Section 6A: Fundamentals of cell compartments and protein sorting

Question 1

Proteins have an address built into them telling them where to go

Answer 1

like a “distribution centre”

Question 2

Lysosome

Answer 2

breakdowns macromolecules

Question 3

ER

Answer 3

builds up macromolecules

Question 4

THES

Answer 4

condition that manifests in intestinal epithelial cells
- proteins that are supposed to be in one part of the cell end up in a different part
- protein DOES NOT make it to apical plasma membrane
- protein is involved in nutrient transport thus, if not in right location, protein CANNOT take up nutrients

Question 5

Why do we care about protein sorting within cells?

Answer 5

because when they don’t localize properly, it can lead to disease (e.g. THES)

Question 6

NHE

Answer 6

Na/H+ transporter has to be sorted by a cell to the apical plasma membrane

Question 7

Membrane-bound organelles

Answer 7

contents are held together by the surrounding lipid bilayer: separates the inside from the outside

Question 8

Membrane-less organelles

Answer 8

no surrounding membrane

Question 9

How can membrane-less organelles stay together and disperse?

Answer 9

membrane-less organelles form because of Scaffold Molecules (proteins)

Question 10

What are the characteristics of Scaffold Molecules?

Answer 10

-sticky: binds to other scaffold molecules
- floppy/loose: no secondary structure
- liquid phase: but separate when found

Question 11

What are Client Molecules?

Answer 11

• these proteins can have secondary structures (α/β) that stick to the scaffold molecules
• allow to concentrate or couple certain types of proteins to work together

Question 12

Some membrane-less organelles are also called __________

Answer 12

Biomolecular Condensates

Question 13

Scaffold Proteins are made up of intrinsically disordered regions (no secondary structure) and interact with various non-covalent interactions:

Answer 13

• electrostatic
• Pi-pi (most favoured, ring structure with delocalized electron interacting)
• cation-pi
• hydrogen bonds
• van der waals interactions

Question 14

What is the Nucleolus?

Answer 14

• an example of a membrane-less organelle
• where rRNA is processed and assembled into ribosomes
• made up of several “layers” of membrane-less organelles

Question 15

Membrane-bound organelles have 3 distinct parts

Answer 15

1. Lumen: the aqueous fluid enclosed by the lipid bilayer of an organelle
2. The cytoplasmic face/leaflet of the bilayer: the outer membrane surface that faces the cytosol
3. The lumenal face of the bilayer: the inner membrane surface that faces the lumen. constantly tidy up/sort proteins to right location or else materials get mixed up

Question 16

How are proteins targeted and transported to specific organelles?

Answer 16

proteins have a built-in signal that tells them where to go

Question 17

What type of molecules can diffuse across a lipid bilayer?

Answer 17

small non-polar, hydrophobic molecules can diffuse through a lipid bilayer

Question 18

No protein on its own will go through a lipid bilayer:

Answer 18

• it needs a transport mechanism
• proteins that are responsible to transfer other proteins into an organelle

Question 19

How do proteins enter membrane bound organelles?

Answer 19

1. Ribosome translating mRNA into polypeptide
2. Soluble proteins (aka anything other than membrane proteins) get sorted to specific organelles after they are made
   OR
3. Transmembrane/Secreted proteins get sorted to ER while/as they’re being made

Question 20

What causes organelle specialization?

Answer 20

• Unique integral membrane proteins
• Unique proteins in the organelle lumen
• Unique peripheral proteins on the organelle surface
• Unique lipids

Question 21

Three important facts about
organelle function

Answer 21

1. Each organelle has a specific set of functions
2. Each specialized function requires a specific set of
   proteins and lipids
3. Organelles are not isolated: they exchange content

Question 22

If organelles are not isolated, how do you keep them separate?

Answer 22

signal sequences act as postal codes to target proteins to the correct membrane-bound organelle
- series of positively (+) charged amino acids to send a protein to the nucleus (e.g. Histones)

Question 23

Where does translation of most proteins occur?

Answer 23

Cytosol

Question 24

How to target proteins to a specific organelle?

Answer 24

Signal peptide sequences target proteins to specific
compartment

Question 25

How to transport proteins to a specific organelle?

Answer 25

• Delivery across a “gate” (Gated Transport): between cytosol and nucleus, controlled by nuclear pore
• Delivery through a translocator/channel (Transmembrane Transport): between cytosol and ER, insertion of proteins (squeeze through) into membrane and lumen during translation by ribosome
• Delivery by transport membrane vesicles (Vesicular Transport): between ER, golgi, PM, endosomes, and lysosomes, transport membrane enclosed vesicles