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MCB1 Block 3 > Mitochondria > Flashcards

Mitochondria Flashcards

1
Q

How many membranes does mitochondria have?

A

2 - outer and inner

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2
Q

Where are ATP synthases located?

A

inner membrane

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3
Q

What is the equivalent to the cytoplasm in the mitochondria?

A

mitochondrial matrix

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4
Q

The majority of proteins for mitochondria are encoded in ____

A

nuclear genome

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5
Q

The mitochondria has ____ that code for itself

A

its own genome

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6
Q

there are enzymes in the matrix that are involved in breakdown of what?

A

food products

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7
Q

What is mitochondria known for?

A

ATP production - power plant

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8
Q

ATP production is what kind of respiration?

A

Aerobic

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9
Q

The number of mitochondria in a cell varies depending on what?

A

That cells energy needs.

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10
Q

What kinds of cells have a lot of ATP?

A

neurons and muscle

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11
Q

What is significant about the outer membrane of mitochondria?

A

It is permeable to ions

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12
Q

What is significant about the inner membrane of mitochondria?

A

It is impermeable to ions

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13
Q

What protein contributes to the impermeability of the inner membrane?

A

cardiolipin

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14
Q

What is between the inner and outer membrane in mitochondria?

A

intermembranous space

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15
Q

The matrix encodes for its own _____

A

ribosomes

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16
Q

Where does actual ATP production occur?

A

matrix

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17
Q

What important reactions happen in the mitochondria inner membrane?

A

ETC, ATP synthesis (the actual production of ATP occurs in matrix)

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18
Q

Oxidative metabolism is the production of ____

A

ATP

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19
Q

What important synthesis happens in outer membrane of mitochondria?

A

Cardiolipin synthesis

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20
Q

Where are TCA cycle enzymes located?

A

matrix of mitochondria

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21
Q

What allows for the free diffusion of ions in outer membrane of mitochondria?

A

Porins

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22
Q

Where do transmembrane proteins cross in mitochondria?

A

Outer & inner membrane

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23
Q

Where is peptidoglycan located in mitochondria?

A

intermembranous space

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24
Q

What is a double phospholipid?

A

Has four fatty acid tails

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25
Q

A cardiolipid is a ____

A

phospholipid

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26
Q

Where is cardiolipid made?

A

Mitochondria

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27
Q

Key words: cardiolipin synthesis, SIDS, high mortality in infants are what disease?

A

Barth syndrome

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28
Q

Defect in cardiolipin is the cause of what disease?

A

Barth syndrome

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29
Q

What is the mode of inheritance for barth syndrome?

A

x-linked

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30
Q

Characteristics: SIDS, cardiomyopathy, generalized muscle weakness, chronic fatigue, neutropenia are what disease?

A

Barth syndrome

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31
Q

What is neutropenia?

A

abnormally low concentration of neutrophils in blood

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32
Q

What is the mechanism for Barth syndrome?

A

defect in cardiolipid -cardiolipid helps create impermeability of inner membrane in mitochondria → lack of structure & permeability → inefficient ATP synthesis → chronic fatigue

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33
Q

Where does glycolysis take place?

A

cytoplasm

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34
Q

What does glycolysis become?

A

pyruvate

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35
Q

Without oxygen, pyruvate goes through what?

A

fermentation

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36
Q

With oxygen, pyruvate goes through what reaction?

A

oxidative phosphorylation

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37
Q

What is pyruvate broken down to in mitochondria?

A

Acetyl CoA

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38
Q

How is the first proton pumped into the intermembranous space in the ETC?

A

NADH has a high energy electron, complex I has higher affinity for electron than NADH, with the coupling of electron a proton is released into inter membranous space

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39
Q

How many complexes are there in the ETC?

A

4

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40
Q

Each time an electron is passed from one carrier to the next in the ETC, what happens?

A

a proton is pumped into intermembranous space

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41
Q

Why are protons pumped into intermembranous space in ETC?

A

to create a proton gradient, want a much higher concentration of protons outside of matrix

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42
Q

How can protons enter into matrix of mitochondria?

A

ATP synthase

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43
Q

How is acetyl CoA metabolised?

A

By TCA, reduces NAD+ to NADH

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44
Q

What is used to pass high energy electrons to first complex in ETC?

A

NADH

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45
Q

When proton enters the cell through ATP synthase, what allows that process to create ATP?

A

mechanical energy rotates enzyme and uses that energy to couple ADP and inorganic phosphate to make ATP

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46
Q

Once ATP is made in mitochondria, what happens to it?

