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Cell Biology > Exam 2b > Flashcards

Exam 2b Flashcards

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1
Q

What do proteins define in each compartment of a cell?

A

function

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2
Q

where are localization signals in a protein

A

they are part of primary or secondary structure

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3
Q

nuclear localization signal (NLS)

A

directs proteins to nuclear pore complex (NPC)

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4
Q

what is in localization signal

A

proline followed by positive amino acids

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5
Q

where can localization sequence be

A

anywhere in protein

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6
Q

what size things can diffuse freely into nucleus

A

5kDa small molecules, dNTP, NTP, small proteins

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7
Q

what size things for sure need assistance getting into nucleus

A

30kDa, large proteins, RNAs

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8
Q

characteristics of nuclear porin

A

huge, has 30 proteins, many copies, approximately 120 Mda

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9
Q

what is NPC center like

A

gelatinous and disordered

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10
Q

how is NPC selective

A

for size

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11
Q

what is nuclear porin gate made of

A

glycine and phenylalanine, which are both nonpolar

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12
Q

key players in nuclear import/export

A

nuclear import receptor, nuclear export receptor, Ran, RanGTP, RanGDP, RanGAP, RanGEP

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13
Q

nuclear importer receptor

A

floating in cytosol, interacts with NLS, directs proteins to nuclear pore

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14
Q

Ran

A

monomeric G protein, binds receptor when bound to GTP in nucleus, shuttles import receptor back out

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15
Q

Ran-GAP

A

in cytosol, releases Ran from receptor GTP to GDP

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16
Q

Ran-GEF

A

in nucleus, converts Ran-GDP to Ran-GTP, maintains Ran-GTP

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17
Q

active and inactive form of Ran

A

Ran GTP is active/ Ran GDP is inactive

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18
Q

what limits NLS exposure

A

ligand binding/conformation

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19
Q

what do nuclear export receptors do

A

go into nucleus, pick up proteins with nuclear export signal and deliver it to cytosol

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20
Q

What role does Ran-GTP play in export

A

promotes cargo association

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21
Q

what role does Ran-GAP play in export

A

induces receptor to hydrolyze GTP to GDP. Then export receptor releases both cargo and GDP in cytosol, the returns to nucleus

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22
Q

how to test if sequence is enough to guide to organelle

A

bind to protein and see if it goes. Cleaving it may just ruin protein so it can’t go anywhere.

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23
Q

endoplasmic reticulum

A

extensive network of membrane/ expansive and dynamic

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24
Q

smooth ER

A

lipid and steroid synthesis

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25
Q

rough ER

A

protein synthesis for entire endomembrane system

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26
Q

signal peptide (SP)

A

for entry into ER or for secretion of bacterial proteins

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27
Q

where is signal peptide and what is it?

A

at the N-terminus, a hydrophobic alpha helix, approximately 15-30 amino acids

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28
Q

when do most proteins enter ER

A

during translation, “co-translational”, reason for RER formation

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29
Q

what happens during ER signal sequence

A

translocation

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30
Q

How does protein bind to ER

A

Er signal sequence on newly formed polypeptide chain binds to SRP, which directs the translating ribosome to the ER membrane. SRP binds to receptor! Receptor calls translocator. Dissociates from protein. Signal enter translocator. Protein on C end comes in and comes through. Signal is cleaved off in membrane.

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31
Q

pH of lumen ER

A

Approximately 6

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32
Q

ph outside lumen of ER

A

7

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33
Q

2 types of ribosomes

A

free ribosomes and membrane bound ribosomes (coat rough ER)

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34
Q

Type I transmembrane protein

A

has signal peptide and is equal to or greater than 1 hydrophobic alpha helix

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35
Q

which side of start-transfer protein ends up facing cytosol?

A

the more positive side stays out

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36
Q

Type II transmembrane protein

A

No SP, has “internal start transfer” sequence

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37
Q

Post-translation

A

fully synthesized,then directed into ER

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38
Q

what translocator do bacteria, archea and eukaryotes all have

A

Sec 61

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39
Q

What complex do eukaryotes use for translocation post-translation

A

Sec 62, 63, 71, 72 complex

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40
Q

what does sec 62, 63, 71, 72 complex do

A

which attaches itself to Sec 61 and deposits BIP molecules onto protein chain as it emerges through translocator.

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41
Q

How does BIP work

A

BIP is ATP driven. Release pull protein into lumen

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42
Q

sec Y

A

translocator complex used by bacteria

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43
Q

what feeds sec Y

A

Sec A ATPase with conformation changes that cause piston like motion in Sec A. only in bacteria.

