Lec 17: Intracellular Compartments and Protein Transport

Question 1

Why are cellular compartments essential to the proper functioning of cells?

Answer 1

Eukaryotic cells carry out many interactions at the same time, some of which are incompatible (glycolysis and gluconeogenesis, for example), so they have to be segregated.

Question 2

Ways to organize chemical reactions within cells:

Answer 2

1) biomolecular condensates/membraneless organelles: aggregate the proteins and molecules needed and hold them separate from surrounding area by fluctuating non covalent interactions.

2) Confine these reactions to within membrane-bound compartments

Question 3

Name the major membrane-enclosed organelles in a eukaryotic cell and their function

Answer 3

9 organelles

Question 4

How are the organelles positioned and moved around the cell?

Answer 4

They are attached to the cytoskeleton, especially the microtubules

Question 5

endomembrane system

Answer 5

Interconnected network of membrane-enclosed organelles in a eukaryotic cell; uncludes hte endoplasmic reticulum, the Golgi apparatus, lysosomes, peroxisomes, and endosomes. The communicate extensively with each other and with the outside of the cell via vesicles.

Question 6

In a typical human secretory cell, which of the membranes has the largest surface area?

Answer 6

rough ER (it can sometimes compose up to half the total membrane present in the cell)

Question 7

How do the interiors of the ER, Golgi apparatus, endosomes, and lysosomes exchange contents with each other?

Answer 7

by small vesicles that bud off one organelle and fuse with another

Question 8

What three mechanisms are used to transport proteins into organelles?

Answer 8

Most proteins are snthesized on ribosomes in the cytosol, except for a few proteins that are made in the mitochondria and chloroplasts. The amino acid sequence contains a sorting signal that directs it to the appropriate organelle.

1) from cytosol into nucleus: transported through nuclear pores which go through inner and outer nuclear membranes. They are selective gates for larger molecules, allow smaller ones to diffuse freely

2) Cytosol to ER, mitochondria, or chloroplasts: protein translocators located in the membrane. Proteins usually have to unfold to get through.

3) moving onward from the ER (or between compartments in the endomembrane system): transport vesicles

Question 9

signal sequences

Answer 9

amino acid sequence that directs a protein to a specific location in the cell, such as the nucleus or mitochondria. They are often removed from the mature protein once it has reached its destination, but some keep it (nuclear membranes, ex, to be allowed back into nucleus after daughter cells split)

Question 10

Nuclear envelope

Answer 10

double membrane surrounding the nucleus. Consists of inner and outer membranes perforated by nuclear pores

Question 11

nuclear pores

Answer 11

channel through which selected large molecules move between the nucleus and the cytoplasm.

Small proteins can just diffuse through.

For larger proteins, pore proteins look for particular tags and pull those proteins through.

This only works when the nuclear membrane is intact. During cell division, the nuclear membrane break down so other proteins can get in then

Question 12

Endoplasmic reticulum

Answer 12

labrynthine membrane enclosed compartment in the cytoplasm of eukaryotic cells where lipids and proteins are made

Many of the proteins that enter the ER enter as they are still being synthesized…they are made by ribsomes that are attached to the cytosolic side of the ER membrane, creating the rough endoplasmic reticulum. They are bound by the proteins that transport proteins into the ER. They come from a common pool of free ribosome subunits.

Question 13

Rough endoplasmic reticulum

Answer 13

region of the ER associated with ribosomes and involved in the synthesis of secreted and membrane-bound proteins

Question 14

Answer 14

B: free ribosomes are structurally identical to those that are bound to the ER. When a ribosome happens to be amking a protein with an ER signal sequence, the signal sequence directs the ribosome to the ER membrane

Question 15

Which organelle cannot receive proteins directly from the cytosol?

Answer 15

Golgi apparatus: they are delivered from the ER or from other components of the endomembrane system

Question 16

How does vesicle budding happen?

Answer 16

It is driven by the assembly of a protein coat. They have distinctive proteins on their surface that help make sure only correct proteins are contained in them.

Question 17

Clathrin

Answer 17

a cytosolic coating of a type of vesicle that buds either from the Golgi apparatus on the outward secretory pathway or from the plasma membrane on the inward endocytic pathway. The clathrin starts to make a pit.

Adaptins then create a second coat that helps select which molecules to transport.

Question 18

How are transport vesicles moved

Answer 18

often actively transported by motor proteins that move along cytoskeletal fibers.

Question 19

Rab proteins

Answer 19

small GTP binding proteins that help ensure transport vesicles only fuse with the correct membranes

Question 20

tethering protein

Answer 20

filamentous transmembrane protein involved in the docking of transport vesicles to target membranes

Question 21

SNAREs

Answer 21

one of a family of membrane proteins responsible for the selective fusion of vesicles with a target membrane inside the cell. For the membranes to fuse, the hydrophilic groups on the cytosolic side must have their bonds broken with the water moelcules. SNAREs help do this

Question 22

How to vesicles recognize and dock with the correct other membrane?

Answer 22

Rab proteins on the vesicle are recognized by corresponding tethering proteins on the cytosolic side of the target membrane. SNAREs then recognize each other, and help fuse the two membranes together

Question 23

Vesicle budding is driven by what?

Answer 23

Assembly of a protein coat.

Cargo receptors recruit adaptin proteins, which recruit clathrin, which starts the budding process.

Dynamin and associated proteins wrap around the stalk and pinch it off.

