Outline for Lecture 12

C2006/F2402 '10 OUTLINE OF LECTURE #12

Handouts: 12A. Modes of communication between cells. 12B -- Signal Hypothesis -- Co-translational Import & 12C = How proteins insert into ER membrane.

I. How do cells signal to other cells?

A. Why & when is cell-cell communication needed?

1. For development to work properly

2. To co-ordinate functions in adult -- between cells, tissues and organs (w/o using nerves)

3. For nerve-nerve and nerve-target communication

B. Major types of secreted Signals -- classified here by type of cell that makes them and/or target location. See Handout 12A for pictures -- numbers of pictures match numbers below.

1. Endocrine:

a. Signal molecule secreted by specialized cells in ductless (endocrine) gland

b. Gland secretes signal molecule (hormone) into blood.

c. Target cell is often far away. Acts long range. For an example see Becker fig. 14-23 (14-22).

d. Examples: Insulin, testosterone, TH (thyroid hormone)

e. Signal molecule is not always a protein -- can be a protein (insulin & many others) or not (testosterone or other steroid or TH)

2. Paracrine: See Becker fig. 14-1 & table 14-4 (6th ed) for paracrine (or autocrine) vs. endocrine.

a. Usually secreted by ordinary cells

b. Target cell is near by -- Receptor is on adjacent cells. Act locally.

c. Example -- many growth factors (such as EGF); Wnt proteins (products of WNT genes), AMH (AntiMullerian Hormone -- not an endocrine, in spite of name)

3. Autocrine: Like paracrine, except receptor is on same cell. ex. = some growth factors

4. Neurocrine:

a. Neuron secretes signal molecule.

b. Signal molecule acts as a neurotransmitter (NT)

c. NT acts on receptors on neighbor (gland, another neuron or muscle). Acts locally, like a paracrine.

d. Examples: norephinephrine, acetyl choline. Details when we get to nerves. (Note these are small molecules, not proteins.)

5. Neuroendocrine:

a. Neuron secretes signal molecule, as in previous case.

b. Signal molecule acts like a hormone (travels through blood to target).

c. Example: Epinephrine (adrenaline).

6. Exocrine:

a. Exocrine gland secretions are released by ducts to outside of body (or to inside of body cavity)*.

b. Examples: sweat, tears.

c. Secretions on outside can carry signals → target in different individual = pheromones (detected by olfactory receptors in mammals).

*Exocrine secretions (not involved in signaling) can be released to spaces inside of the body that connect with the outside, such as the GI lumen. Example: enzymes of pancreas.

C. Other types of Signaling

1. Gap Junctions -- allow ions & currents to flow directly from cell to cell -- used in smooth muscle → synchronized contractions. Sadava fig. 15.19 (15.16).

2. Juxtacrine. Cell surface proteins from two different cells contact -- used in immune system. Similar to basic system, but signal molecule is not secreted -- remains on cell surface.

II. How do cells make secreted proteins?Sorting of Proteins to their Proper Place: Overview & Review (See handout 7C & Becker fig. 22-14 (20-14) or Sadava 12.15 (12.14) -- terminology in Sadava is slightly different.)

A. Fate of proteins made on free ribosomes

1. Soluble Cytoplasm This is the default location for a soluble protein. If there are no "tags" at all, proteins stay in the cytoplasm.

2. Organelles that are not part of the endomembrane system (EMS). Proteins with the appropriate "tags" or localization signals can be imported post-translationally into organelles outside the EMS -- nuclei, mito, chloro or peroxisomes.

B. Fate of proteins made on attached ribosomes -- these become part of the endomembrane system and/or leave the cell.

1. They enter the ER primarily by co-translational import. (There is some post-translational import, esp. in unicellular eukaryotes.) Protein can

Remain inserted in membrane -- become a transmembrane protein -- single or multipass(details below)

Pass all the way across the membrane and end up in lumen of ER

2. Most proteins travel from ER to Golgi (a few may remain in ER) -- vesicles carrying protein bud off ER, travel to Golgi and fuse with cis side of Golgi (side nearest to nucleus).

3. Most proteins are sorted and processed in the Golgi and packed into vesicles that bud off the trans side of Golgi (also called TGN = trans Golgi network).