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44
Q

two post translational modifications in ER

A

N-linked glycosylation; Disulfide bond formation

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45
Q

when does glycosylation happen? To what?

A

-as proteins enter or after;-both soluble and transmembrane proteins

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46
Q

sequence for attaching oligosaccharide

A

Asn-X-Ser/thr

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47
Q

how does N-glycosylation end

A

in three sugar residues

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48
Q

why n-glycosylation

A

increase solubility of protein; prevent proteolysis, can become part of glycocalyx if transmembrane, part of zip code for lysosome, keeps misfolded proteins in ER

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49
Q

how does it prevent proteolysis

A

protein can have many oligosaccharides attached to it, and they shield it from proteases

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50
Q

how are misfolded proteins kept in ER

A

misfolded proteins are held back; are recognized by glucose residues still attached to it; chaperone protein calnexin binds to glucose residues of protein; Protein is released from clanexin when glucosidase removes terminal glucose residues;Glucosyl transferase determines whether folded correctly or not;if it isn’t, the transferase adds new glucose from UDP-glucose

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51
Q

what happens if protein never folds correctly

A

;chaperones, disulfide isomerases and lectins are involved

-go to cytosol;ubiquitylated, deglycosylated and degraded in proteasome

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52
Q

how does n-glycosylation work

A

Oligosaccharide is attached to PM, neighboring a growing peptide chain. Oligosaccharide protein transferase transfers oligosaccharide to peptide chain.

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53
Q

what forms SS bond

A

protein disulfide isomerase or pdi;-helps correct disulfide bonds to form

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54
Q

There are no disulfides in cytosolic proteins. Why?

A

because of reducing environment, which means there is glutathione that breaks SS bonds

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55
Q

where do SS bonds exist

A

only inside organelles and extracellularly

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56
Q

what happens to SS bonds in cytosol

A

become SH sulfhydryl groups

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57
Q

what do sulfhydryl groups mean to ER

A

a signe of incomplete disulfide bond formation

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58
Q

can there be SS bonds in nucleus

A

no. it has a reducing environment like cytosol

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59
Q

What is the endomembrane system?

A

ER, Golgi (has cisternae), PM, endosomes, lysosomes/vacuoles, vesicles, peroxisomes

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60
Q

what is entry point to endomenbrane system

A

ER

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61
Q

what make EM a system

A

exchange of materials

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62
Q

what kind of transportation does EM rely on

A

vesicular transport

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63
Q

what is pH of ER

A

6

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64
Q

is lumen of EM acidic or basic

A

acidic

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65
Q

what is pH of lysosome. Why?

A
  1. due to H+ATPase, which adds protons
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66
Q

what happens to pH as proteins move farther into EM

A

gets more acidic

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67
Q

three parts of vesicular transport

A

formation (budding), movement to target membranes, fusion with target membranes

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68
Q

what are players in vesicle formation

A

cargo, receptor, adaptor, coat proteins, dynamin

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69
Q

vesicle formation steps

A

initiate bud, coat proteins drive vesicle formation, adaptors have clathrin triskeleon, then dynamin pinches off vesicle, coat falls off

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70
Q

what does dynamin use to pinch off vesicle

A

GTP; wraps around and pinches off

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71
Q

are adaptors always open

A

no, they are locked sometimes

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72
Q

with what do different adaptors associate

A

different membranes and different coat proteins via phosphoinositides in cytosolic leaflet

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73
Q

what can be modified in phosphoinositides

A

three OH groups after carbon 1

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74
Q

how are different PIPs produced

A

phosphorylation of 1, 2 or 3 carbons can form a variety of species

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75
Q

do animal cells only have one PI or PIP

A

no, they have various

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76
Q

what catalyzes PIP production

A

PIP phosphatase

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77
Q

where do PIPs live

A

in different membranes and different domains

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78
Q

what are PIPs associated with

A

specific vesicle transport events

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79
Q

vescicle membrane steps

A

Has PIP, fuses with PM, PI kinase adds P, recruits adaptor protein, initiate clathrin coated pit, vesicle hydrolizes and loses coat

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80
Q

how do coat proteins drive vesicle formation

A

via autoassembly

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81
Q

what is triskeleon made of

A

three heave clathrin chains and three light chains

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82
Q

types of coat proteins

A

clathrin, COPI, COPII

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83
Q

what do different coat proteins do

A

select different cargo

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84
Q

how does vesicle move

A

via cytoskeleton, does not float, motor proteins move vesicle along microtubule towards, for example, cis golgi

