Chapter 15

Question 1

What is the purpose of the endocytic pathway? Where does it start and where does it end?

Answer 1

The endocytic pathway is responsible for the ingestion and degradation of extracellular molecules. It moves materials from the plasma membrane through endosomes to lysosomes.

Question 2

Define Receptor Mediated Endocytosis

Answer 2

Special type of endocytosis in which receptor proteins on the cell surface are used to capture a specific target molecule

Question 3

What do low density lipoproteins (LDL) do?

*Might not need to know

Answer 3

They travel with molecules like cholesterol because they are not soluble

Question 4

What does clathrin do? (general) What is its structure?

Answer 4

Forms a protein coat with vesicles traveling between membranes, three-legged or triskeleton

Question 5

Where is clathrin used? What partner does it require?

Answer 5

From the golgi on the outward secretory pathway and from the plasma membrane on the inner, GTPase (makes vesicle release cargo)

Question 6

What does clathrin form at the plasma membrane? Why does it hang out around the plasma membrane?

Answer 6

Coated pits, it is involved in endocytosis

Question 7

What is the purpose of protein coats? How many types are there (general-> 1, 3, lots)

Answer 7

Help shape membranes into buds and help capture distinct/specific molecules

Protein coats differ depending on the origin of the vesicle

Question 8

What is the role of adaptin in endocytosis?

Answer 8

It binds to cargo receptors on the plasma membrane to take up molecules

Question 9

What is the role of dynamin in endocytosis?

Answer 9

It circles the end of the vesicle bud and helps separate it from the plasma membrane

Question 10

What are the three possible fates for receptors used in endocytosis?

Answer 10

Recycled from the endosome back to the plasma membrane by budding and fusion of vesicles

They can continue to the lysosome along with the cargo from degradation

They can be used for transport in vesicles to another region of the membrane

Question 11

What do lysosomes do? How can they do their job?

Answer 11

They are the principal site of inner cell digestion and contain many acid hydrolases that are kept functional by the acidic environment created by proton pumps

Nucleases for nucleic acids, proteases for proteins, glycosidases for carbohydrates, lipases for lipids

Question 12

What is the first step in the formation of the proteins that will become a part of a lysosome?

Answer 12

Since they are part of the secretory pathway, they have ER signal sequences and are inserted into the lumen of the ER

Question 13

How do the proteins that will become a part of a lysosome move from where they are translated to the lysosome? (include intermediate destinations)

Answer 13

An oligosaccharide is added in the ER, then it moves to the cis golgi where its mannose sugar is phosphoylated, then the trans golgi where a receptor protein will bind to mannose and it is placed in a vesicle

The vesicle will fuse with the late endosome, turning it into a lysosome

Question 14

What is an endosome?

Answer 14

A precursor to lysosome that has a lowish pH that breaks cargo-receptor bonds in endocytosis

Question 15

What are the three main pathways to the lysosome?

Answer 15

Endocytosis: Early endosomes contain cargo from endocytosis and pH is lowered to turn it into the late endosome (needs proteins to turn into lysosome)

Autophagy: Old organelles will be packaged by autophagosomes inside of a double membrane, which fuses with a lysosome

Phagocytosis: Large molecules that the cell has taken up fuse with late endosomes

Question 16

What are peroxisomes and how do they get their proteins?

Answer 16

Organelle containing one or more enzymes that break down hydrogen peroxide and also synthesize some phospholipids

A short import signal on their proteins is reognized by receptors in the cytosol and moved to the peroxisome by protein translocators

Question 17

What are the four functions of the rough endoplasmic reticulum?

Answer 17

Begin glycosylation of proteins
Catalyze disulfide bond formation
Quality control of protein folding
Response to unfolded proteins

Question 18

Define glycosylation

Answer 18

the covalent attachment of oligosaccharide chains to proteins from a membrane lipid

Question 19

What is(are) the purpose(s) of glycosylation? When does it happen?

Answer 19

Protect the protein from degradation, act as a transport signal, and participate in cell-cell recognition

During translation

Question 20

Describe the process of glycosylation (and the two types?)

How does it occur at the beginning

Answer 20

The oligosaccharide comes attached to a lipid in the ER membrane (usually dolichol)

Oligosaccharide transferase catalyzes the transfer of the oligosaccharide from the lipid

It attaches on a asparagine amino acid and the process is called n-linked glycosylation

It attaches on the hydroxide group of serine or threonine and is called o-linked glycosylation

Question 21

What do chaperone proteins in the ER do?

Answer 21

Bind to proteins and prevent misfolded ones from leaving

They will help them fold correctly, or lead to protein degradation (ER associated degradation) ERAD

Question 22

Describe the Unfolded Protein Response (UPR) and its possible actions

Answer 22

Response to large amounts of misfolded proteins that is triggered by binding to receptors

1) Produce more ER membrane
2) Increase transcription/translation of chaperone proteins
3) Increase rate of ERAD
4) Decrease protein production
5) Undergo apoptosis or programmed cell death

Question 23

Where do properly folded proteins in the ER go?

Answer 23

golgi

Question 24

What is different about the ribosomes on the RER? What do they do? How did they get to the RER?

Answer 24

They happen to be synthesizing proteins that are part of the secretory pathway (otherwise identical) and are going to the golgi, endosomes, lysosomes, or cell surface

They translate proteins as inserts into the RER, where glycosylation occurs immediately

Signal sequences on the protein direct the ribosome to the RER, where the sequence is bound by signal-recognition particles (SRPs) that are then bound to their own receptors and lead the protein to a translocation channel

Once in the channel, a signal peptidase cleaves the signal sequence

Question 25

What is the process of inserting an ER membrane protein that crosses the membrane only once?

