1 What is compartmentalization? • Mainly in eukaryotic cells. • Biochemical reactions take place in an organized way in cells (different reactions with different requirements at the same time) → these reactions have to take place in a spatially separated (compartmentalized) way • cell nucleus • mitochondria • endoplasmic reticulum • Golgi • secretory vesicles • endosomes • lysosomes • peroxisomes • cytoskeleton • centrosome • ribosome • nucleolus • Cajal bodies, … Organelles: specialized structures in cells that have specific functions (less restrictive definition) membrane-bounded organelles: according to the generally accepted, more restrictive definition only these are considered to be organelles, i.e. specialized structures having specific function bounded by a membrane
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What is compartmentalization?...• transport across compartment boundaries is complex and often energy requiring What are the realizations of compartmentalization? 1. ... What is
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1
What is compartmentalization?
• Mainly in eukaryotic cells.
• Biochemical reactions take place in an organized way in cells (different reactions with different requirements
at the same time)→ these reactions have to take place in a spatially separated (compartmentalized) way
• cell nucleus
• mitochondria
• endoplasmic reticulum
• Golgi
• secretory vesicles
• endosomes
• lysosomes
• peroxisomes
• cytoskeleton
• centrosome
• ribosome
• nucleolus
• Cajal bodies, …
Organelles: specialized structures in cells that have
specific functions (less restrictive definition)
membrane-bounded
organelles: according
to the generally
accepted, more
restrictive definition
only these are
considered to be
organelles, i.e.
specialized structures
having specific
function bounded by
a membrane
2
What is the advantage and disadvantage of compartmentalization?
Advantage of compartmentalization:
• membrane-bound organelles establish special conditions favoring a given set of biological functions
(e.g. lysosome – hydrolytic degradation, mitochondrion – ATP generation, etc.)
• different reactions with different requirements at the same time
Disadvantage of compartmentalization:
• transport across compartment boundaries is complex and often energy requiring
What are the realizations of compartmentalization?
1. „Virtual compartments” (without membranes):
2. Compartmentalization (by membranes, only in eukaryotes) →
transmembrane transport is necessary which is often energy-
consuming.
B) Droplet organelles (generated by liquid-liquid phase separation – liquid
droplets) → diffusion takes place inside them and they exchange
material with their surroundings (e.g. nucleolus, Cajal bodies, etc.)
A) Enzyme complexes (in eukaryotes and prokaryotes) → efficient since
there is no need for diffusion (e.g. mammalian fatty acid synthase)
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What is endosymbiosis? Which compartments were generated by endosymbiosis?
• eukaryotic organism, already equipped with adequate
cytoskeleton and internal membrane systems
• phagocytosed a prokaryotic organism (engulfed)
• they started to live together for their mutual benefit.
• Mitochondria came about when an aerobic prokaryote
performing oxidative phosphorylation was internalized.
The origin of peroxisomes is similar.
What are the proofs for the bacterial origin of mitochondria?
cytosolnucleus
extracellular space
vesicleslysosome
ER, nuclear membrane
mitochondrion
peroxisome (?)
Golgi
1. DNA
• circular DNA
• no introns
• polycistronic mRNA
• The genetic code of mitochondria is different from the universal
code in some cases.
2. Ribosomes resembling prokaryotic ribosomes
3. Size of mitochondria (similar to the size of bacteria (~ 1 μm)).
4. Two membranes (the composition of the inner membrane is similar
to that of bacterial membranes).
5. Mitochondria divide independently of the host cells by binary
fission, like bacteria.
What about the peroxisome?
4
How can you classify the compartments from the stand point of intracellular transport?
cytosol
extracellular space
vesicleslysosome
ER, nuclear membrane
mitochondrion
peroxisome
nucleus
Golgi
1. endomembrane system: ER, Golgi, lysosome,
vesicles (endo- and exocytic, transport) and the
lumen of the nuclear membrane (+EC space,
plasma membrane)
2. cytoplasmic compartment:
2a. cytosol
2b. organelles communicating with the
cytosol by non-vesicular transport: nucleus,
peroxisome and the mitochondrion
transport between individual
organelles by means of vesicular
transport
diffusion/directed motion +
transmembrane transport
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What is the distance which can be covered efficiently (in a couple of seconds) by diffusion in a
living organ? Why?
• diffusion is an efficient way to transport molecules up to ∼∼∼∼100 µµµµm
• it is not efficient for transport to larger distances
• mean squared displacement:
2 2 2 26r x y z Dt∆ = ∆ + ∆ + ∆ = average displacement t∼
= ⇒ ∼ ∼3
1 1kTD D
f f MW
k – Boltzmann constant
T – absolute temperature
f – form factor
MW – molecular weight
glycine
(MW=75)
glucose
(MW=180)
ordinary (40
kDa) protein
D (µm2/s) 103 5�102 102
distance travelledtime of diffusion (sec)
protein glucose glycine
1 µm 0.0017 0.00033 0.00017
10 µm (size of a
eukaryotic cell)0.17 0.033 0.017
100 µm (max. distance
of cells from capillaries)16.7 3.3 1.7
1 mm 1667 333 166.7
1 cm 166667 33333 16667
weak dependence on MW
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Why does the diffusion rate of proteins decline steeply with their molecular weight?
The rate of diffusion is decreased by:
• molecular weight dependent, static filtering effect of the cytosolic matrix with a pore size of ~50 nm
• dynamic filtering effect of macromolecules
• specific interaction of proteins with the cytoskeleton (or DNA in the nucleus)
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What are the main functions of the smooth endoplasmic reticulum (SER)? Which organs
contain a large amount of it?
• SER belongs to the endomembrane system
• storage and release of Ca2+ (heart, skeletal muscles → sarcoplasmic reEculum)