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85
Q

what does vesicle fusion with target membrane require

A

Rab and SNAREs

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86
Q

what form of Rab is active

A

Rab-GTP

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87
Q

what does Rab-GTP do

A

identifies target membrane

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88
Q

what do SNAREs do

A

drive vesicle fusion

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89
Q

how are SNARES built

A

have hydrophobic side and hydrophilic side extracellularly, so form coiled coils;have one transmembrane domain and one or two long amphipathic alpha helices

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90
Q

Coiled coils

A

nonpolar wrap around each other (two alpha helices, eg.);can join both in parallel and antiparallel direction

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91
Q

Types of SNAREs

A

v-SNARE –vesicular-attaches to vesicle;t-SNARE – target membrane – attaches to membrane

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92
Q

Vesicle fusion Steps

A
  1. Rab effectors does initial tether of vesicle to target membrane;2. the two different SNARE membranes pair;3. vesicle docks;4. fusion – Rab GAP hydrolyzes Rab GTP to Rab GDP, which then dissociates from membrane and returns to cytosol bound to GDI (keeps Rab soluble and inactive)
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93
Q

what happens to membrane orientation during fusion

A

;Membrane orientation is maintained with each budding and fusion event;one leaflet always faces cytosol

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94
Q

Botulism case

A

Man eats food contaminated with clostridium botulinum, which has toxin protease that cleaves SNAP25, t-SNARE no longer available, vesicle can’t bind to membrane in neuron terminal, so neurotransmitters can’t be released;With no vesicular fusion, there can be paralysis or death.

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95
Q

dissociation of SNARE pairs by NSF after fusion

A

;NSF binds to SNARE complex;has accessory proteins help; hydrolyzes ATP to pry SNAREs apart

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96
Q

membrane orientation during vesicular formation

A

-membrane orientation maintained with budding and fusion; that is, if C terminus is facing cytosol in organelle, it will face it in vesicle and in target membrane

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97
Q

charge of amino acid terminus

A

positive

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98
Q

golgi apparatus

A

– condensed stacks of membrane near cell center

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99
Q

golgi parts

A

cis golgi – receives from ER; trans golgi – stuff leaves golgi from here

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100
Q

major functions of golgi

A
  1. modification/synthesis of glygolipids and glycoproteins;2. golgi is post office
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101
Q

Secretory (anterograde) pathway

A

ER secretes vesicles vesicles form vesicular tubule cluster proteins marked with KDEL use retrograde pathway and return to ER other vesicles go to cis Golgi vesicles leave cis Golgi and go to cis, medial and trans Golgi cisternae vesicles go to trans Golgi vesicles leave trans Golgi and head to plasma membrane

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102
Q

The Golgi as post office

A

sorts to lysosome -sends proteins with mannose-6-phosphate (MSP) marker to lysosomes via endosomes; sorts to plasma membrane - -sends items to PM to be secreted or to become part of PM

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103
Q

Two types of secretion:

A

. constitutive and regulated

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104
Q

constitutive secretion

A

-all cells do constitutive exocytosis to maintain PM and extracellular space

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105
Q

regulated secretion

A

-signal mediated;-special, glandular cells send insulin, neurotransmitters, etc.;-dense vesicles aggregate and wait for signal so they can then cause short burst of a lot of protein

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106
Q

Exocytosis vs endocytosis in endomembrane system:

A

In growing, dividing cells : exo > endo;In nongrowing cells : exo = endo

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107
Q

Endomembrane system is:

A
  1. acidic ~ pH 5;2. has high Ca2+ concentration;3. causes soluble proteins to aggregate and form dense vesicles (not all proteins aggregate under acidic conditions)
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108
Q

Zip code for secreted proteins:

A

N-| SP | —————————— |-C; SP and nothing else – protein will be secreted from cell

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109
Q

golgi to lysosome zip code

A

Zip code: mannose-6-phosphate at N-glycosylation site ;N-| SP | ————Asn – X – Ser/Thr ————|-C;Has SP to get in ER;Golgi kinase uses ATP to ADP to phosphorylate sugar residue on protein (adds mannose-6-phosphate)

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110
Q

Trip to lysosome

A

ER Golgi endosome lysosome

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111
Q

Lysosome function

A

-recycling bin-acidic, pH ~ 5-H+ATPases – constantly pumps H+ into lysosomes-filled with digestive enzymes – acid hydrolases-has many exporters on surface

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112
Q

List of acid hydrolases:

A

Nucleases Proteases Glycosidases Lipases Phosphatases Sulfatases Phospholipases

113
Q

how does protease in lysosome treat protein

A

Protease in lysosome takes protein, degrades to amino acids and allows amino acids to be used to build other proteins

