How Proteins are Targeted to the Rough E.R.

Note from Mr. W on 11/30. If you’re seeing this message, then you’re one of my first viewers on this page. Please send me an email letting me know what you think (and kindly let me know if you see any typos or errors).

1. Introduction: Free v. Bound Ribosomes

In a eukaryotic cell, ribosomes can be found in two places: in the cytoplasm (shown at “5” at left), or bound to the rough endoplasmic reticulum (also known as the rough ER, shown at “2”). Ribosomes that are floating in the cytoplasm are called free ribosomes, and indicated by “3.” The ribosomes attached to the rough ER are called bound ribosomes, and are shown at “4.”

Schematic diagram of parts of the endomembrane system

When a free ribosome synthesizes a protein, it will release that protein directly into the cytoplasm. By contrast, bound ribosomes make proteins that are released into the ER lumen (the fluid space inside the ER). Afterwards, these proteins will pass from the rough ER to the smooth ER (“3,” at right). This will be followed by transfers to vesicles (“4”), then the Golgi Apparatus (“5”), then more vesicles (“6”).

In the diagram at right, several possible fates for these proteins are possible: the protein might integrate itself into the membrane; or the protein might be exported by the cell, or the protein might be encapsulated within a membrane bound vesicle like a lysosome (shown at “7”).

Before going on, interact with these diagrams to make sure that you understand them. Doing so will help you review the endomembrane system, and also prepare you to understand protein targeting below.

[qwiz random=”true”] [h]

The ER and  Endomembrane System (Review)

[i]

[q] The nucleus is at

[textentry single_char=”true”]

[c*] 1

[f] Yes. The nucleus is at “1.”

[c] Enter word

[f] No.

[c] *

[f] No. The nucleus is the large, dark body on the far left.

[q] The rough ER is at

[textentry single_char=”true”]

[c*] 2

[f] Yes. The rough ER is at “2.”

[c] Enter word

[f] No.

[c] *

[f] No. The rough ER is a series of membrane-bound channels studded with ribosomes. The ribosomes are represented by the dark black dots.

[q] A vesicle moving materials from the smooth ER to the Golgi is at

[textentry single_char=”true”]

[c*] 4

[f] Yes. Number “4” represents a vesicle that’s moving materials from the smooth ER to the Golgi.

[c] Enter word

[f] No.

[c] *

[f] No. Here’s a hint. First find the Golgi (a series of membrane-bound, flattened sacs). Then find  a vesicle that’s moving towards it from the smooth ER.

[q] The Golgi is at…

[textentry single_char=”true”]

[c*] 5

[f] Yes. The Golgi is at “5.”

[c] Enter word

[f] No.

[c] *

[f] No. The Golgi is a series of flattened sacs.

[q] An “outbound” vesicle heading toward the membrane or an organelle immediately after the protein it is carrying has been been processed by the Golgi is at

[textentry single_char=”true”]

[c*] 6

[f] Yes. Number “6” is a vesicle with a protein that has just been processed by the Golgi apparatus.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Find the vesicle that’s closest to the the Golgi, and which is on the Golgi’s outer side.

[q] The nucleus is at

[textentry single_char=”true”]

[c*] 1

[f] Yes. Number “1” is the nucleus

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. The nucleus is generally in the center of the cell, so find the part of this diagram that is most central (you might have to imagine the entire diagram as a circle).

[q] The rough ER is at

[textentry single_char=”true”]

[c*] 2

[f] Excellent. Number “2” is the rough ER

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Rough ER is a series of interconnected membrane bound channels, studded with ribosomes. Which numbered item above could fit that description?

[q] Free ribosomes are indicated by which number?

[textentry single_char=”true”]

[c*] 3

[f] Nice. Number “3” indicates four “free” ribosomes, floating in the cytoplasm.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Free ribosomes float freely in the cytoplasm. If the cytoplasm is number 5, which ribosomes (represented by blue spheres) would qualify as being “free?”

[q] Bound ribosomes are indicated by which number?

[textentry single_char=”true”]

[c*] 4

[f] Great job. Number “4” indicates three “bound” ribosomes, each attached to the membrane of the rough ER.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Free ribosomes float freely in the cytoplasm. If the cytoplasm is number 5, which ribosomes (represented by blue spheres) would qualify as being “free?”

