Department of Medical Biochemistry

Semmelweis University

Subcellular biochemistry
February-March 2017
 Subcellular biochemistry
(biochemical aspects of cell biology)

Miklós Csala
Semmelweis University
Dept. of Medical Chemistry, Molecular
Biology and Pathobiochemistry
 TOPICS

• COMPARTMENTATION

Basic structural and functional principle of the eukaryotic cell

organization

• MEMBRANES

Plasma membrane, intracellular membranes, nucleus

• MOVEMENT AND TRAFFIC OF ORGANELLES

Cytoskeleton, microfilaments, microtubuli, actomyosin, vesicular

transport

• METABOLISM AND TRANSPORT

Principles of metabolome, metabolic profile of various organelles

 COMPARTMENTATION

Basic structural and functional

principle of the eukaryotic cell
organization
 Cellular membranes
The endomembrane system
• nuclear envelope
• endoplasmic reticulum (ER)
• Golgi apparatus
• lysosome (phagosome, autophagosome)
• endosome
• transport vesicles
• cell membrane
• peroxisome (?)

Mitochondria
• inner and outer mitochondrial membranes
Biological membranes:
the fluid mosaic model
 Biological membranes:
Amphipathic membrane lipids
 Biological membranes:
Amphipathic membrane lipids
 Biological membranes:
Amphipathic membrane lipids
 Biological membranes:
Amphipathic membrane lipids
 Biological membranes:
Amphipathic membrane lipids
 Biological membranes:
Amphipathic membrane lipids
Biological membranes:
Lipid bilayer
 Biological membranes:
Integral and peripheral membrane proteins
 Associated membrane proteins
With transmembrane helices or β-barrels
 Integral membrane proteins
With lipid anchors
Glycophosphatidylinositol (GPI) anchor
Carbohydrate layer around the cell membrane
 Roles of cellular membranes
• Separating cell contents from the outside environment (plasma membrane).
• Cell recognition and signaling.
• Creating separated intracellular compartments (endomembranes and mitochondrial
membranes).
• Holding the components of some metabolic pathways in place (compartment or
membrane).
• Regulating the transport of materials into or out of cells.

Roles of membrane proteins

 Mitochondrial respiratory chain:
a central metabolic process based entirely on
compartmentation and membrane structure
 Compartment

• membrane-encompassed
• characteristic proteome
• characteristic metabolome
• characteristic pH, redox and ion millieu
• separation and connection
• driving cellular specialization and development of tissues
and organs
 Cellular compartments
• cytosol

Formed by the endomembrane system

• nucleus
• endoplasmic reticulum (ER)
• endoplasmic reticulum - Golgi intermediate compartment (ERGIC)
• Golgi apparatus
• lysosome (phagosome, autophagosome)
• endosome (early, late, MVT)
• transport vesicles
• peroxisome (?)
• lipid droplet
• autophagic vacuole

Formed by mitochondrial membranes

• mitochondrial matrix
• mitochondrial intermembrane space
Plasma membrane
 Plasma membrane:
Membrane microdomains: lipid rafts

Cholesterol- and
sphingolipid-enriched,
highly dynamic,
submicroscopic (25–100
nm diameter) assemblies,
which float in the liquid-
disordered lipid bilayer in
cell membranes.
 Plasma membrane:
Caveola - invaginated lipid rafts

Roles in signal transduction and endocytosis

Plasma membrane:
Asymmetry

Phosphatidylcholine and
glycolipids

Phosphatidylserine and
phosphatidylinositols
 Plasma membrane:
Asymmetry

ATP ATP

Apoptosis: „eat me” signal

Platelet factor 3

Lipid raft organization

and endocytosis

Signaling protein recruitment

The endomembrane system
 The endoplasmic reticulum

The origin of the

endomembrane system

Function
protein synthesis (RER)
lipid synthesis
biotransformation
Ca2+-storage
glucose production
The dinamic endoplasmic reticulum
 ER subdomains and the specialized ER

• Rough ER (RER)
• Smooth ER (SER)
• Transitional ER (tER) / ER exit site (ERES)
• Junctional ER (jER) / sub-plasmalemmal ER /
plasma membrane associated membrane
(PAM)
• Mitochondrion-associated membrane (MAM)
• Sarcoplasmic reticulum (SR)
The (ER-directing) signal sequence
Attachment at the translocon channel
Ribosome
cycles and
SRP cycle
Signal peptidase
N-glycosylation in the ER
 Golgi-appartus
Distribution and Shipping Department

Function
glycoprotein maturation
O-glycosylation
limited proteolysis
protein sorting
synthesis of sphingomyelin
and glycolipids
synthesis of proteoglycans,
polysaccharides and
glucosaminoglycans
 Lysosome
Its enzymes can break
up almost anything.

• Acid hydrolases
– DNAse, RNAse
– proteases (e.g. cathepsins)
– glycosidases
– lipases
– phosphatases
– sulfatases etc.
• V-ATPase (vesicular type proton ATPase)
• Fusion with late endosome or autophagosome
• Lipofuscin „wear and tear” pigment granules
accumulating in aging cells around the nucleus
 Autophagosome
Degrading the cell's own
components using the
lysosomal machinery
Endosomes and lysosomes
 Recicling endosome
Lysosome

Early endosome

Multivesicular
body
LDL-cholesterol uptake
 Peroxysome
Function
oxidative catabolism with low energy conservation
certain processes of lipid synthesis (ether-phospholipid,
cholesterol, bile acids)

hydrogen peroxide production and elimination

Crystalloid core
Lipid droplet
 Nucleus
The control center of the cell

DNA (nuclear genome)

Histones and non-histone proteins
Transcription factors
RNA synthesis and processing
Synthesis of ribosomes (nucleolus)
Regulation of gene expression
 Nucleus
Double bi-layer

Nuclear lamina (lamin protein)

Nuclear pores across two membranes

Outer membrane continuous with the

RER (ribosomes on both)

Perinuclear space continuous with the

RER lumen
The nuclear pore
The Ran GTPase cycle
 Nuclear import / export with Ran
Ran-GTP makes the import receptor unloaded or the export receptor loaded
 Evolution of endomembranes
and
formation of mitochondria by endosymbiosis
 Mitochondria
Power Plants of the Cell

Function
Oxidative phosphorylation
ATP synthesis (energy conservation)
driven by oxidative catabolism of fuel
molecules
Oxidative catabolism of fatty acids,
pyruvate and amino acids (β-
oxidation, PDH and citrate cycle)
Urea cycle, hem synthesis
Ca2+ buffering and storage
Heat production
 Mitochondria

Matrix
nucleoid,
ribosomes,
large enzyme
complexes

Inner membrane
impermeable
protein:lipid ratio > 3:1
- transporters for metabolites and proteins Outer membrane
- enzymes of oxidative phosphorylation pores (porin)
- proteins of fusion and fission permeable for up to 5 KDa
Mitochondrial genome

mtDNA:
• circular, double stranded
• heavy (G) and light (C) strands
• 100-10000 copy/cell
• replicated by DNApolγ
• 37 genes
• no introns
• little noncoding sequences
• unique code (mitochondrial
tRNA)
 Mitochondrial genome

13 proteins
22 tRNAs
2 rRNAs
Comparison between human nuclear and
mitochondrial genomes
 Mitochondrial diseases

Unique inheritance
Mitochondrial
encephalomyopathy,
lactic acidosis, and
stroke

Motor neuron
diseases Myoclonic
epilepsy with
ragged red fibers
Mitochondrial
genome
genetic relationships of
individuals or groups
within a species,
phylogeny among
different species