114
Q

Lysosomal Storage Disease:

A

-proteins don’t reach lysosomes-end up with overaccumulation-Inclusion cell disease – problems with transport of all hydrolytic enzymes to lyposomes-Tay-sachs – problems degrading glycolipids

115
Q

Pinocytosis

A

-small stuff-means cell drinking-via vesicular trafficking-all eukaryotes-regulated vs constitutive

116
Q

constitutive pinocytosis reason

A

to rejuvenate PM and extracellular space

117
Q

regulated pinocytosis reason

A

for specific material, receptor mediated

118
Q

regulated example in liver

A

Liver synthesizes LDL – bloodstream – LDL receptor – adaptin – clathrin coat – coat off – endosome – lysosome; From acidic endosome, receptor disassociates LDL and recycled back to PM; In lysosome, cholesterol is digested and secreted into cytosol

119
Q

More on the endosome

A

-first place pinocytosed materials go-acidic, receptors release cargo, go back to PM-acts like trans Golgi Network (TGN) (sorting);receptors back to PM or other stuff to lysosomes

120
Q

homotypic fusion

A

Endosomal fusion

121
Q

where do digestive enzymes fuse with endosomes

A

TGN

122
Q

what do endosomes have internally

A

multivesicular; have RNA

123
Q

Phagocytosis =

A

-large stuff-cell eating-foreign cells, cell debris (digested in lysosome)

124
Q

what does phagocytosis

A

white blood cells, amoebae, protists

125
Q

Autophagy:

A

self eating-for damaged organelles or starvation conditions, especially mitochondria

126
Q

Four degradation pathways

A
  1. from PM to phagosome to lysosome 2. from PM to phagosome to endosome to lysosome 3. from PM, endocytosed, early endosome, late endosome, lysosome 4. autophagy (double membraned autophagus)
127
Q

Inner mito membrane characteristics

A

-has no cholesterol, has infolding to form cristae, has electron transport system and ATP synthase, has enzymes for lipid synthesis

128
Q

why is inner membrane space more acidic than matrix space?

A

Protons are pumped into this space by the complexes in the ETC.

129
Q

Outer membrane characteristics

A

-has cholesterol, contains import receptors and porins for import of large molecules

130
Q

What encloses matrix compartment?

A

Inner membrane

131
Q

What does matrix compartment contain?

A

The DNA and dense concentration of proteins including those for transcription and translation activities, and enzymatic reactions like the citric acid cycle and fatty acid oxidation.

132
Q

What is inner membrane compartmentalized into? 2

A

Inner boundary membrane and crista membrane.

133
Q

Three distinct spaces in the mitochondrium

A

Inner membrane space, crista space, and the matrix.

134
Q

What is crista junction?

A

Joins cristae to inner boundary membrane

135
Q

What led to an aerobic eukaryotic cell?

A

The uptake of a bacterial cell with ability for respiration

136
Q

What was initial host cell of this bacterium? How did it gain a competitive advantage?

A

An anaerobic primitive eukaryotic cell or a type of archeal cell. With help of endosymbiont.

137
Q

To where did genes from endosymbiont move? How may proteins do modern mitochondrial genomes code for?

A

To the nucleus. 13 proteins.

138
Q

What is Rickettsia prowazekii?

A

An obligate intracellular parasitic bacterium that causes typhus.

139
Q

What is important about R. prowazekii?

A

It provides clues about the origins of mitochondria. Its bacterial genome is most closely related to mitochondrial genomes. It has 834 open reading frames – ten times more than most mito genomes.

140
Q

What gave rise to chloroplasts?

A

An endosymbiotic oxygen loving cyanobacterium (cyan)

141
Q

From what did mitochondria arise?

A

Alpha-proteobacterium

142
Q

What are the nearest relatives of mitochondria?

A

Three closely related groups of alpha-proteobacteria – the rhizobacteria, agrobacteria, and rickettsias.

143
Q

What kind of photosynthesis did ancestral fermenting bacteria do?

A

H2S

144
Q

What did ancestral fermenting bacteria evolve into?

A

Reducing atmosphere – green sulfur bacteria and purple sulfur bacteria. Oxidizing atmosphere – green filamentous bacteria, purple nonsulfur bacteria, and cyanobacteria.

145
Q

What happened before the rise of cyanobacteria?

A

H2O photosynthesis

146
Q

What three types of bacteria did purple nonsulfur bacteria break into?

A

Beta proteobacteria, alpha proteobacteria, and gamma proteobacteria

147
Q

What is extranuclear inheritance?

