Lecture I Flashcards
What is mitochondria important in?
neurodegenerative disorders, diabetes, cancer, and many other multifactorial diseases
What is the endosymbiotic theory?
in ancient time, gram- proteobacterium was engulfed by an ancestral cell, conferring oxidative phosphorylation to the ancestral eukaryotic cell
Describe the mitochondria:
2 membranes (outer and inner)
What is the inner membrane of the mitochondria divided into?
inner boundary membrane (translocons and transporters) and cristae (invaginations that are the site of oxidative phosphorylation)
What is the shape of the cristae important for?
it is needed to maximize the functionality of the respiratory chain
What is the function of the inter membrane space?
space between the 2 membranes and the matrix
What is located in the matrix of the mitochondria?
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.
What is important to remember in regards to mitochondria?
posses their own DNA so they cannot by generated de novo
What do mitochondria derive from?
fission events of pre-existing organelles
Describe the lipid composition of the mitochondria’s inner membrane:
there is a lipid called cardiolipin, which is absent in the other membrane
How can we analyze mitochondria?
via electron tomography
What is a mitochondria deprived of the outer membrane called?
mitoplast
What are the criastae the sites of?
oxidative phosphorylation
What is important in regards to the 5 respiratory chain complexes?
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
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?
mitochondria
Describe the mitochondrial proteome:
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
How small is the mitochondrial DNA?
16kb circular dsDNA (very small)
How is mitochondrial DNA packaged?
nucleoids
What are nucleoids?
associations of mitochondrial DNA with TFAM, which is a mitochondrial TF
Why is mitochondrial DNA fully dependent on the nuclear DNA?
machinery that is needed for its replication, transcription, and translation comes from the nucleus
What is POLGA?
polymerase devoted to mtDNA replication
What is Twinkle?
helicase that unwinds the mtDNA allowing replication
What is TFAm and all the other factors?
nuclear encoded
Describe the figure:
it is a fibroblast:
blue is the nucleus
red is the mitochondrial network
green is the nucleoids
What are 2 considerations regarding mitochondria?
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
How many genes does mitochondrial DNA encode for?
37 genes
What are the 2 strands of mitochondrial DNA?
heavy strand (outer) and light strand (inner)
What interrupts the heavy strand?
red circles, which are genes encoding for tRNA (which are necessary for the transcription and translation of mtDNA when grouped with rRNAs
How many genes are transcribed by the light strand?
only 1 gene (ND6)
How many promoters are on mtDNA?
only 1, so it is a polycistronic transcript
What is a moncistronic transcription?
every gene can be regulated individually
Where is the regulation of mRNA, tRNA, and rRNA established?
at the post-transcriptional level
The protein that are encoded by the mitochondrial DNA are all components of the _______.
respiratory chain
Why are all but 30 genes transferred to the nucleus?
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
What are the 3 main players in the transcriptional program of mitochondrial biogenesis?
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
What is the mass regulator of the mitochondrial biogenesis process?
PGC-1𝛼, which is a coactivator
What happend when PGC-1𝛼 increases in transcription and protein level?
it can bind and promote the transcription and translation of mitochondrial DNA and nuclear genes encoding for mitochondrial proteins
What are primary mitochondrial diseases?
diseases caused by mutations in the mitochondrial DNA
What are the 3 pathways for the translation of proteins encoded by the nucleus?
pathway mediated by PUMILIO1 (PUM1)
co-translational import
post-translational import
Describe the pathway mediated by PUM1
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
How are the vast majority of nuclear encoded proteins imported?
in a post-translational manner
What does it mean if proteins are imported in a post-translational manner?
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
What is co-translation import like?
it is like what happens in the ER:
protein is synthesized after being imported into the organelle
There are 5 major protein import pathways: which 2 pathways have a pre-sequence?
the classical pathway
protein containing cysteine residues
*proteins in the matrix and inner membrane have the pre-sequence
What is the presequence?
short sequence that varies from 15-50 aa, which form amphipathic 𝛼-helices
What is methionine usually a presequence for?
cytochrome C oxidase from yeast
What is the difference between the + charged aa and the hydrophobic aa?
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)
Describe how proteins can be translocated from the outside of the mitochondria to the inside of the mitochondria:
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
What is special about Tom40?
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
Describe the presequence pathway:
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
What are the 2 presequence pathways?
TIM23 SORT: proteins that are highly hydrophobic and reside in the IM
TIM23 MOTOR: proteins that are translocated into the matrix (soluble protein)
Review the following:
https://www.youtube.com/watch?v=wbH-5LARKyQ
What are the most important carriers in the IM?
pyruvate carriers: allow the passage of pyruvate across the IM
ANT carrier
*they are very hydrophobic and have 6 transmembrane domains
What happens after the proteins have been internalized through the TOM40 complex?
small chaperones maintain the unfolded state and the proteins are passed to the TIM22 insertase and laterally released
Where are proteins that contain disufate bonds located?
only in the intermembrane space of the mitochondria and in the ER
What is the MIA complex?
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
What 2 types of proteins are found in the outer membrane?
β-barrel proteins: integral to the membrane thanks to multiple transmembrane β-strands
𝛼-helical membrane proteins
WHat is important in regards to TOM40?
it is always present and all proteins need to be internalized by TOM40
Review the pathway for β-barrel proteins:
Review the pathway for the insertion of 𝛼-helical proteins to the OM:
Remember the summary:
!!
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
