C2006/F2402 '07 OUTLINE OF LECTURE #8

(c) 2007 Dr. Deborah Mowshowitz, Columbia University, New York, NY. Last update 02/12/2007 06:23 PM

Handouts: 7B (Hand drawn; not on web.)

I. Lysosomes -- an example of sorting after the Golgi

    A. The Normal Pathway (See Becker fig. 12-9 & handout 7B) --  covered last time.

    B. Scavenger Pathway & Lysosomal diseases -- see Handout 7B, top.

1. I-cell disease -- what happens if the enzyme that catalyzes formation of M6P is missing.

a. The primary defect: In I-cell disease, the defect is in the gene for an enzyme that modifies all the soluble hydrolases. So many hydrolases are affected, not just one. (Hydrolases that are membrane proteins are not affected.) Step 3 is skipped.

b. What happens to the hydrolases: All the soluble acid hydrolases lack M6P. So all the hydrolases that would normally stick to M6P receptors go to the wrong part of the Golgi. The hydrolases then end up in default vesicles. (Step 11) The default vesicles fuse with the plasma membrane and the hydrolases exit the cell. (Step 12) The hydrolases never reach the lysosomes.

c. The consequences: Inclusion bodies form = vesicles full of undigested materials that are normally degraded in lysosomes. ("Lysosomes" contain substrate, but no hydrolases to degrade the substrate.) Note that not all tissues are affected in I (inclusion) disease. This implies that there are other pathways for directing hydrolases to the lysosomes. Different enzymes and/or pathways must be critical in different tissues.

2. Standard lysosomal storage diseases

a. What is a lysosomal storage disease? It's what happens if one hydrolase is missing or defective. A different enzyme is missing in each disease.

b. Examples: Gaucher's disease & Tay-Sach's disease. In these cases, only one hydrolase is missing due to a defect in the gene for that enzyme. All other hydrolases reach the lysosomes and function normally. 

c. How is I disease different? In I disease, most of the hydrolases are missing from lysosomes -- the hydrolases are made, but are not transported to lysosomes. The defect is not in the gene for a particular hydrolase. The defect is in a gene for an enzyme that modifies the sugars attached to many different hydrolases.

d. Genetics: Each standard lysosomal storage disease or I disease is caused by a single, recessive mutation -- but the mutation in each disease is different. 

3. Salvage (scavenger) pathway -- recovers normal hydrolases that accidentally end up outside the cell.

a. Some M6P receptors are "misdirected" : they are not recycled to Golgi -- instead they reach plasma membrane in some cells (by default pathway?). 

b. Some normal hydrolases (with M6P) are "misdirected" -- they reach extra-cellular fluid (by default pathway?) -- "escape" from cell.

c. Misplaced receptors can trap misplaced hydrolases: M6P receptors on the plasma membrane bind any extra-cellular hydrolases that "escaped" the cell (since these are normal hydrolases with M6P attached) . This is the "scavenger" part. 

d. "Escaped" Hydrolases can be recovered by RME: Hydrolases bound to receptors are internalized by RME endosome lysosome = where they belonged in the first place. This is the "salvage" or recovery part. ("Misdirected" and "escaped" are in quotes above, because this may be a normal pathway that some hydrolases always use to reach the lysosomes.)

4. Use of Salvage Pathway to treat Gaucher's Disease -- Enzyme Replacement Therapy

a. Missing lysosomal enzymes can be added: In cells with salvage pathway, added lysosomal hydrolases (containing M6P) can be taken up from outside. Hydrolases will be retrieved by RME and localized to lysosomes as explained above.

b. Practical Use: This method is currently used to treat Gaucher's disease (one hydrolase missing) at annual cost of $50,000 per patient for added enzyme. Enzyme is so expensive because M6P addition (& glycosylation in general) cannot yet be done in bacteria. Enzyme must be obtained from eukaryotic cells grown in tissue culture -- in bottles. Several other lysosomal diseases have been treated by enzyme replacement therapy at a similar cost per patient.

c. Can't treat I-cell disease this way. Note only one enzyme is being replaced here, not an entire set of hydrolases (as would be required to treat I-cell disease).