A

It is exported to cytoplasm for use

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47
Q

Why is it called oxidative phosphorylation?

A

oxidation: generating high energy electrons
phosphorylation: the electrons are used to couple ADP to inorganic phosphate to create ATP

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48
Q

What is the gradient across the inner and intermembrane space called?

A

electrochemical proton gradient

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49
Q

Why is it called the electrochemical proton gradient?

A

Chemical: the intermembrous space has lower pH b/c of all the protons
electro: charge is more positive in intermembrous space

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50
Q

What drives ATP synthesis?

A

Electrochemical proton gradient

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51
Q

What does the proton couple with at the end of the ETC?

A

Oxygen - makes water

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52
Q

Where is the proton carrier located in ATP synthase?

A

transmembrane

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53
Q

Where is the head located in ATP synthase?

A

matrix

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54
Q

What does the head do in ATP synthase?

A

binds ADP to inorganic phosphate, it does this via rotation and conformation change

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55
Q

How does the head attach ADP to inorganic phosphate (Pi) in ATP synthase?

A

rotation and conformational change

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56
Q

What does ATP synthase do?

A

couples oxidation to phosphorylation

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57
Q

What assists ATP in leaving the mitochondria and going to the cytoplasm?

A

mitochondrial gradient (there is different pH and voltage gradient)

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58
Q

What does the TCA cycle create?

A

CO2 & NADH

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59
Q

How do the concentrations of ions in cytoplasm and intermembranous space of mitochondria compare?

A

They are similar

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60
Q

Protons fall down ______ ______ through ATP synthase, making ATP

A

electrochemical gradient

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61
Q

What is the exception to the way mitochondria make ATP?

A

thermogenesis - brown fat

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62
Q

What do the TCA and ETC produce in brown fat?

A

heat

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63
Q

What does UCP stand for?

A

uncoupling protein

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64
Q

What is another name for uncoupling protein?

A

thermogenin

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65
Q

What does thermogenin do?

A

It uncouples oxidation from phosphorylation to make heat

it allows protons to “leak “ from cytoplasm to matrix

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66
Q

Electrons have a very high affinity for what?

A

Oxygen

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67
Q

What happens when an electron reacts with oxygen?

A

Free radical (reactive oxygen species)

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68
Q

There is high probability of what bad thing happening in mitochondria?

A

free radicals being created

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69
Q

What does ROS stand for?

A

reactive oxygen species

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70
Q

ROS is very damaging to what?

A

ETC, protein, DNA, RNA

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71
Q

Why is ROS in mitochondria so dangerous compared to say, a ROS in nucleus?

A

mitochondrial genome does not have repair mechanisms that are in place in nucleus

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72
Q

Mutations in mitochondrial genes will affect what?

A

ETC

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73
Q

Explain how ROS can lead to snowball affect

A

More ROS leads to more damage of DNA, ETC, etc. the more damaged the DNA & ETC is, the more ROS is created, and the cycle continues

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74
Q

What is the function of superoxide dismutase?

A

It converts ROS to hydrogen peroxide

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75
Q

What is the function of glutathione peroxidase?

A

converts hydrogen peroxide to water

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76
Q

What does SOD2 stand for?

A

superoxide dismutase

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77
Q

What does GPX stand for?

A

glutathione peroxidase

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78
Q

Describe the extrinsic pathway for apoptosis

A

Cell: death receptor → death ligand binds death receptor → recruits proteins → activate caspase →activates more caspases →digest cell→ scramblase inhibitor broken down → scramblase puts phosphotidyl serine on outside

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79
Q

Describe the intrinsic pathway for apoptosis in mitochondria

A

DNA damage → opening of pores in outer membrane of mitochondria → cytochrome C leaks to cytoplasm → cytochrome C combines w/ cytosolic protein Apaf1 → activates caspases → cell death

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80
Q

What is caspase important for?

A

apoptosis

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81
Q

Bcl-2 is a family of proteins that control what?

A

control pore formation in mitochondria

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82
Q

What do pro-apoptotic bcl-2 proteins do?

A

promote pore formation in mitochondria

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83
Q

Pore formation in mitochondria promotes what?

A

apoptosis

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84
Q

What do anti-apoptocic bcl-2 proteins do?

A

inhibit the pro-apoptotic bcl-2 proteins, which stop apoptosis

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85
Q

BAX & BAD are examples of what?

A

pro-apoptotic bcl-2 proteins

86
Q

What does Bcl-2 inhibit?