Question 24

Botulism is a potentially fatal foodborne diesase caused by the bacterium C. botulinum. It produces different toxins, several of which are proteases that cleave neuronal SNARE proteins. What normal process is blocked by cleavage and inhibition of SNARE proteins?

Answer 24

Fusion of vesicles with target membranes. This means that neurotransmitters can’t be released into synaptic clefts, leading to paralysis.

Question 25

Exocytosis

Answer 25

the process by which most molecules are secreted from a eukaryotic cell. These molecules are packaged in membrane-enclosed vesicles that fuse with the plasma membrane, releasing their contents to the outside.

Each molcule that gets secreted travels through a pathway of membrane-enclosed organelles, often getting chemically modified en route. (usually cytosol to ER to Golgi apparatus to plasma membrane)

Question 26

How are proteins modified in the ER?

Answer 26

Generally this is where covalent disulfide bonds are added.

Glycosylation also happens there: attachment of short, branched oligosaccharide bonds.

Glycosylation can dramatically change the function of a protein, and can change how the antibodies bind to the protein. These alterations can change the same proteins across species. The problem with studying this is that sugars are unstable

Question 27

How do chaperone proteins function in the ER?

Answer 27

They are an important quality control step

They bind to misfolded proteins, and prevent them from being exported.

They can also help proteins fold correctly

Question 28

Unfolded protein response

Answer 28

When a build-up of improperly folded proteins happens in the ER, this response is triggered. It allows the cells to expand the ER and make more of the machinery responsible for proper protein folding and processing

Question 29

What is the role of the Golgi apparatus?

Answer 29

Further modifies and sorts proteins. Usually located near the cell nucleus. Made up of flattened, membrane-enclosed sacs.

Question 30

secretory vesicles

Answer 30

membrane-enclosed organelle in which molecules that are destined for secretion are stored prior to release. Sometimes they wait for the right signal before they are released.

Question 31

What distinguishes proteins destined for regulated secretion?

Answer 31

Their surface properties allow them to form aggregates that are packaged into secretory vesicles. (It is not because they have specific signal sequences that mark them for being packed into the vesicles)

Question 32

How are newly made lipids supplied to the plasma membrane?

Answer 32

Via the constitutive pathway of exocytosis. This enables the plasma membrane to expand prior to cell division, and replaces old lipids in non-proliferating cells

Question 33

Endocytosis

Answer 33

the process by which cells take in materials through the plasma membrane which surrounds the ingested material in a membrane-enclosed vesicle.

Question 34

Phagocytic cells

Answer 34

A cell such as a macrophage of neutrophil that is specialized to take up particles and microorganisms by phagocytosis. An important part of the immune system

Question 35

phagocytosis

Answer 35

the process by which particulate material is engulfed (eaten) by a cell. Prominent in predatory cells like amoeba and the immune system

Question 36

pinocytosis

Answer 36

a type of endocytosis where soluble materials are taken up from the environment and incorporated into vesicles for digestion. (cell drinking). Often indiscriminate, but can sometimes be more selective

Question 37

lysosomes

Answer 37

membrane-enclosed organelles that breakdown worn out proteins and organelles and other water materials. Contains digestive enzymes, and often maintained at a lower pH (5.0, vs. the cell’s 7.2)

The digestive enzymes only work at the lower pH, so if they get loose into the cell, they won’t digest everything in sight

Question 38

Viruses such as influenza and HIV enter cells via which process?

Answer 38

receptor-mediated endocytosis. They bind to the cell-surface receptors and are taken in by clathrin-coated vesicles

Question 39

What happens to the final products of the digestion of macromolecules in the lysosome?

Answer 39

They are transferred to the cytosol through transporters in the lysosomal membrane. They are then reused by the cell or secreted.

Question 40

Answer 40

Question 41

How do you “add” the signaling sequence to the other protein?

Answer 41

You can add signaling sequence to the protein by fusing the corresponding DNA sequence of the signal tag in frame to the gene of interest in the DNA. This can be accomplished through molecular cloning or using genome editing approach to “knock-in” the sequence into the genome.

Question 42

How do proteins get into the mitochondria?

Answer 42

proteins are pulled through both membranes, one amino acid at a time

Sometimes there is a stop transfer sequence that pulls the protein only through the first membrane, and not through the second

Question 43

How are proteins synthesized directly into the ER?

Answer 43

translation and transport happen at the same time.

Question 44

How are membrane proteins made?

Answer 44

They are translated in the ER, and then a stop-transfer signal lodges it partway through. There can be different ways that this happens, and different orientations where it gets stuck

Question 45

Answer 45

If the stop-transfer doesn’t exist, it will be a single-pass membrane protein only. The n-terminus will be in the cytosol, the c-terminus will be in the lumen.

Question 46

What is the process that membrane proteins go through before they reach the membrane?

Answer 46

Most membrane proteins are made the the membrane protein in the ER. Then they are sent to teh GOlgo apparatus for further modifications, and then to the cell membrane. The intra-lumen part becomes the extracellular cellular part, and the cytosol side stays in the cytosol.

Question 47

Answer 47

a) no adaptins: clathrin won’t attach, still no budding

b) no clathrin: still nothing

c) no dynamin: forms buds, but nothing gets pinched off

Question 48

Answer 48

Strain A is mutated: proteins associated with vesicle transportation, particularly from the ER to the Golgi apparatus