Answer 25

ER membrane proteins are pulled in and the signal peptidase cleaves the start-transfer sequence

This is the same as before, but this protein also has a hydrophobic stop-transfer sequence that stays in the translocation channel

Start-transfer -> stop-transfer

Question 26

What is the process of inserting an ER membrane protein that crosses the membrane twice?

Answer 26

ER membrane proteins that cross twice have an internal hydrophobic start sequence and a hydrophobic stop-transfer sequence

Start-transfer sequence is caught in the channel, and the protein loops around so the stop sequence is caught in the channel (continuous loop on lumen side, two ends on cytosol side)

Internal start-transfer -> stop-transfer

Question 27

What do COP-coated vesicles do?

Answer 27

Transfer material between the ER and cis golgi network and transfer material from the trans golgi back to the cis golgi or ER

Question 28

Describe the golgi apparatus, its parts, and its location

Answer 28

Made of a series of flattened sacs called cisternae (in stacks from 3-20)

Cis side that faces the ER and trans side where proteins leave to go to the lysosome or PM

Often located near nucleus/centrosome

Question 29

What is the purpose of the golgi apparatus? How does it do its job?

Answer 29

continue the glycosylation of proteins by taking the proteins that enter the cis face and add or remove sugars as it passes through via many different enzymes on the two faces

sulfation and phosphoylation of proteins

Question 30

Describe the process of proteins leaving the golgi (short)

Answer 30

they are sorted and packaged into vesicles for secretion or transport into the lysome

Question 31

Define exocytosis and describe the two types

Answer 31

the process by which vesicles that leave the golgi will fuse with the plasma membrane

Constitutive Secretion: Default, no signal required, automatically goes to plasma membrane

Regulated Secretion (not in all cells): Many vesicles hang out near the plasma membrane waiting for signal before cytosis, Can release mucus, hormones, or digestive enzymes

Question 32

HOW WE KNOW…..

Describe the in vitro protein assays that can determine the purpose of a signal sequence

Answer 32

Uses a protein without a signal sequence, one with, and a isolated organelle
(proteins can be labeled with radioactive amino acids)

A) Mix all together, proteins in organelle will sink to bottom of centrifuge tube

B) Mix all together, organelle will protect labeled protein from protease, unless detergent is added

Question 33

HOW WE KNOW…..

Describe the use of yeast secretory pathway mutants

Answer 33

Some mutations result in temperature sensitive alleles where transport proteins only work at low temp

Shifting cells to high temperature will show where the transport protein works

Will accumulate in organelle at the start of the normal transport

Question 34

HOW WE KNOW…..

Describe the use of GFP fusion proteins

Answer 34

Can be used in conjunction with secretory pathway mutants

Will show where the accumulation is and where it goes when the temp is lowered again

Question 35

What are the four functions of the smooth ER?

Answer 35

Lipid synthesis (membrane lipids and steroid hormones)
Storage of Ca++ (used in signaling)
Drug detoxification
Carbohydrate metabolism

Question 36

What are the three general transport types?

Answer 36

Through nuclear pores (requires unfolding and protein translocators)
Across membranes
By vesicles

Question 37

What is the endomembrane system?

Answer 37

The nuclear membranes and the membranes of the ER, Golgi, endosomes, and lysosomes originated from invagination of the plasma membrane

These are all members of the endomembrane system

Question 38

Describe the purpose of Ran and SNARE proteins in vesicle transport

Answer 38

they direct vesicle interaction with target membranes

Rab binds a tethering protein

V-SNARES on vesicles bind to T-SNARES on the target membrane

SNARES facilitate/catalyze membrane fusion

Question 39

What is the role of the cytoskeleton in celllar transport?

Answer 39

The cytoskeleton forms tracks for the vesicles

Question 40

Describe the nuclear envelope

Answer 40

The nuclear envelope encloses the nuclear DNA and defines the nuclear compartment. It is formed by two concentric membranes, the inner membrane with proteins that act as binding sites for both chromosomes and the nuclear lamina (fibrillar network, supports envelope), and the outer membrane that is continuous with the ER membrane.

Question 41

Describe the nuclear pores. What do molecules need to enter?

Answer 41

Nuclear pores are large, elaborate structures with many proteins and symmetry. Many have unstructured regions of disordered polypeptide chains that form a mesh that stops large molecules while allowing in small, soluble ones. Large molecules must have a sorting signal to enter, the nuclear localization signal (NLS).

Question 42

Describe the process of the importation of large molecules into the nucleus via the nuclear pores. Include names of helper proteins and their end fate

Answer 42

The nuclear import signal (NLS) is bound by a nuclear import receptor (importin)

The cytosolic fibrils then help the protein/receptor through the network of nuclear fibrils

Ran and GTP binds to the receptor, causing it to release its cargo

Back out in the cytosol, Ran hydrolyzes its GTP and dissociates from receptor

Question 43

Describe how proteins are imported into mitochondria and chloroplasts

Answer 43

Imported proteins must have their signal sequence (mitochondria makes some of its own)
They are transported simultaneously across both membranes
As they are transported, they are unfolded and their signal sequence removed
Chaperone proteins help the protein across and fold it when it is inside

Question 44

Are signal sequences on the N-terminus or C-terminus

Answer 44

N-terminus