A

BAX

87
Q

Bcl-2 is what kind of protein?

A

anti-apoptotic

88
Q

Cytochrome C in cytosol activates what for apoptosis?

A

caspase cascade

89
Q

How do mitochondria replicate/divide?

A

lengthen and then go through fission (similar to bacteria)

90
Q

Explain the bottleneck affect in mitochondria

A

There are lots of mitochondria, but only a few are taken to create an egg. The egg could have all normal cells, all mutant cells, or any combination. Depending on the mitochondria in the egg, and then how that replicates, will determine if child will express disease

91
Q

What is heteroplasmy?

A

Variability of mitochondrial diseases. can’t say recessive or dominnat b/c of all the mitochondria in cell.

92
Q

What is homoplasmy?

A

All mitochondria are the same - can be wild type or mutant (almost all homoplasmy mutants will die)

93
Q

How does mitotic segregation affect the way wild type and mutant mitochondria divide and affect a child?

A

Certain cells can end up having way more mutant mitochondria than others, and certain tissues can be more affected than others

94
Q

What cells are most affected by mitochondrial inheritance?

A

muscle & neuron

95
Q

What does mRNA have to have to enter mitochondria?

A

mitochondrial signal sequence

96
Q

Where are mRNA that are destined to mitochondria folded?

A

In mitochondria

97
Q

What is the purpose of Hsp70?

A

Prevents mitochondrial protein from folding in cytoplasm

98
Q

Where are Hsp70 proteins located?

A

In cytoplasm and matrix of mitochondria. They have different functions in both locations. in cytoplasm prevents folding of protein, in mitochondria it helps fold protein

99
Q

What is TOM?

A

A protein in outer membrane of mitochondria that Hsp70 will bind to

100
Q

What happens once Hsp70 binds to TOM?

A

the unfolded protein travels across membrane, signal sequence is removed by protease, protein spontaneously folds or is helped by Hsp60

101
Q

What does TOM stand for?

A

translocase of outer membrane

102
Q

What helps protein fold in mitochondria?

A

Hsp60

103
Q

How many proteins are encoded for in mitochondria?

A

13

104
Q

How many total genes are in mitochondrial DNA?

A

37

105
Q

How many tRNA genes are in mitochondrial DNA?

A

22

106
Q

How many rRNA genes are in mitochondrial DNA?

A

2

107
Q

What are the two strands of the mitochondrial genome called?

A

H-strand & L-strand

108
Q

H-strand is rich in what?

A

G

109
Q

L-strand is rich in what?

A

C

110
Q

How many genes are encoded for in H strand?

A

12 of the protein - coding genes

111
Q

How many genes are encoded for in L-strand?

A

1 protein coding gene (and some tRNA)

112
Q

What controls the replication and transcription of mitochondrial DNA?

A

D loop

113
Q

What does D loop stand for?

A

Displacement Loop

114
Q

How many origins of replication are there no the mitochondrial genome?

A

2

115
Q

How are mitochondrial strands transcribed?

A

polycistronically (at the same time)

116
Q

Which is the heavy mitochondrial strand?

A

H-strand

117
Q

Which is the light mitochondrial strand?

A

L-strand

118
Q

What is the promoter for the heavy strand?

A

HSP

119
Q

What is the promoter for the light strand?

A

LSP

120
Q

How are the promoter regions for the two mitochondrial strands related to each other?

A

H promoter (Oh) is at twelve o clock, L promoter (OL) is at 8 o clock

121
Q

Which complex in ox phos pathway contains only nuclear-encoded proteins?

A

Complex II

122
Q

Complex I contains how many genes encoded for by mitochondria?

A

7

123
Q

Complex III contains how many genes encoded for by mitochondria?

A

1

124
Q

Complex IV contains how many genes encoded for by mitochondria?

A

3

125
Q

Complex V contains how many genes encoded for by mitochondria?

A

2

126
Q

What surrounds every protein coding gene in mitochondrial genome?

A

tRNA coding genes

127
Q

What is one purpose of tRNA coding genes in mitochondrial genome?

A

Act as spacers b/w different genes

128
Q

Which complexes in mitochondria carry out oxidative phosphorylation?

A

I, III, IV

129
Q

Replication occurs _____ for mitochondrial DNA (symmetric or not?)

A

Asymmetrically

130
Q

To complete replication, mtDNA has its own ____ and ____

A

polymerase and helicase

131
Q

One cell may contain how many mtDNA genomes?

A

thousands

132
Q

Are there okazaki fragments in mtDNA replication?

