Lecture 12 - Intracellular compartments and Protein Sorting Part II

Question 1

Peroxisomes

Answer 1

Spherical organelles with a fine granular matrix, sometimes with crystals

Question 2

The ER is in close contact with

Answer 2

Peroxisomes

Question 3

Peroxisomes only have a

Answer 3

Single membrane, no DNA

Question 4

Peroxisomes are

Answer 4

Multi-purpose
Ubiquitous, dynamic organelles with high plasticity
Essential for health

Question 5

Peroxisomes respond to

Answer 5

Environmental stimuli

Question 6

Function of peroxisomes (3)

Answer 6

Lipid metabolism (produce lipids)
Protective function (detoxification of lipids)
Central regulatory role

Question 7

Peroxisomes produce what during lipid metabolism?

Answer 7

Myelin lipids

Insulation for axons in the brains

Question 8

Dysfunctions of peroxisomes normally cause

Answer 8

Neurological disease

myelin

Question 9

In fungi, what is produced in the peroxisome?

Answer 9

Penicillin

Question 10

In fireflies, what do the peroxisomes do?

Answer 10

Light producing reaction in the lantern organ

Question 11

Peroxisomes react to environmental stimuli by (3)

Answer 11

1. A change in number
2. A change in enzyme composition
3. A change in positioning in the cell

Question 12

Peroxisomes can import

Answer 12

Completely folded, oligomeric or co-factor proteins

Question 13

Co factor Protein

Answer 13

Non-protein chemical compound or metallic ion that is required for an enzyme’s activity
Cofactors can be considered “helper molecules” that assist in biochemical transformations

Question 14

Oligomer

Answer 14

A macromolecular complex formed by non-covalent bonding of a few macromolecules like proteins or nucleic acids

Question 15

Peroxisomes can be produced

Answer 15

De novo (dogma breakers)

Question 16

Examples of how peroxisomes are odd

Answer 16

They can import large proteins that should need a gate without needing a gate (transient pore)
They can form de novo (against biochemical dogma)

Question 17

PTS

Answer 17

Peroxisome Targeting Signal

Amino acid sequence that targets a protein to the peroxisome

Question 18

PTS1 is found at the

Answer 18

C terminus of the protein (3 a.a)

Question 19

PTS2 is found at the

Answer 19

N terminus of the protein (9 a.a.)

Question 20

PTS1 and PTS2 are recognised by

Answer 20

Specific receptors

Pex 5 and Pex 7 respectively (soluble cytosolic proteins)

Question 21

Pex 5 and Pex 7 are involved in

Answer 21

Peroxisome biogenesis

Question 22

Catalase is a key enzyme

Answer 22

In peroxisomes

Degrades H202 produced by Oxidases

Question 23

Oxidases produce

Answer 23

H202 in peroxisomes

Question 24

Peroxisomes probably have

Answer 24

A transient pore
Allows them to import large proteins
Not been visualised by electron microscopy

Question 25

The transient pore model

Answer 25

Pex proteins (Pex5) has bacterial toxin-like properties, can insert into the membrane, interact with lipids Pex5 forms the pore and releases the PTS1 cargo inside No ATP required

Question 26

In the transient pore model, Pex5 is removed by

Answer 26

Pex1, 6, and 26 form a 'lever arm' Grab Pex5 when it is ubiquinitated Pulls it out of the membrane ATP required

Question 27

After it is removed from the membrane, Pex5 can either be

Answer 27

Recycled or degraded

Question 28

If Pex5 is going to be degraded, it is

Answer 28

Polyubiquitinated

Question 29

Pex5 is degraded by the

Answer 29

26S Proteosome

Question 30

Ubiquitination requires

Answer 30

ATP

Question 31

Pex1 and 6 are

Answer 31

ATPases

Question 32

Pex13, 14 and 17

Answer 32

Aid in tethering and of Pex5 and translocation of the cargo

Question 33

Example of PBDs | Peroxisome biogenesis disorders

Answer 33

Zellweger syndrome | Cerebro-hepato-renal syndrome

Question 34

Proteins go into the ER

Answer 34

Co translationally

Question 35

Co translational transport

Answer 35

While the proteins are made, they go in | 'synthesised into'

Question 36

Only certain proteins go into the ER (3)

Answer 36

1. Extracellular proteins (sent to the Golgi to packaged into vesicles) 2. Plasma membrane proteins 3. Lysosomal proteins (sent to the Golgi) and Golgi proteins of course!

Question 37

SRP

Answer 37

Signal recognition particle

Question 38

Structure of the SRP

Answer 38

Made out of RNA and 6 proteins | Hydrophobic pocket lined with methionines recognises N terminus signal sequence

Question 39

The SRP

Answer 39

Has a translational pause domain (like a finger that stops the ribosome translating) Brings the ribosome to the ER SRP binds to SRP receptor in the ER membrane Translation continues and translocaction begins

Question 40

Once the co translated protein is in the ER

Answer 40

The signal peptide is cleaved and the protein is folded

Question 41

What does the ER do to the incoming proteins?

Answer 41

``` Glycosylation (important in extracellular signalling) Disulfide bridging (stabilises proteins) Folding ```

Question 42

Quality control in the ER

Answer 42

Checks if proteins are properly folded and will refold or degrade them if they are not

Question 43

When proteins leave the ER

Answer 43

They are sent to the ER for further processing

Question 44

Sec61

Answer 44

Protein translocator in the ER | Hetero trimeric complex

Question 45

Structure of Sec61

Answer 45

Bundled alpha helices with a central pore Pore is usually closed by a small a-helix 'plug' Signal peptide displaces the plug allowing transport of the protein

Question 46

Two mechanisms of ER transport (4)

Answer 46

1. Soluble proteins 2. Single pass TM proteins I 3. Single pass TM proteins II 4. Multi pass TM proteins

Question 47

ER transport: Soluble proteins

Answer 47

Polypeptide binds to ER signal sequence Polypeptide is completely transferred into ER lumen Signal is cleaved

Question 48

ER transport: Single pass TM proteins I

Answer 48

Polypeptide binds to ER signal sequence Polypeptide contains stop transfer signal (hydrophobic sequence) Signal is cleaved C terminus remains in cytosol

Question 49

ER transport: Single pass TM proteins II

Answer 49

Polypeptide binds to ER signal sequence Then: More positive residues before stop transfer signal = N terminus translocation inhibited Complete transfer of C terminus part OR More positive residues after stop transfer signal = C terminus translocation inhibited Complete transfer of N terminus part

Question 50

ER transport: Multi pass TM proteins

Answer 50

(multiple domains have to span the membrane) Start transfer signals begin Until a stop transfer signal is encountered For more than 2 membrane passes, second start transfer signal sequences re initiate translocation

Question 51

Stop and start transfer signal sequences are

Answer 51

Internal signal sequences | Same sequences, just depends on where they are

Question 52

Transmembrane transport is used to

Answer 52

Deliver proteins to mitochondria, plastids, peroxisomes and ER First three occur post translationally, ER is co translational

Question 53

What do signal sequences do?

Answer 53

Facilitate interactions between polypeptides and receptors/translocators