4. Where do the proteins and/or vesicles go next?

a. Secretory vesicles (vesicles involved in regulated secretion) → area near plasma membrane

(1). Vesicles fuse with plasma membrane only in response to signal (such as hormone, change in local Na⁺ concentration, etc.)

(2). The 'signal' usually causes an increase in intracellular Ca⁺⁺, which directly triggers the fusion, causing exocytosis.

(3). Fusion results in: Release of contents outside cell and/or addition of material to cell membrane. Click here for animation #1 -- annotated & animation #2 -- larger but not annotated.

b. Default vesicles (vesicles involved in constitutive secretion) → plasma membrane → fuse automatically (constitutively) and release contents. Same as in (a) -- leads to addition of material to membrane or outside it. HOWEVER no signal is required for fusion. This is probably the "default" for proteins that are directed to the ER but have no additional directional information.

c. Vesicles containing hydrolases → Lysosomes (details to be discussed in future lectures).

d. Vesicles containing other enzymes → other parts of EMS (Some enzymes may stay in trans Golgi, but others bud off and go back to other parts of Golgi, ER, etc.)

C. Labeling -- How do you follow newly made molecules moving through the cell and/or on their way out? How do we know newly made proteins go from RER to Golgi etc.?

In examples of detection discussed previously, emphasis was on following molecules going in to the cell. This example is about following newly made molecules on their way out.

1. General idea -- Add labeled precursors (small molecules) and measure incorporation into macromolecules.

a. Add labeled precursors, and take cell samples after increasing time intervals.

b. For each sample, wash out unused ('unincorporated') small molecules -- removes labeled molecules not used for synthesis so not incorporated into macromolecules. Radioactivity remaining in dif. parts of the cell is in macromolecules.

c. Use autoradiography for measurement of radioactivity in each cell part, or measure amounts in each isolated fraction.

2. A specific example -- following secreted proteins out. See graphs on handout 6C. Re-label the curves, left to right, with Rough ER, Golgi, Vesicles, Outside the cell.

a. Continuous label vs pulse-chase results (See graphs on handout 6C & fig. 12-10 of Becker. 6th ed. has curves; 7th ed. has autoradiographs.)

b. Implications: newly made proteins to be secreted go → RER → Golgi → secretory vesicles → outside (See Becker fig. 12-8.) Click here for animation.

To review labeling of newly made material, try 3-4D.

D. Another Type of Labeling -- Cell makes its own labeled (fluorescent) protein containing GFP

GFP has been mentioned before. Here are the details.

1. What is it? GFP = green fluorescent protein = small fluorescent protein made by jelly fish. (Click here for page with pictures of GFP and related fluorescent proteins.)

2. What is it good for? GFP is used as tag to follow proteins inside the cell.

3. How is GFP added to proteins? GFP is not added from outside. Instead, genetic engineering is used to splice the gene for GFP to the gene for the protein of interest. The recombinant gene makes a fusion protein = normal sequence of amino acid + sequence of amino acids in GFP. Fusion protein (including GFP) is made internally by the cell; the functioning protein part and the GFP part fold up separately (each forms a separate domain).

4. How does fusion protein work?

a. GFP part fluoresces. In other words, cell makes its own fluorescently tagged version of the protein.

b. Functioning protein part usually works normally, but location of protein can be easily followed in cell, because protein has GFP attached. GFP labeled protein is used for many purposes, including following newly made protein through the cell.

5. Examples. For examples of use of GFP, see Becker fig. A-14, or Purves p. 885 (7th ed). Not in 8th ed. (Sadava).
GFP is often used to identify cells that express (turn on) a particular gene. For an example see this picture. The cells that "light up" are the only ones that express (turn on) the fusion gene. Only these cells produce a fusion protein containing GFP. (This example also illustrates why people use small, transparent organisms as "model organisms.") For a really startling picture, t ry this picture. For the accompanying article, click here.

See problem 2R-4 for an example of the use of GFP labeling.

To review the material so far, you can try problems 3-1, A & B, 3-16, A & B, & 3-17. Alternatively, you may find it easier to wait until after section III.

