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Molecular Cell Biology > Lecture I > Flashcards

Lecture I Flashcards

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1
Q

What is mitochondria important in?

A

neurodegenerative disorders, diabetes, cancer, and many other multifactorial diseases

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2
Q

What is the endosymbiotic theory?

A

in ancient time, gram- proteobacterium was engulfed by an ancestral cell, conferring oxidative phosphorylation to the ancestral eukaryotic cell

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3
Q

Describe the mitochondria:

A

2 membranes (outer and inner)

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4
Q

What is the inner membrane of the mitochondria divided into?

A

inner boundary membrane (translocons and transporters) and cristae (invaginations that are the site of oxidative phosphorylation)

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5
Q

What is the shape of the cristae important for?

A

it is needed to maximize the functionality of the respiratory chain

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6
Q

What is the function of the inter membrane space?

A

space between the 2 membranes and the matrix

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7
Q

What is located in the matrix of the mitochondria?

A

mitochondrial DNA where many metabolic processes take place like Krebs (crucial for the respiratory chain as it provides the NADH and FADH₂), β-oxidation of fatty acids, steroidogenesis, the generation of heme, etc.

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8
Q

What is important to remember in regards to mitochondria?

A

posses their own DNA so they cannot by generated de novo

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9
Q

What do mitochondria derive from?

A

fission events of pre-existing organelles

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10
Q

Describe the lipid composition of the mitochondria’s inner membrane:

A

there is a lipid called cardiolipin, which is absent in the other membrane

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11
Q

How can we analyze mitochondria?

A

via electron tomography

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12
Q

What is a mitochondria deprived of the outer membrane called?

A

mitoplast

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13
Q

What are the criastae the sites of?

A

oxidative phosphorylation

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14
Q

What is important in regards to the 5 respiratory chain complexes?

A

there is an electron transfer from complex I to complex IV coupled with the proton passage to the inter membrane space and this is crucial as it creates a proton gradient essential for the functionality of the organelle

*loss of the proton gradient is related to organellar pathology in most cases

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15
Q

What is the name for cellular metabolic hubs for anabolic processes and catabolic processes that are also involved in calcium signaling and mediated the pathway of apoptosis through the release of cytochrome c?

A

mitochondria

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16
Q

Describe the mitochondrial proteome:

A

there are more or less 1100 proteins related to protein biogenesis, mitochondrial gene expression, respiratory chain and metabolism

many of these reside in the nucleus and only 13 polypeptides derive from the mitochondrial DNA

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17
Q

How small is the mitochondrial DNA?

A

16kb circular dsDNA (very small)

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18
Q

How is mitochondrial DNA packaged?

A

nucleoids

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19
Q

What are nucleoids?

A

associations of mitochondrial DNA with TFAM, which is a mitochondrial TF

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20
Q

Why is mitochondrial DNA fully dependent on the nuclear DNA?

A

machinery that is needed for its replication, transcription, and translation comes from the nucleus

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21
Q

What is POLGA?

A

polymerase devoted to mtDNA replication

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22
Q

What is Twinkle?

A

helicase that unwinds the mtDNA allowing replication

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23
Q

What is TFAm and all the other factors?

A

nuclear encoded

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24
Q

Describe the figure:

A

it is a fibroblast:
blue is the nucleus
red is the mitochondrial network
green is the nucleoids

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25
Q

What are 2 considerations regarding mitochondria?

A

mitochondria form a very interconnected network so it is more appropriate to talk about them as a mitochondrial network since they are highly dynamic and continuously fuse and divide

the nucleoids are spread along the network

26
Q

How many genes does mitochondrial DNA encode for?

A

37 genes

27
Q

What are the 2 strands of mitochondrial DNA?

A

heavy strand (outer) and light strand (inner)

28
Q

What interrupts the heavy strand?

A

red circles, which are genes encoding for tRNA (which are necessary for the transcription and translation of mtDNA when grouped with rRNAs

29
Q

How many genes are transcribed by the light strand?

A

only 1 gene (ND6)

30
Q

How many promoters are on mtDNA?

A

only 1, so it is a polycistronic transcript

31
Q

What is a moncistronic transcription?

A

every gene can be regulated individually

32
Q

Where is the regulation of mRNA, tRNA, and rRNA established?

A

at the post-transcriptional level

33
Q

The protein that are encoded by the mitochondrial DNA are all components of the _______.

A

respiratory chain

34
Q

Why are all but 30 genes transferred to the nucleus?

A

these are integral to the membrane, and they are very hydrophobic proteins, so the proteins cannot be folded and then unfolded and transported via the classical translocons of the mitochondria due to their hydrophobicity

35
Q

What are the 3 main players in the transcriptional program of mitochondrial biogenesis?

A

nuclear respiratory factor 1 and 2 (NRF-1 & NRF-2): important for the transcription of genes encoding for the subunits of the respiratory chain and TFAM (transcription factor needed for mitochondrial DNA transcription)

PPAR𝛼: controls the expression of genes of fatty acid β-oxidation

Estrogen-related receptors (ERRs): control TCA cycle genes, respiratory chain genes and other oxidative phosphorylation-related genes

36
Q

What is the mass regulator of the mitochondrial biogenesis process?