A

Phenotype does not segregate with nuclear genes.

148
Q

Yeast example of extranuclear inheritance

A

petite mutants grow very slowly and are deficient in respiration. The phenotype disappeared in cross of petite mutants to wild type strains. All diploid progeny were wild type. When these strains were sporulated, all haploid progeny were wild type. Poky phenotype did reappear sporadically as the haploid progeny continued to divide. They showed non-Mendelian inheritance.

149
Q

How many mitochondria do cells contain?

A

Multiple

150
Q

How many copies of DNA does each mitochondrion contain?

A

Multiple

151
Q

What did yeast progeny cells contain mitochondria wise?

A

They were heteroplasmic – contained multiple mitochondria, some mutant and some wild type.

152
Q

When did mutant yeast phenotype get expressed?

A

When WT mito fell into minority.

153
Q

What was the name of the mutant Neurospora crassa fungus?

A

Poky

154
Q

What is unusual about neurospora crassa crosses?

A

The females provide nucleus and cytoplasm. The males only provide nucleus. In crossing poky females to wt males, progeny were poky. If females were wt, progeny were wt.

155
Q

What happened when cytoplasm from “poky” cells was injected into wild type cells?

A

The wild type recipients became “poky”. The mitochondria had the ability to induce the “poky” phenotype. The poky mito have a replicative advantage over wt mitochondria and quickly become the dominant mitochondria in the cell.

156
Q

From where does a human inherit the mitochondria?

A

The mito DNA is inherited only from the mother’s egg. The sperm contributes a nucleus only.

157
Q

What DNA do human mitochondria contain?

A

A circle 5 microns in length, containing 16 kb of DNA.

158
Q

How is yeast mito DNA different from human?

A

It is five times larger, but has the same amount of genetic information.

159
Q

What do mitochondrial genomes encode?

A

All the tRNAs and ribosomal RNAs necessary for translation in the mitochondria.

160
Q

How many tRNA genes are there in mammalian mito?

A

22 tRNA genes

161
Q

How long is human mito DNA? Yeast mito DNA?

A

5microM vs 25 microM

162
Q

Are there introns in human mito DNA?

A

No

163
Q

What are the two strands of DNA in human mito genome?

A

Light strand and heavy strand

164
Q

What does human mito light strand encode?

A

1 protein and several tRNAs

165
Q

What does human mito heavy strand encode?

A

12 proteins, ribosomal RNAs, and several tRNAs

166
Q

where are tRNA genes placed on human mito heavy strand?

A

Between coding sequences so that they punctuate the genome

167
Q

What does the human mito genome control region contain?

A

Two promoters and one origin of replication.

168
Q

Where is human mito heavy strain transcribed from?

A

A “strong” promoter that produces many copies of the rRNAs

169
Q

What does human mito weak promoter do?

A

Results in one long polycistronic transcript that is cleaved to liberate the tRNAs. After cleavage, transcripts are polyadenylated. In some cases, the first base of the polyA tail is the last base of the stop codon.

170
Q

How does yeast mito genome compare to human mito DNA?

A

It has many more noncoding sequences. The tRNA genes in yeast mito are placed in clusters. The order of the genes is different than in mammalian mito. The genes have introns, some which encode transposases.

171
Q

What two things get imported into mito from cytosol? What happens to them?

A

Fatty acids and pyruvate. They get oxidized.

172
Q

What does oxidation of fatty acids and pyruvate generate in the Krebs cycle?

A

Acetyl CoA and NADH

173
Q

What does NADH contribute to ETC?

A

Electrons

174
Q

What does ETC do?

A

Pump protons into the inner membrane space, resulting in acidification of this space

175
Q

How is ATP produced in mitochondria?

A

Protons move down their concentration gradient through ATP synthase and produce ATP.

176
Q

What are the 3 major protein complexes of ETC?

A

NADH dehydrogenase complex, cytochrome c reductase, and cytochrome c oxidase

177
Q

NADH dehydrogenase complex characteristics

A

22 protein subunits, 7 encoded by mitochondrial genes

178
Q

What does NADH dehydrogenase complex pass electrons to?

A

The mobile carrier ubiquinone

179
Q

What does carrier ubiquinone pass electrons to?

A

The cytochrome b-c1 complex

180
Q

Characteristics of cytochrome b-c1 complex

A

15 protein subunits, 1 encoded by a mitochondrial gene

181
Q

Where are electrons from cytochrome b-c1 complex passed to?

A

The mobile carrier cytochrome c

182
Q

What does mobile carrier cytochrome c pass electrons to?