A

no

133
Q

What is the dedicated helicase for mtDNA called?

A

Twinkle

134
Q

How many mitochondrial DNA polymerase are there?

A

1

135
Q

What is the name of the mitochondrial DNA polymerase?

A

DNA polymerase gamma

136
Q

What is the function of DNA polymerase gamma?

A

mostly replication, some repair

137
Q

What does the PLOG gene encode?

A

Catalytic subunit

138
Q

Mutations in PLOG are associated with what?

A

reduced levels of mtDNA and/or mutations in the mtDNA

139
Q

What is Ophtalmoplegia?

A

Weakness or paralysis of muscles that move the eye

140
Q

Key words: bilateral ptosis, mtDNA depletion/deletion, polymerase gamma are what disease?

A

Progressive External Ophtalmoplegia (PEO)

141
Q

PEO stands for what?

A

Progressive External Ophtalmoplegia (PEO)

142
Q

Characteristics: Bilateral ptosis – progressive weakening of external eye muscles, proximal muscle weakness and wasting, exercise intolerance are what disease?

A

PEO - Progressive External Opthalmoplegia

143
Q

What is the most common mode of inheritance for PEO?

A

Autosomal dominant, but can be autosomal recessive

144
Q

How many genes are involved in PEO disease?

A

5

145
Q

If PLOG or TWINKLE is the mutated in PEO disease, what is the mode of inheritance?

A

AD

146
Q

What is the mechanism for PEO?

A

mtDNA depletion or large deletion - usually is large deletion

147
Q

What two proteins may affected by mutations in PEO?

A

Twinkle & PLOG

148
Q

What kind of mutation is more damaging to the mtDNA and will have more sever clinical outcomes?

A

Missense mutations

149
Q

What is the name of a nucleoside used to treat HIV?

A

AZT

150
Q

Describe AZT

A

A nucleoside used to treat HIV. It is thymidine analogue - has thymidine without hydroxyl group at 3’ and with a bunch of nitrogens at 2’

151
Q

What is Zidovudine?

A

Another name for AZT - drug used to treat HIV

152
Q

What is the mechanism AZT/Zidovudine works?

A

It doesn’t affect DNA Pol delta (in nucleus) but DNA Pol gamma (in mitochondria) is inhibited. B/c it is attached to methylated thymine, thymine will insert itself onto mtDNA and cause deletion of DNA. It protects against HIV because it competes with dTTP for incorporation into DNA by viral reverse transcriptase

153
Q

What is myopathy?

A

disease of muscle

154
Q

What is a side effect of AZT?

A

Myopathy

155
Q

What are the names of the two promoters in control region of mtDNA?

A

HSP & LSP

156
Q

What processes the giant transcripts from mitochondria?

A

RNA endonuclease

157
Q

What does RNA endonuclease recognize in the mitochondria to excise certain genes?

A

It recognizes secondary structure in tRNA of the giant transcripts

158
Q

mRNAs in mitochondria are ______ but not _____

A

poly adenylated but not capped

159
Q

How does protein synthesis in mitochondria resemble that of bacteria?

A

It starts with N-formyl methionine

160
Q

Which has more repeats, nuclear or mitochondrial DNA?

A

nuclear

161
Q

How many tRNAs are involved in mitochondrial translation?

A

22

162
Q

Explain the difference b/w tRNA in mitochondria and the rest of the cell

A

There is more wobble in tRNA in mitochondria, there is less tRNA available to recognize all the codons

163
Q

What is the exception to the universal genetic code? Give example

A

Mitochondria codons do not code for the same thing as codons for everything else. Ex: UGA is usually stop codon, in mitochondria it codes for Trp

164
Q

What is the size of the nuclear genome compared to mitochondrial?

A

Nuclear: 3 billion bp
Mitochondrial: 16 thousand bp

165
Q

Are there introns in mitochondrial DNA?

A

No

166
Q

Compare the % of coding DNA in nuclear genome vs. mitochondrial

A

Nuclear: 3%
Mitochondrial: 93%

167
Q

What is the mutation rate of mitochondrial DNA? Why?

A

10x faster than in nuclear DNA. b/c of oxygen radicals formed after ox/phos

168
Q

Mitochondrial DNA is very variable, meaning it is _____

A

polymorphic

169
Q

Why is mtDNA so polymorphic?

A

the high mutation rate

170
Q

The variations in mtDNA are mostly what?

A

SNP’s (single nucleotide polymorphism) & small deletions/insertions

171
Q

What are the 3 major types of mutations in mtDNA?