III. ER -- How does Co-translational Import Work?

A. Signal hypothesis -- How ribosomes get to the ER & Protein enters ER -- See handout 12B. Steps listed below refer to handout. See Becker fig. 22-16 or Sadava fig. 12.16 (12.15).

1. What is the Signal Hypothesis? Ribosome unattached to ER starts making protein. (Step 1.) If nascent (growing, incomplete) peptide has a "signal peptide," then ribosome plus growing chain will attach to ER membrane, and growing chain will enter ER as it grows.

2. How does ribosome get to the ER?

a. Signal peptide (SP) = section of growing peptide (usually on amino end) does not bind directly to the ER. Binds to 'middleman' called SRP. (Step 2.)

b. SRP = signal recognition particle = example of an RNP (ribonucleoprotein particle)

    Role: temporarily blocks translation; ferries nascent protein to ER.

    Structure: SRP contains proteins + RNA = Large particle containing both ribonucleic acid & protein like a ribosome or spliceosome.

    Helps attach ribosome to ER, so growing chain can enter pore (translocon) in ER.

3. How does Growing Chain enter ER? Takes two steps (3 & 4)

a. ER has SRP receptor. Receptor is also called docking protein. SRP binds to SRP receptor/docking protein, not directly to pore. (Step 3.)

b. ER has Translocon (gated pore or channel through membrane) which allows growing chain to pass through membrane as chain is made. Pore is closed until ribosome with growing chain gets into position.

Note on terminology: The term "translocon" is used in (at least) 2 different ways. Sometimes it is used to mean only the channel itself, and sometimes it is used to mean the whole complex of proteins required for translocation of proteins across the membrane -- the channel, SRP receptor, etc. It should be clear from context which usage is meant at any one time.

c. Ribosome/translocon complex formation occurs. (step 4 = complex step involving several events)

SRP is released, recycles -- GTP split

Ribosome binds to pore/translocon

Translocon opens & peptide enters (as loop).

Ribosome resumes translation.

d. Role of Middleman. Middleman needed for entry into ER through translocon or entry into nucleus through nuclear pores. Processes probably similar. In each case there is a protein system with three components -- Protein with LS (NLS or SP) binds to "middle man" or "ferry proteins" (importins or SRP) which bind to pore. Additional proteins (that we will ignore) are required as well, and GTP is used to drive transport in both cases. See Becker fig. 18-30 for a model.

What You Need -- Category	to Get into Nucleus**	to Get into ER
Address/Localization Sequence	NLS	SP
Middle Man or "ferry protein/particle"	Transporter proteins (importin)*	SRP
Surface receptor protein(s)	Nuclear Pore Complex	Docking Protein (SRP receptor)

*A middle man protein is required to enter or exit the nucleus, but different ones are used in for entry vs exit. Exportin is needed to get out of the nucleus, while importin is needed to get in.

** This is how soluble nuclear proteins are imported into the nucleus Integral (transmembrane) proteins of the nuclear membrane (nuclear envelope) are probably made on the ER, and slide laterally into the outer & inner nuclear membranes (continuous with the ER). Once in place, TM proteins are anchored by binding to lamins or other internal nuclear proteins.

4. How does a new protein end up in the lumen?

a. Translation (and movement through translocon) continues (step 5)

b. Translation (and translocation) are completed, translocon closes. (step 6)

c. Signal Peptidase cuts off signal peptide at arrow. (step 7)

Protein is released into lumen of ER

Ribosome and mRNA are released

Now try problem 3-13, especially part D. (If some of the parts are not obvious, wait until later.)

B. How do proteins cross or enter the ER membrane? (See handout 12C and/or fig. 22-17 of Becker)

1. How proteins enter/pass through the membrane -- important points

a. SP probably forms loop not arrow. Loop enters channel (translocon) in membrane. SP loop is probably what opens (gates) the channel on the cytoplasmic side.

b. Protein enters as it is made. In humans, growing protein chains usually enter the ER as the chains are synthesized (co-translational import).