[/qwiz]

2. How do proteins get made at the right ribosome (“free” or “bound”)?

Now let’s step back for a moment and think about how protein synthesis works. A molecule of mRNA is synthesized in the nucleus and enters the cytoplasm. In the cytoplasm, a ribosome assembles itself around that mRNA, and starts synthesizing whatever protein that the mRNA is coding for. As we’ve just seen, some of these proteins (those headed for export, the membrane, or organelles like lysosomes) have to be made by ribosomes at the rough E.R. How does the cell ensure that proteins that need to be made at the rough ER get to bound ribosomes, as opposed to free ones?

Based on what you know about biology, speculate about a mechanism. You can write these down on any piece of paper, or on your student study guide for this module.

3. Protein targeting works through a signal polypeptide that binds to a signal recognition particle

Almost everything in biology works by touch and feel. Why does adenine bind with thymine? Because of complementary shapes. That’s also why enzymes bind with substrates, or why the anticodon on a tRNA can bind with its corresponding codon on messenger RNA.

The process by which proteins destined for the ER wind up at the ER happens through a similar mechanism. Study the diagram before reading the text that follows, and see if you can explain to yourself what’s happening. Then read the text to confirm your hypothesis. Note that when you read, you can scroll the text while keeping the image stationary.

The first thing to realize is that all ribosomes start as free ribosomes. It’s the protein that the ribosome is synthesizing that determines whether or not the ribosome will dock at the ER membrane and become a “bound” ribosome. Here’s how it works:

  • STEP 1: At “1” you see a ribosome that’s starting to synthesize a protein. In ribosomes that are destined to make their proteins at the rough ER, the first few amino acids will make up a signal polypeptide, shown at “B.” The signal polypeptide will not be a part of the protein that’s released into the lumen of the rough ER (shown at letter “E”). Rather, the signal polypeptide’s function is to  bind with a  signal recognition particle, shown at letter “A.”
  • STEP 2: At “2” you can see the signal recognition particle, bound to a signal polypeptide. The signal recognition particle (SRP) has a second binding site (in addition to the one that binds with the signal polypeptide),that’s complementary to a translocation complex, a protein that’s embedded in the membrane of the rough ER. The binding of the SRP to the signal polypeptide also temporarily halts protein synthesis.
  • STEP 3: While the arrow in diagram 2 seems to show that the ribosome/SRP heads to the translocation complex with the determination of a hawk swooping down on its prey, it’s important to keep in mind that the ribosome is floating around randomly. When the ribosome, with its attached SRP, bumps into the ER’s membrane in the right spot and in the right orientation, the SRP binds with the translocation complex (just as any ligand binds with its receptor). This is what you see at step number “3.”
  • STEP 4: The translocation complex is both a membrane channel and a membrane-embedded enzyme. The substrate of the enzyme is the signal polypeptide. At “4” you can see the signal polypeptide bound to the translocation complex. This binding allows the SRP to float back into the cytoplasm, where it will drift until it binds with another signal polypeptide.  Binding of the signal polypeptide with the translocation complex also restarts protein synthesis. with the rest of the polypeptide being threaded into the ER lumen.
  • STEP 5: At “5” the enzyme in the translocation complex goes to work, cutting the signal polypeptide off of the rest of the growing polypeptide chain.
  • STEP 6: At “6,” the ribosome has reached the stop codon on the mRNA. This causes the ribosomal subunits to dissociate, the mRNA to be released into the cytoplasm, and the protein to be released into the rough ER’s lumen.

Note that while our focus above has been on how ribosomes making certain proteins find their way to the rough ER, that this kind of signaling is the basis for how many things find their right place within cells. Signal polypeptides are like the addresses on an envelope. These signals are bound by signal recognition particles that have affinities to specific organelles within the cell. In other words, protein targeting is how a cell sends proteins to its mitochondria, its lysosomes, or any other organelle.

Got it? Try this quiz.

4. Protein Targeting Quiz

[qwiz random = “true” style=”width: 600px !important;”]

[h]Protein Targeting

[i]

[q] In the diagram below, a free ribosome that has synthesized a signal polypeptide, but which has not yet bonded with a signal recognition particle, is shown at

[textentry single_char=”true”]

[c*] 1

[f] Excellent! “1” shows a free ribosome. This ribosome has already translated the signal polypeptide, but that signal polypeptide has not yet bonded with the signal recognition particle.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Here’s a hint. Free ribosomes are ribosomes that haven’t docked at the ER membrane. Once you find a free ribosome, hone in on the one that hasn’t bonded with the signal recognition particle (at “A”)

[q] In the diagram below, a free ribosome that has a signal recognition particle attached to its signal polypeptide is shown at

[textentry single_char=”true”]

[c*] 2

[f] Nice! “2” shows a free ribosome. This ribosome has already translated the signal polypeptide, and signal polypeptide has bonded with the signal recognition particle.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Here’s a hint. Free ribosomes are ribosomes that haven’t docked at the ER membrane. Once you find a free ribosome, hone in on the one that’s bonded with the signal recognition particle (at “A”).