A

deletions or duplications
point mutations in tRNA
Missense mutations in coding regions

172
Q

What do most mtDNA mutations affect

A

ox/phos - ultimately ATP production

173
Q

Describe a ragged red muscle fibers

A

It has defective mitochondria, so more mitochondria are produced. If you biopsy and stain with certain dye, it will look ragged and stain red, it has a lot more mitochondria.

174
Q

What is the threshold hypothesis for mtDNA disorders?

A

the proportion of mutated mtDNA molecules must exceed a certain threshold before clinical consequences

175
Q

Mitochondrial diseases often exhibit what?

A

reduced penetrance

176
Q

The _____ of consequence of mitochondrial mutations correlates with _____ of mutated molecules

A

severity, proportion

177
Q

People can survive giant mutations in mtDNA but not if it’s ______

A

homoplasmic

178
Q

Giant deletions are usually inherited how?

A

Spontaneously - not passed down

179
Q

A giant deletion is easy to detect using what method?

A

southern blot

180
Q

How will a giant deletion present on a southern blot compared to a normal mitochondrial DNA?

A

normal will have one blot. Mutated will have 3, because of the deletion. They will be thicker b/c there is more mitochondria b/c cell is compensating for it not working well

181
Q

The ____/______ of bottleneck with oocytes can cause very different levels of heteroplasmy in children

A

restriction/ampmlification

182
Q

key words: no bone marrow involvement, late onset, ragged red fibers are what disease?

A

Kearns-Sayre Syndrome (KSS)

183
Q

KSS stands for?

A

Kearns-Sayre Syndrome

184
Q

Characteristics: late onset, typical ragged red fibers (>80% mutated mtDNA), PEO, retinopathy, cerebellar ataxia, heart block are what disease?

A

Kearns-Sayre Syndrome

185
Q

What is the mode of inheritance for KSS?

A

mitochondrial

186
Q

What is the mechanism for KSS?

A

giant mtDNA deletion

187
Q

What does MELAS stand for?

A

Mitochondrial Encephalomyopathy, Lactic Acidosis and Stroke-like episodes

188
Q

What is mutated in MELAS?

A

leucine tRNA

189
Q

Key words: tRNALeu, short, stroke, diabetes are what disease?

A

MELAS

190
Q

Characteristics: short stature, stroke-like episodes (vomiting, headaches, visual disturbances), diabetes, sensorineural hearing loss are what disease?

A

MELAS

191
Q

MELAS is always what?

A

heteroplasmic

192
Q

key words: tRNALys, ragged red fibers, epilepsy are what disease?

A

MERRF

193
Q

characteristics progressive myoclonic epilepsy and seizures are what disease?

A

MERRF

194
Q

MERRF stands for?

A

Myoclous Epilepsy and Ragged Red Fibers

195
Q

MERRF is always

A

heteroplasmic

196
Q

What is the mutated gene in MERRF?

A

lysine tRNA

197
Q

What does LHON stand for?

A

Leber’s Hereditary Optic Neuropathy

198
Q

What is the only mitochondrial disease that might be homoplasmic?

A

LHON

199
Q

What kind of gene mutation is in LHON?

A

missense

200
Q

key words: mutated Complex I gene, optic nerve damage, homoplasmy, bilateral vision failure are what disease?

A

LHON

201
Q

characteristics: subacute painless bilateral visual failure, male:female 4:1 (X-chromosome penetrance), ~24 years old are what disease?

A

LHON

202
Q

What complex is affected in LHON?

A

Complex 1

203
Q

key words: ATPase 6 gene, ataxia, retinopathy, pigmentation, Leigh Syndrome Note: Maternally inherited Leigh Syndrome is a more severe form with a larger portion of mutated mtDNA are what disease?

A

NARP

204
Q

characteristics: late childhood or adult onset peripheral neuropathy, ataxia, pigmentary retinopathy are what disease?

A

NARP

205
Q

NARP is always

A

heteroplasmic

206
Q

What does NARP stand for?

A

Neurogenic muscle weakness, Ataxia, and Retinitis Pigmentosa

207
Q

What kind of mutation is in NARP?

A

missense

208
Q

what gene is mutated in NARP?

A

ATPase 6 gene of Complex V

209
Q

NARP is a ____variation of Leigh syndrome

A

milder

210
Q

Describe 3 parent babies

A

mother with affect mtDNA can have unaffected children, nuclear genome of affected zygote transferred to another zygote from unaffected donor.

MCB1 Block 3 (15 decks)

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