Note: In unicellular organisms, soluble proteins destined for the ER lumen often enter the ER after they are finished (post-translational import). Post translational import into the ER will be ignored here, but is covered at length in cell biology.

c. How do transmembrane proteins get anchored in the membrane? A hydrophobic sequence may trigger opening of the pore sideways, so protein slides out of pore, laterally, into lipid bilayer. These hydrophobic sequences are called 'stop-transfer' sequences and/or 'anchor' sequences.

d. Where will protein end up? Protein can go all the way through the membrane and end up as a soluble protein in the lumen (as in example above, on 12B) or protein can go part way through and end up as a transmembrane protein. Depends on sequence of protein.

2. Types of Proteins that can result (see handout 12C)

a. Soluble protein in lumen. Happens if protein passes all the way through the membrane and SP (on amino end) is removed, as above.

b. Integral membrane protein anchored in membrane by SP with no cytoplasmic domain. This happens if SP is on the amino end and is not removed.

c. Single Pass transmembrane protein -- get one of 2 possibilities:

(1). Type 1: Amino end is on lumen side of membrane (on E side); Carboxyl end is in cytoplasm (on P side of membrane)
One way this could happen: If SP is on amino end, and SP removed, and there is a hydrophobic sequence (acting as a stop-transfer or anchor sequence) in the middle of the peptide.

(2). Type 2: Carboxyl end is on lumen side of membrane (on E side); Amino end is in cytoplasm (on P side)
One way this could happen: If SP is in the middle, not on amino end. SP in this case is not removed -- it becomes the transmembrane domain of the protein. (SP doubles as stop-transfer or anchor sequence.)

d. Multipass transmembrane protein. (Requires one SP and several hydrophobic (start/stop) sequences.

(1). Hydrophobic sequences can stop the process (of moving through pore) and anchor protein in membrane, as explained above.

(2). Hydrophobic sequences in the middle of the peptide can restart looping → multipass protein. These are usually called "start-transfer" sequences (see 4).

(3). 'Start-transfer' and 'stop-transfer' sequences are probably equivalent. Role depends on where in protein they occur. (Both start- and stop-transfer sequences are also called 'topogenic sequences' as they determine the topology of the finished peptide.)

(4) A sequence that starts or restarts passage of a protein through the translocon is usually called a 'start transfer sequence' even if it also doubles as a stop or anchor in the membrane.

e. Lipid Anchored Proteins (FYI): Proteins to be anchored to lipids on the outside of the plasma membrane are generally made as follows: Protein is made on RER and inserted into the ER membrane. After the protein reaches the plasma membrane, the extracellular domain is detached from the rest of the protein and attached to lipid. (Proteins to be anchored to the plasma membrane on the inside are made on cytoplasmic ribosomes.) See Becker if you are curious about the details.

By now you should be able to do problems 3-1 to 3-3 & 3-4, A-B.

IV. What Else Happens in/on the ER?

A. What happens inside ER

1. Terminal SP usually removed. Signal peptidase (enzyme) inside ER recognizes a particular sequence of amino acids next to the SP. If this sequence is present in the protein, signal peptidase cuts the peptide chain at that point. (If this sequence is absent, SP is not removed.)

2. Folding of protein -- requires chaperones.

a. Chaperones (also called chaperonins) -- proteins needed to assist in protein folding. Chaperones are used every time a protein remains unfolded or becomes unfolded to cross a membrane (or refolds on the other side). Different chaperones are found in different parts of the cell.

b. Chaperones are of two major types (families) -- HSP 60 (forms barrel) or HSP 70 (binds to hydrophobic regions). Differ in molecular weight (60 K vs 70 K) and mode of action. (See an advanced text if you are curious about the mechanisms.)

c. The major chaperone inside the ER is a member of the HSP 70 family, also called "BiP"

d. Why are chaperones named HSP 60, HSP 70? HSP = heat shock protein. Chaperones, aka HSP's, are made in large amounts after exposure to high temperatures. (That's how they were first discovered.)

e. Final shape. Amino acid sequence of protein determines final, folded shape, but chaperone is needed to help reach final state.

3. Enzymatic Modifications. The appropriate enzymes inside the ER catalyze the following:

a. Making of S-S bonds. In eukaryotes, all S-S bonds are formed in proteins inside the ER. Proteins made in the cytoplasm do not have S-S bonds. Cytoplasmic proteins do contain cysteines and have free SH groups.

b. Start of N-glycosylation. Oligosaccacharides are added to the N of the amide of asparagine side chains (this is called N glycosylation.) See Becker fig. 12-7 if you are curious about the biochemical details. Additional steps of glycosylation occur in the Golgi; details below.

c. Removal of SP as above.