A

PGC-1𝛼, which is a coactivator

37
Q

What happend when PGC-1𝛼 increases in transcription and protein level?

A

it can bind and promote the transcription and translation of mitochondrial DNA and nuclear genes encoding for mitochondrial proteins

38
Q

What are primary mitochondrial diseases?

A

diseases caused by mutations in the mitochondrial DNA

39
Q

What are the 3 pathways for the translation of proteins encoded by the nucleus?

A

pathway mediated by PUMILIO1 (PUM1)

co-translational import

post-translational import

40
Q

Describe the pathway mediated by PUM1

A

this pathway is needed for the translation of proteins encoded by the nucleus:

protein binds the 3’ of specific mRNAs

PUM1 is localized to the OMM → allows the co-translational import of proteins because the ribosomes are located close to the OMM and PUM1 targets the mRNAs to have to be imported close to the OM

41
Q

How are the vast majority of nuclear encoded proteins imported?

A

in a post-translational manner

42
Q

What does it mean if proteins are imported in a post-translational manner?

A

proteins are translated into free polysomes in the cytosol and after that (thanks to chaperones) they are positioned in close proximity to the OMM and imported into the organelle

43
Q

What is co-translation import like?

A

it is like what happens in the ER:

protein is synthesized after being imported into the organelle

44
Q

There are 5 major protein import pathways: which 2 pathways have a pre-sequence?

A

the classical pathway

protein containing cysteine residues

*proteins in the matrix and inner membrane have the pre-sequence

45
Q

What is the presequence?

A

short sequence that varies from 15-50 aa, which form amphipathic 𝛼-helices

46
Q

What is methionine usually a presequence for?

A

cytochrome C oxidase from yeast

47
Q

What is the difference between the + charged aa and the hydrophobic aa?

A

the + side are the typical import signal for mitochondrial protein

elements of the amphipathic 𝛼-helix are recognized by the receptors of the OM (translocons)

48
Q

Describe how proteins can be translocated from the outside of the mitochondria to the inside of the mitochondria:

A

cis-binding site
Tom20
Tom22
Tom40
Tom22IMS
trans-binding site

this is the pore in which the proteins can be translocated from the outside of the mitochondria to the inside

49
Q

What is special about Tom40?

A

contains both hydrophilic and hydrophobic aa in the internal part of the pore

it is also a big channel of the OM and belongs to the β-barrel proteins, composed mostly of β-strands

50
Q

Describe the presequence pathway:

A

proteins are synthesized in the cytoplasm from nuclear encoded mRNAs

the presequence carrying porteins are then handed over to TOM and then the translocons of the IM, which are called TIM complex (TIM23)

presequence is followed by a hydrophobic stretch, which is the signal for the protein to be laterally sorted in the IM

the protein then travels to the intermembrane space and presents a hydrophobic domain

the presequence is then removed by mitochondrial peptidase of the matrix

51
Q

What are the 2 presequence pathways?

A

TIM23 SORT: proteins that are highly hydrophobic and reside in the IM

TIM23 MOTOR: proteins that are translocated into the matrix (soluble protein)

52
Q

Review the following:

A

https://www.youtube.com/watch?v=wbH-5LARKyQ

53
Q

What are the most important carriers in the IM?

A

pyruvate carriers: allow the passage of pyruvate across the IM

ANT carrier

*they are very hydrophobic and have 6 transmembrane domains

54
Q

What happens after the proteins have been internalized through the TOM40 complex?

A

small chaperones maintain the unfolded state and the proteins are passed to the TIM22 insertase and laterally released

55
Q

Where are proteins that contain disufate bonds located?

A

only in the intermembrane space of the mitochondria and in the ER

56
Q

What is the MIA complex?

A

composed of oxireductase (Mia40) and cooperates with sulfhydryl oxidase (Erv1) and it is devoted to the intermembrane space to reach the final folding of the protein

57
Q

What 2 types of proteins are found in the outer membrane?

A

β-barrel proteins: integral to the membrane thanks to multiple transmembrane β-strands

𝛼-helical membrane proteins

58
Q

WHat is important in regards to TOM40?

A

it is always present and all proteins need to be internalized by TOM40

59
Q

Review the pathway for β-barrel proteins:

A
60
Q

Review the pathway for the insertion of 𝛼-helical proteins to the OM:

A
61
Q

Remember the summary:

!!

A

the presequence pathway describes proteins residing in the matrix and the inner membrane

must remember the features of the presequence

actors of the TOM complex

actors of the TIM complex

carriers do not have a presequence and they are highly hydrophobic

carriers for pyruvate

carriers for ATP and ADP (ANT carrier)

proteins containing disulphate bonds in the intermembrane space are folded by the Mia complex

β-barrel and 𝛼-helix proteins are of the outer membrane

Oxa1 is located on the intermembrane and it is important for the insertion of the mtDNA-encoded proteins, which are part of the respiratory chain complexes located in the inner membrane

Molecular Cell Biology (10 decks)

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