A

The cytochrome oxidase complex

183
Q

Characteristics of cytchrome oxidase complex

A

8 protein subunits, 3 encoded by mitochondrial genes

184
Q

what happens as electrons pass through the electron transport chain?

A

There are drops in free energy

185
Q

How does ATP synthase produce ATP?

A

It uses the energy from the proton gradient to produce ATP

186
Q

Characteristics of ATP synthase

A

12 subunits, two encoded by mitochondrial genes

187
Q

Does the control region of the mammalian mito DNA maintain exact nucleotide sequences?

A

No

188
Q

What does control region have?

A

One origin of replication and promoters for heavy strand and for light strand

189
Q

What type of cells do mito defects often affect?

A

Those that have a large ATP requirement such as optic nerve and muscles

190
Q

What diseases might be linked to mitochondrial defects?

A

Deafness, neuromuscular disease, alzheimers, parkinsons

191
Q

What do some mito diseases result from?

A

Mutations in mito tRNA gene

192
Q

Database of mitochondrial diseases

A

MITOMAP

193
Q

When may mito diseases develop?

A

When somatic tissues acquire spontaneuous mutations in mito DNAs

194
Q

Can mito repair their DNA?

A

They don’t have a strong DNA repair system

195
Q

What do reactions on the cristae do to cause mutations?

A

Generate high levels of free radicals (superoxides)

196
Q

What do mutations in the control region of human mito DNA do?

A

Suppress mito DNA replication and transcription

197
Q

How many patients with mito disease have same mutation?

A

70-80%

198
Q

How do mito mutations accumulate? What type of mutations are they?

A

With aging. They are somatic, not germline, mutations.

199
Q

How do cells change as patients age?

A

They increase in heteroplasmy.

200
Q

When do cells die because of mito disfunction?

A

Once a critical threshold is reached (loss of more than ~15% wild type mito

201
Q

What is alzheimer’s disease?

A

Neurons die due to oxidative stress

202
Q

What is amyloid beta-peptide (Abeta)?

A

A 40-42 amino acid peptide that is a component of amyloid plaques found in the brains of alzheimer’s patients.

203
Q

How does Abeta interact with mitochondrial alcohol dehydrogenase?

A

It inhibits its function

204
Q

How does alpha beta peptide enter mitochondria?

A

It is imported into mito and localizes to cristae.

205
Q

What may cause mitochondrial diseases to develop in humans?

A

When somatic tissues acquire spontaneous mutations in mitochondrial DNAs. These mutations accumulate with aging.

206
Q

What kind of gene is the mitochondrial DNA polymerase?

A

A nuclear gene

207
Q

What two domains does the mitochondrial DNA polymerase have?

A

A polymerizing domain and a proofreading domain

208
Q

What mito DNA polymerase domain was mutated in mice in an aging experiment?

A

The proof-reading domain

209
Q

What happened to the mice that were homozygous for the mito DNA polymerase proof-reading domain mutation?

A

The mice aged much more rapidly than wild-type mice and lived only about half as long.

210
Q

How many mitochondria does a cell have?

A

Many

211
Q

How many copies of mito DNA does each mitochondrion have?

A

Many

212
Q

Would a somatic mutation in one copy of the mito DNA have a detectable phenotype?

A

Not initially, but over time the mutant mito may come to dominate the population.

213
Q

Until when is tissue normal when there are mito DNA mutations?

A

Until about 85% of mitochondrial DNA copies contain the mutation. Then the tissue crashes and function is lost.

214
Q

Where are there numerous mutations found in mitochondria?

A

tRNA genes and protein coding genes

215
Q

How many mitochondria do oocytes have?

A

~10,000

216
Q

How are defective mitos treated in oocyte?

A

They are screened out and removed as the oocyte develops by a mechanism that is not understood.

217
Q

What happens if defective mitos are not removed from oocyte?

A

Mutant mito DNA will pass to the progeny.

218
Q

Is there a germline gene therapy for inherited mitochondrial diseases?

A

The 3-parent baby is a new approach that has been approved by british parliament and is being considered by FDA.

219
Q

What is the 3-parent baby approach?

A

The chromosomes, contained on the meiosis I spindle, are removed from the oocyte that contains defective mitochondria. It is injected into a second oocyte (with normal mito) from which the spindle has been removed. The result is an oocyte with mito from one mother and nuclear genome from a second mother. The sperm can then fertilize the resulting egg.

220
Q

What is heteroplasmy?

A

The condition in which some mitochondrial DNA copies in a cell are wild-type while other copies contain a mutation.

221
Q

Two ways to prevent rare mitochondrial diseases?

