9 Cell organelles

• compartmenalization

• Separation of biochemical pathways

• Substrate availability

• Membrane permeability: channels and transporters

• Maintainance of ion gradients

• -Production of all transmembrane proteins

• Production of all luminal and secreted proteins

• Soluble proteins for secretion and the lumen of ER, Golgi and lysosomes

• Lipid synthesis

• Storage of Calcium

• Lipid metabolism (S)

• Detoxification (S, liver cells)

Co-translational Transport

Guided transport via SRP

• SRP recognises target sequence in the translated protein

• Guides it to the membrane

• By binding to the pore, it opens for the Proteine

• N-glycolysations can be conducted via dolichol: the whole sugar tree is built on dolichol and then it can be transferred to the protein

• In the Golgi-complex those N-linked oligosaccharide structures are trimmed and modified

The most important chaperone proteins are

• PDI= protein disulphide iseomerase: make sure that disulphide bond is right (folding)

• BIP (binding protein): makes sure that the proteins are folded correctly

• Calnexin-calreticulin System (Slow flucosidase activity, protein disulphide isomerise)

The KDEL sequence makes sure that certain proteins stay in the ER

The unfolded protein response is a mechanism which reacts to stress in the ER (=too many unfolded proteins)

First the translation needs to be stopped so no more proteins are produced-> stop the accumulation

Misfolded proteins can bind to the lumenal side of three branch proteins in the membrane.

• IRE1 (+XPB1)

• ATF6

• PERK

They also upregulate the chaperone expression and can induce apoptosis.

• ERAD makes sure to eliminate misfolded proteins

• Misfolded proteins are targeted by attaching Ubiquitin, so it can be transported out of the ER (into the Cytosol/ proteasome)

• Degradation via proteasome

the ER plays an important role in Membrane biosynthesis

It can store lipids in lipid droplet’s

• Phospholipids

• Cholesterol

• Triacyglycerols

• Ceramide (basis for sphingolipids

The ER has many (different) contact sites to all other organelles to exchange molecules and ions.

In obese mouse is less sheet ER, more tubular and a change of protein climp-63 (changed metabolism of liver cell to make it healthy again-> tolerance)

• protein processing and distribution

• Glycosphingolipid and sphingomyelin synthesis

• Vesicular Transport and/ or cisterns maturation

• polarity in structure and function

• Entry of molecules at the cis Golgi

• Golgi stacks (medial and trans)

• Exit at the trans Golgi

• Important for: signal transduction, molecular tracking, cell-cell communication, immunity

• N-linked oligosaccharides are further modified in the Golgi to yield high mannose and complex oligosaccharides

• A precise sub- compartmentalisation of the enzymes is required. The gradient can be maintained by vesicles which carry back the enzymes and cysternae movement

• Mannosidase trims down the 9-mannose residues from the dolichol

• Transferases put on other sugars

• Complex oligosaccharides contain sialic acid which is the only sugar with a negative charge

• Mannose 6-phosphate is a marker for lysosomal enzymes. These are transported by mannose phosphate receptors (MPRs) via endosomes to lysosomes. MPRs recycle to the Golgi apparatus

• Important for proteins to get into the endocytic pathway in the lysosomes

• Delivery of newly synthetized acid hydrolases with a M6P recognition moiety to lysosomes

• Generated by 2 enzymes:

  First ads a mannose residue

  Second reveals the M6P recognition signal

• Serin or Threonin residues, sometimes Tyrosine

• O-Gal NAc glycosylation

• Less common: O-fucosylation, O-glycosylation

• B: Interaction with carbohydrate-binding proteins

• C: Shielding proteins from proprotein-convertases

• D: Resistance to proteolytic cleavage

• E: Interaction with the immune system

• F: Host-pathogen interaction (mucosal surfaces)

• G: Ligand binding

• Anterograde vesicular transport between stable compartments

• Cisternal progression (whole cisternal goes anterograde)

• Hybrid: Cisternal progression with heterotypic tubular transport

• Coated adapter proteins facilitate the budding of the needed vesicles

• COP1, COP2

• Clathrin take care between early endosomes, plasma membrane, endocytosis

• The endo-lysosomal system is the uptake and digestion system of the cell

Membrane heterogeneity

• lipid domains (different PIP2)

• Protein recruitment

• Cargo recognition by adaptor proteins

• Specific membrane tethering by Rab-GTPases

• Formation of vesicles: actin, dynamin, clathrin

• membrane lipid heterogeneity

• Lipids can be brought into membrane domains and determine which proteins can bind there

• Different endocytic compartments: sorting endosome, endocytotic recycling compartment

• Rab proteins are important for budding

• SNARE-mediated fusion of transport vesicles with the target membrane

• ARF: coat recruitment and unloading for fusion

• Recognize and deliver cargo destined for degradation

• mediating inward membrane budding during endosomal sorting and other membrane remodeling processes

• Modulation of signal transduction by controlling the levels, cell- surface receptors availability and signaling mediators

• cholesterol can not be degraded by cells. It’s degraded by the liver

• LDL receptor transports cholesterol into the blood system, liver cells, early/ recycling endosome, late endosome and lysosomes

• Cholesterol transport is transported to the ER. When there is enough it’s stored in Lipid droplets

• Cholesterol is then localised in Calveolae

• Degradation of ligands and cargo (growth hormones)

• Receptor downregulation

• Autophagy

• Degradation of phagocytoses pathogens

• Macroautophagy

• Exosome release

• Cholesterol homeostasis

• MHC class 2 antigen presentation

• Defects in lysosomal function cause lysosomal storage disorders

• positioning via cytoskeleton and motor proteins

• Multiple contacts to ER

The shape of the Cristal is telling something about the metabolic function of the Mitochondria. -> can adapt t metabolic needs.

Mitochondria are enclosed by a double membrane: the outer mitochondrial and the inner mitochondrial membrane (IMM).

The IMM is sub-structured into the inner boundary membrane and the cristae junction that connects the cristae to the inner boundary membrane

2 separate genetic systems

• mitochondrial genome: mitochondrial translation

  Mitochondrial diseases via mothers, because sperm doesn’t have mitochondria

• Nuclear DNA encoded mitochondrial proteins

  protein import system into mitochondria

involved in…

• primary energy-generations system

• Intermediary metabolism

• Calcium signaling

• Apoptosis

Energy production

• Production of reduction equivalent (NADH) by TCA cycle or fatty acid oxidation

• Electron transport chain and proton pumping

• Redox-equivalents (NADH/FADH) from glycolysis (cytosol) and the TCA –cycle (mitochondrial matrix) are converted to a H+ gradient by the electron transport chain (import into cristae lumen)

  The H+ gradient drives the ATP-synthase when protons flow back to the matrix side

• Cytochrome c oxidase

Catabolism of

• glutamine branched AA

• Fatty acids

Involved in biosythesis of

• Nucleotides

• Glucose and heme

• Fatty acids and Cholesterol

• Amin acids

Metabolic waste management

• ammonia (NH3)

• H2S

• ROS

• H2O2