: to large unit of ribosome

85
Q

where does a SRP bind to a ribosome?

A

to the large unit of ribosome at the elongation factor

and binds to the ER signal sequence of the protein being translated

86
Q

describe steps of co-translational translocation

A 
SRP binds ribosome
SRP binds ER signal seq.
translation paused
travel to ER
bind to SRP receptor
translation restarts
protein fed thru translocator
SRP recycled
87
Q

where are the SRP receptors located?

A

next to translocators on ER membrane

88
Q

describe ER translocators

A

circular shape
3 subunits
largest surrounds pore
central pore

89
Q

describe ER translocator pore

A

water filled
core = Sec61 complex
gated by short helix
opens and closes as needed

90
Q

what are the 2 states of the ER translocator?

A

open — full circle, pore plugged

closed — 3/4 circle shape, pore plug displaced
signal seq. bound in open 1/4

91
Q

signal sequence that interacts with a specific site within the pore

A

start-transfer signal

also interacts with lipid components of ER membrane. acts as dual recognition to ensure specificity

92
Q

what does the start-transfer signal do?

A

activates the pore opening
allowing entry to lumen

peptidase cleaves it off

93
Q

integration of TM proteins to ER - requirements

A

some portion of the protein must pass thru the translocator before a stop-transfer signal is reached

94
Q

what initiates integration of TM proteins in the ER?

A

N terminus

95
Q

describe a stop transfer signal

A

a hydrophobic region in the polypeptide that stops translocation

peptidase cannot cleave because it becomes integrated into bilayer via the lateral gate of the translocator

96
Q

can a TM protein be multi-integrated?

A

yes, single or multiple

depends upon the combination of start and stop transfer signals

97
Q

in an ER TM protein which side of the membrane does each terminus of the protein end up on?

A

either side

they both can exist on the same side too

98
Q

ER integration predictions

A

we can utilize software to predict the amount of integration of a protein

based upon the physical properties of the sequence itself

Biology Exam 2 (9 decks)

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