A

Maternal spindle transfer; pronuclear transfer

222
Q

Maternal spindle transfer

A

Chromosomes are removed from oocyte that has mutated mito DNA; these are added to an unfertilized donor egg that has had its nucleus removed; this fused egg is fertilized in vitro; the egg develops normally to form an embryo.

223
Q

Pronuclear transfer

A

An egg with mutated mito DNA is fertilized in vitro; the resulting pronucleus is removed; this is transferred to a fertilized donor egg that has had its pronucleus removed; the fused egg develops normally.

224
Q

Cytosolic S Ribosomes vs michondrial S ribosomes

A

80 S vs 55 S

225
Q

Cytosolic rRNA vs mito rRNA

A

Both Lg rRNA, Sm rRNA

226
Q

Cytosolic RNA vs mito RNA

A

5S RNA, 5.8S RNA vs nothing

227
Q

cytosolic tRNAs vs mito tRNAs

A

60 tRNAs vs 22 tRNAs

228
Q

inhibitors of mitochondrial ribosomes

A

chloramphenicol; erythromycin; vancomycin; lincomycin

229
Q

chloramphenicol

A

broad-spectrum antibiotic causes aplastic anemia in children (non-reversible damage)

230
Q

CIPRO

A

Antibacterial drug that can target mitochondria. CIPRO inhibits bacterial DNA gyrase and also inhibits mito DNA gyrase.

231
Q

How are the very hydrophobic proteins encoded by mito DNA synthesized in the aqueous environment of the matrix and then imported?

A

Answer is in mito ribosome and its unusual structure. Proteins functionally replace rRNA to some extent. Ribosomal proteins dock the ribosome to the OXA complex. As they exit from the ribosome, nascent proteins are directed immediately into a channel in the PXA complex for insertion into the membrane.

232
Q

What percent of mito proteins is encoded in nucleus?

A

More than 90%

233
Q

Where are mRNAs translated?

A

On cytosolic ribosomes

234
Q

When does transport into mitochondria occur?

A

Only post-translationally

235
Q

What do proteins destined for import into mito contain?

A

A presequence (leader sequence, targeting sequence).

236
Q

What happens to the mito protein presequence when the protein is folded?

A

The sequence becomes amphiphilic – plus charges on one side, nonpolar on the other.

237
Q

How do mito protein leader sequences get to the TOM complex?

A

Receptors on the outer membrane bring these leader sequences to the TOM complex.

238
Q

TOM complex

A

Translocase of the outer membrane; contains 7-8 proteins but only two proteins required form import: TOM 22, TOM 40

239
Q

TIM complex

A

Translocase for the inner membrane – TIM 22, TIM 23

240
Q

How do TOM and TIM work together?

A

They line up together in regions where the inner and outer membranes are closely spaced. An extension of the TIM complex interacts with the TOM complex.

241
Q

What experiments revealed mitochondrial pre-sequence (targeting sequence)?

A

So basically, create a protein with radioactive amino acid labels. Add mito in early translation and late translation and see that it is smaller in SDS because it has been imported and pre sequence was cleaved off. If we treat the mito with protease to remove proteins from surface, or remove membrane potential, or deplete ATP, the mito can’t import the protein, so pre-sequence is never cleaved.

242
Q

Cytosolic HSP70

A

Heat shock proteins and chaperones

243
Q

Role of chaperones in cytosol

A

Bind mitochondrial precursor proteins (client proteins) in cytosol and keep them unfolded

244
Q

What is required for HSP70 to release the client protein

A

ATP hydrolysis

245
Q

What happens to N-terminus of protein when it is imported into mito?

A

It is threaded first through TOM complex and adjacent TIM complex. Then mito HSP70 in matrix binds the protein and pulls it into the matrix using ATP dependent “ratchet” mechanism.

246
Q

What happens to protein once it has been imported into mito matrix?

A

Signal peptidase cleaves the signal peptide and the HSP70 continues to “pull” the remainder of the protein into the matrix.

247
Q

What is required in mito matrix to fold proteins?

A

An HSP60 protein

248
Q

What mechanisms are used to sort proteins into inner mito membrane?

A

Different mechanisms, including the OXA complex on the inner membrane. Some proteins enter matrix and then associate with the OXA complex to insert into the inner membrane.

249
Q

How do proteins import into different mito compartments?