4. Some proteins stay in ER (in lumen or membrane); most move on to Golgi.

5. What happens to proteins in ER that do not fold properly? See Becker p. 750-752 (755-757) .

a. Transport to cytosol -- Unfolded proteins are transported back to the cytosol (through the translocon -- mechanism unknown).

b. Ubiquitin addition -- in cytosol, proteins (from ER or cytosol) to be degraded are marked for destruction by addition of a multiple molecules of a small protein called ubiquitin to side chains of lysine. (See Becker or advanced texts if you are interested in the enzymatic details.)

c. Role of Proteasome = a large protein complex in cytosol that degrades ubiquitinylated proteins to fragments, at expense of ATP. Major site of degradation of intracellular proteins. (Proteins from outside are generally degraded in lysosomes.)

d. What goes to the proteasome? Proteins that are misfolded, damaged, or have served their function.

A major proportion of all proteins made in cell do not fold properly and are degraded.

Destruction of many proteins is regulated -- level of protein activity can be controlled by protein degradation as well as by rate of synthesis, feed back of activity, modification, etc. More details and/or examples to follow.

e. 2004 Nobel Prize for Chemistry was awarded to Aaron Ciechanover, Avram Hershko and Irwin Rose for the discovery of the ubiquitin/proteasome system.

B. What happens on outside of ER (besides protein synthesis)

1. Lipid synthesis --

a. Insertion: Lipids made and inserted on cytoplasmic side (cytoplasmic leaflet) of membrane by enzymes attached to/in membrane.

b. Flipping: Enzymes ('flippases' = transporters) are required to move amphipathic lipids from one leaflet (P side) of membrane to other leaflet (E side). If lipids are moved preferentially from one side of membrane to the other, transport is active and requires ATP.

c. Transport: Lipids can reach parts of cell not connected to ER through vesicles and/or transport (exchange) proteins.

2. Some detoxifications and other reactions are catalyzed by proteins on the cyto side of ER. See text for details if interested.

To review the structure and function of the ER, try problem 3-4.

V. Golgi Complex -- Structure & Function

A. How things get there -- from ER in coated vesicles (coat made of protein called coatomer or COP instead of clathrin). For animation of how materials pass from ER to and through Golgi click here.

B. Structure & Overall Traffic Flow - See Sadava, fig 4.11 (4.12) or Becker fig. 12-4 & 12-8

1. Two sides of stack

a. cis/forming face (side closest to nucleus & ER)

b. trans/maturing face (away from nucleus)

2. Three basic parts or compartments in a stack

a. CGN (cis-Golgi network) or cis Golgi -- may include fusing vesicles

b. medial cisternae (sacs) -- part in between 'cis' and 'trans' Golgi

c. TGN (trans-Golgi network) or trans Golgi -- may include budding vesicles

3. Different marker enzymes/functions found in different parts. (See Becker figs 12-5 & 12-6) Enzymes unique to any one cell organelle or compartment are called 'marker enzymes' = their presence is a 'marker' for the presence of that compartment or organelle.

4. Sacs in stack connected by vesicle traffic -- not completely clear which way transport vesicles go or what they carry. (See next time.) It is clear that newly made protein and lipid passes through the Golgi from the cis face to the trans face, as shown on this animation.

C. Function -- what reactions take place inside Golgi?

1. Finish N glycosylation -- oligosaccharide that was added to glycoproteins in ER is modified. These oligosaccharides are attached to "N" of amide side chains of asparagines (asn's).

2. Do O glycosylation of glycoproteins. Sugars are added to "O" of the hydroxyl of the side chain of ser & thr.

3. Assemble sugars of proteoglycans (linear chains of repeating sequence = GAGs)

4. Concentrate, sort proteins. This occurs at trans face (TGN). Different areas of Golgi have receptors that trap proteins going to different destinations.

To review how proteins are directed to the right place and modified in the ER and Golgi, try problem 3-2.

Next time: Wrap up of Golgi structure; then -- How are materials transported through the Golgi stacks?