12. Protein processing and the endomembrane system

Question 1

after translation, all proteins must be sorted to their destinations:
some proteins:

Answer 1

1. remain in the cytoplasm
2. move to cellular compartments by the cytoplasm
3. enter the endomembrane system, where they are modified and transported through a series of membrane-bound organelles

Question 2

transport of proteins in the endomembrane system

Answer 2

1. enter the endoplasmic reticulum
2. move by transport vesicles (budding and fusing “carriers” b/w other compartments)
3. to golgi, then to the :
4. trans-golgi network, then to:
   a) lysosomes or b) storage vesicles or c) secretory vesicles and plasma membrane

Question 3

in addition to the lumen or ER (interior space), the proteins may _______, _______ and _______ within the membranes of each these compartments.

Answer 3

reside, transfer and function

Question 4

general pathways of new proteins

Answer 4

starts in the cytoplasm: 1. nucleus

                                   2. mitochondrion
                                   3. R.E.R
                                          * golgi: lysosome or secreted

Question 5

ER structure

Answer 5

network of membranous tubules in the cytoplasm of a cell

two types: rough and smooth

Question 6

ER is involved in..

Answer 6

the production of phospholipids, proteins, and other functions

Question 7

Rough ER:

Answer 7

studded with ribosomes, continuous with nuclear envelope

• in most cells:
• synthesis of all proteins to be compartmentalized in lysosomes secretory vesicles
• synthesis of integral (membrane bound) proteins
• membrane biosynthesis (can assume some SER functions)
• glycosylation of many proteins

Question 8

Smooth ER:

Answer 8

no ribosomes; site of synthesis of specialized enzymes, functions
-concentrated in specialized cells:
skeletal muscle, kidney tubules, some endocrine glands, secretory cells
synthesis of steroids in gonad and adrenal cortex
synthesis of detoxification enzymes in liver
enzymes involved in glucose release from liver
release Ca2+ ions used in muscles contraction
lipid biosynthesis (membrane biosynthesis)

Question 9

biosynthesis

Answer 9

production of chemical compound by living organism

Question 10

chemical modifications of proteins in the ER and golgi

Answer 10

1. disulfid bond formation (cysteines) and folding
2. addition of extra chemical groups (methyl,acetyl,formyl,sulfate,hydroxyl.)
3. addition of lipids: lipoproteins are molecules of the cell membranes
4. formation of multimeric proteins (quaternary structure)
5. proeolytic cleavage
6. glycosylation

Question 11

disulfide bond formation and folding:

Answer 11

• protein folding: proteins have a correct or native state; the tertiary structure of a protein needs to be correct for it to work properly. if can be mis folded or denatured
• molecular chaperones are proteins that bind to and alter the folding of newly forming protein
  * quality control: proteins that misfold cannot bind to chaperones properly and are destroyed
  * with several cysteines, the order in which the disulfide bonds form is important-a protein disulfide isomerase in the lumen of ER can help

Question 12

glycosylation

Answer 12

most proteins destined for secretion, the extracellular matrix, the endomembrane system and the plasma membrane are glycoproteins

Question 13

RER is the site of synthesis of proteins destined for :

Answer 13

• secretion
• integral membrane proteins and proteins within lumen of the endomembrane system
• endoplasmic reticulum, golgi, lysosomes, vesicles, plant vacuoles

Question 14

proteins for the following locations are made within the cytoplasm, not the RER :

Answer 14

• cytosolic proteins
• peripheral proteins of the cell membrane
• proteins sent to the nucleus
• proteins destined for chloroplasts, mitochondria, peroxisomes

Question 15

what is different about the protein that is destined for the rough endoplasmic reticulum?

Answer 15

the main difference is that is has a hydrophobic signal sequce

Question 16

hydrophobic signal sequence

Answer 16

• after the signal sequence is synthesized, protein synthesis temporarily stops until the signal sequence is detected by a protein complex on the RER
• the signal peptide enters the ER through a channel and it guides the protein into the lumen of the RER. protein synthesis resumes and the rest of the protein is inserted in the lumen
• a signal peptidase near the inner surface of the membrane works to cleave the signal sequence from the growing peptide

Question 17

all proteins are made on ________ in the cytoplasm

Answer 17

ribosomes

some ribosomes are free in cytoplasm and some become attached to endoplasmic reticulum

Question 18

polyribosomes can be found on the RER

Answer 18

• the fluidity of the membrane allows the ribosome to be docked at its receptor site and also move along the mRNA
• translocons can move around on the ER membrane, because the membrane has fluidity
• polyribosomes can form, to speed up translation rate

Question 19

integral proteins

Answer 19

proteins embedded in the membrane
-some proteins get incorporated into the membrane- they do not end up in the ER Lumen
-some proteins have a single transmembrane domain-a stretch of at least 15 hydrophobic amino acids that is embedded in the lipid bilayer
-the translocon can open to allow lateral movement of the hydrophobic segment into the lipid bilayer
translocon opens a side door to let hydrophobic sequence move into a hydrophobic environment

Question 20

orientation of the integral protein is dependent on amino acids next to hydrophobic sequence

Answer 20

• presence of positively charged amino acids flanking the hydrophobic sequence will determine the orientation of the protein, such that the positive amino acids are pointing toward the cytosolic side (as opposed to the lumen side)
• N terminal could be in the lumen or the cytoplasm, orientation of protein is adjust so that the flanking positively-charged amino acids are aligned with negatively charged translocon amino acids

Question 21

some integral proteins have multiple transmembrane domains

Answer 21

page 15

• here is the insertion of a double pass transmembrane protein within the rough endoplasmic reticulum. the red coloured signal sequence starts the membrane insertion process. this continues until a second hydrophobic signal (orange) is reached. that anchors the second membrane passage
• these alternating hydrophobic regions are called start-transfer and stop transfer sequences

Question 22

multipass transmembrane proteins

Answer 22

membrane proteins that pass through the membrane multiple times have multiple start and stop signals. a hydrophobicity plot can predict the number of transmembrane domains a protein can have

Question 23

roles of transmembrane proteins

Answer 23

• communication b/w cells
• communication b/w organelles and cytoplasm
• ion transport
• nutrient transport
• connections for cytoskeleton
• 25% of cell’s proteins