[q] In the diagram below, the first moment when a free ribosome becomes a bound ribosome is shown at

[textentry single_char=”true”]

[c*] 3

[f] Good Job! “3” shows a a ribosome that is bonding with a translocation complex. The moment a free ribosome binds with the ER membrane, it has become a bound ribosome.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. Here’s a hint. Free ribosomes are ribosomes that haven’t docked at the ER membrane. In the sequence above, find the moment when a free ribosome is binding with the ER membrane.

[q] In the diagram below, the moment when the signal polypeptide has bonded with the translocation complex, and when the the signal recognition particle has detached from the ribosome, is shown at

[textentry single_char=”true”]

[c*] 4

[f] Nice! “4” shows a newly bound ribosome that is has detached from a signal recognition particle.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. Here’s a hint. Look for a ribosome that has bonded with the ER membrane, but which has lost its signal recognition particle (originally indicated by letter “A.”

[q] In the diagram below, the moment when the signal polypeptide has been cleaved from the rest of the protein that the ribosome is synthesizing is shown at

[textentry single_char=”true”]

[c*] 5

[f] Nice! “5” shows the moment when the signal polypeptide has been cleaved from the rest of the protein that the ribosome is synthesizing.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Here’s a hint. The signal polypeptide is at letter “B.” Look for the first moment when this signal polypeptide has been detached from the rest of the protein.

[q] In the diagram below, the moment when the ribosome has dissociated, with ribosomal subunits and mRNA returning to the cytoplasm, is

[textentry single_char=”true”]

[c*] 6

[f] Correct! “6” shows the moment when the ribosome has dissociated.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No.  Look for the moment when you see, in the cytoplasm, both the large and small subunits of the ribosome, along with a strand of mRNA.

[q] In the diagram below, “A” is a signal ___________ particle.

[hangman]

[c] recognition

[f] Great!

[q] In the diagram below, “B” is a signal ___________.

[hangman]

[c] polypeptide

[f] Excellent!

[q] In the diagram below, “C” is a ___________ complex.

[hangman]

[c] translocation

[f] Excellent!

[q] In the diagram below, the signal recognition particle is shown at

 

[textentry single_char=”true”]

[c*] A

[f] Correct! “A” shows the signal recognition particle

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No.  Look for particle that binds with the signal polypeptide (shown at “B.”)

[q] In the diagram below, the signal polypeptide is shown at

[textentry single_char=”true”]

[c*] B

[f] Terrific! “B” shows the signal polypeptide.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No.  Look for a piece of the polypeptide that this ribosome is synthesizing that 1) binds with the signal recognition particle, and 2)  isn’t ultimately a part of the protein.

[q] In the diagram below, the translocation complex is shown at

[textentry single_char=”true”]

[c*] C

[f] Awesome! “C” shows the translocation complex.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No.  Look for a channel that’s located within the ER membrane.

[q] In the diagram below, the rough ER Membrane is shown at

[textentry single_char=”true”]

[c*] D

[f] Good work! “D” shows the ER membrane.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No.  Look for a something that looks like a membrane between the cytosol (in white) and the ER lumen (in blue)

[q] In the diagram below, the protein that has been released into the ER lumen is shown at

[textentry single_char=”true”]

[c*] E

[f] Good job! “E” shows a protein that has just been released into the ER lumen.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] o.  Look for a something that looks like a membrane between the cytosol (in white) and the ER lumen (in blue)

[q multiple_choice=”true”] Which of the following statements is true?

[c*] All ribosomes start out free. Some become bound.

[f] Yes! All ribosomes become free. Only those that synthesize a protein that starts with a signal polypeptide become bound.

[c] All ribosomes start out bound. Some become free.

[f] No. All ribosomes start out free. Only those that produce a protein with a signal recognition particle become bound.

[x][restart]

[/qwiz]

What now?

This tutorial ends this module about genes and proteins. Click here to return to the Module 14 (From Genes to Proteins) Menu. Or click the AP Biology link above to find another tutorial