A

a. N-terminal signal sequence initiates import into matrix space (after going through TOM). A hydrophobic sequence binds to TIM 23 and stops translocation. Remainder of the protein is then pulled into the intermembrane space through TOM, and hydrophobic sequence is released into the inner membrane to anchor protein. B. inner membrane intergration – protein goes into matrix space completely. Signal sequence cleaved off, revealing hydrophobic sequence that uses OXA dependent pathway to insert itself in inner membrane and pull rest of protein out into intermembrane space. C. soluble intermembrane space proteins released into intermembrane space by a second signal peptidase which has active site in intermembrane space and removes hydrophobic signal sequence. D. soluble intermembrane proteins oxidized by Mia40 during import from outer membrane. Mia40 forms covalent intermediate through intermolecular disulfide bond, which pulls protein through TOM. Mia40 becomes reduced in process and is reoxidized by ETC, so it can catalyze next import round. E. multipass inner membrane proteins that function as metabolite transporters contain internal signal sequences and snake through TOM complex as a loop. Bind to chaperones in intermembrane space that guide them through TIM22.

250
Q

What is TIM 22 specialized to do?

A

Insert multipass inner membrane proteins

251
Q

How many pores does Tom complex have?

A

Two. They work together.

252
Q

Which proteins can’t be removed from TOM complex for import?

A

TOM40 and TOM22

253
Q

Role of peroxisomes

A

Like mito, play a role in oxidative pathway in cells

254
Q

Do peroxisomes have DNA?

A

No

255
Q

Do peroxisomes have a double membrane layer?

A

No. a single membrane.

256
Q

How many enzymes do peroxisomes have? What do they do?

A

50-60 enzymes, most involved in detox reactions

257
Q

two step peroxisome detox process

A
  1. substrates like uric acid and aa are oxidized to form H2O2. Very long-chain fatty acids are oxidized in detox reactions. 2. Catalase breaks down the H2O2.
258
Q

How do fireflies use peroxisomal enzyme luciferase?

A

To oxidize a substrate luciferin to emit visible light from cells in the abdomen.

259
Q

What causes zellweger syndrome?

A

Mutations in genes required for import of proteins into peroxisomes. Peroxisomes are not functional and patients die at an early age.

260
Q

What happens to catalase antibody in some patients with zellweger’s?

A

Catalase antibody does not detect catalase in peroxisomes, but does detect PMP70 from the peroxisomal membrane. So peroxisome membranes are present but empty.

261
Q

What was observed in some fusion combinations of fibroblasts from different patients?

A

Rescue or “complementation” of the defect.

262
Q

How many genes have been identified that can cause zellweger’s when mutated?

A

18-20

263
Q

How have genetic mutations that cause zellweger’s been used?

A

To identify the assembly steps for peroxisomes

264
Q

What kinds of peroxisomes mutations are there?

A

Those that cause defects in 1 formation of peroxisomes 2. Import of proteins into peroxisomes and 3 function of protein (enzymes) in the peroxisomes.

265
Q

Peroxisome biogenesis

A

Peroxisomal membranes are derived from vesicles budding from ER

266
Q

How are additional proteins to peroxisomes?

A

By import from cytosol. Membrane and matrix proteins are imported.

267
Q

How can peroxisomes fuse and divide?

A

By fission

268
Q

What do peroxisomal matrix proteins contain?

A

A targeting sequence (PTS1) at the C-terminus which is recognized by Pex 5 receptor.

269
Q

What receptor does Pex5 work with?

A

Pex14 receptor, located on peroxisome membrane.

270
Q

What happens to matrix protein=Pex5 complex?

A

It is transferred to a set of membrane proteins (Pex 10, 12 and 2) that are necessary for translocation into the peroxisomal matrix by an unknown mechanism.

271
Q

What happens to Pex5 after protein has been translocated?

A

It dissociates from the matrix protein and returns ot the cytosol, a process that involved the Pex2/10/12 complex and addl membrane and cytosolic proteins not shown.

272
Q

Can folded proteins be imported into peroxisome?

A

Yes. Their targeting sequence is not removed in the matrix.

273
Q

What genes encode peroxisomal proteins?

A

Nuclear genes

274
Q

Where are peroxisomal proteins synthesized?

A

On cytosolic ribosomes and folded in cytosol.

275
Q

What is SKL?

A

A targeting sequence at C terminus of peroxisomal proteins

276
Q

What does Pex5 become during protein import?

A

Part of the translocation pore (transient pore)

277
Q

Is unfolding of protein required for import into peroxisome?

A

No

278
Q

How is large catalase tetramer imported into peroxisome?

A

In its folded state.

279
Q

What, in general, do receptor proteins for peroxisome do?

A

They shuttle back and forth from the peroxisome to the cytosol to bind peroxisomal proteins and bring them to the peroxisome.

Cell Biology (35 decks)

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