To review lysosomes and lysosomal diseases, try problem 3-9. For a catalog of all lysosomal diseases & current treatment see eMedicine.

II. Mitochondria & Chloroplasts
 How do proteins get into other cytoplasmic organelles that are not part of the EMS? See right fork of flow chart on top of handout 6A.

    A. Some Proteins are made inside the organelles

Some proteins (not many) are made inside mitochondria and chloroplasts using organelle DNA and organelle transcription and translation machinery.  

    B. Most organelle proteins must be imported.

1. Most organelle proteins are made on free ribosomes and then imported (post-translationally) into the organelles. 

2. Organelle Membranes contain translocases. Proteins are imported by passing through pores or transport complexes (translocases) in the organelle membranes. See Becker 22-18 (20-18).

3. Proteins can pass through both mito. membranes at once. Proteins enter matrix by crossing membranes at contact point = point where membranes are very close together and translocases of the inner and outer membrane are aligned. See Becker fig. 22-19 (20-19).

4. Localization signals. A short sequence called a transit peptide on the amino end is the usual localization signal that targets a protein to attach to a mito. translocase and enter the matrix. The TP is removed once the protein enters the matrix of the mitochondrion. (Additional signals are required to direct the protein to a membrane or the intramembrane space. See 7 below.) Similar sequences are used to direct chloroplast proteins to translocases on the organelle and to the correct organelle subcompartment.

5. Entry requires energy in form of ATP and/or electrochemical (proton) gradient. Note that transfer is post-translational so energy of protein synthesis cannot be used to drive entry of protein into organelle.

6. Chaperones (chaperonins) are needed.  Proteins are translocated in an unfolded state. Every time a protein remains/becomes unfolded to cross a membrane (or refolds on the other side) a chaperone is needed. Two or more types of chaperones involved here -- one in cytoplasm and one or two in matrix of organelle. See Becker fig. 22-20 (20-20).

a. Chaperones in cytoplasm keep protein unfolded or loosely folded until it reaches mitochondrion.

b. Chaperones inside organelle may help "pull protein in" and help protein fold properly once it enters. 

c. Release of chaperones requires hydrolysis of ATP.

7. How do proteins reach parts of the organelle other than the matrix? Proteins destined for the membranes or the intramembrane space may enter the outer membrane, cross only part way in, and never reach the matrix -- the proteins could lodge in the appropriate membrane (if they have a 'stop' transfer sequence) or stay in the intramembrane space. Alternatively, the proteins may enter the matrix and then use a 'start' sequence to cross back out to the membranes or intramembrane space from the matrix. Different proteins probably use different pathways. In any case, proteins destined for sites other than the matrix require additional localization signals and/or stop/transfer sequences.

8. Comparison of Mitochondria vs Lysosomes

  Feature Lysosomes Mitochondria
1 Membrane(s) around organelle Single Double
2 Contain DNA? No Yes
3 Grow & Split? No Yes
4 Where are organelle proteins made? Where are the ribosomes? On Rough ER Free in Cytoplasm & inside organelle
5 Protein import is co-translational post-translational (while unfolded)
6 Localization Signal #1 signal peptide transit peptide
7 Additional LS signal to add M6P stop transfer &/or others (depends on final location)
8 Function of organelle Degradation of macromolecules Energy Metabolism

III. Peroxisomes -- summary of structure, function and synthesis.
 For more details see Becker  pp. 354-358 (358-362).

    A. Structure -- comparison to mitochondria and lysosomes (see table above)

1. Summary Table -- compare to table above

  Feature Peroxisomes
1 Membrane(s) around organelle Single
2 Contain DNA? No
3 Grow & Split? Yes; may also arise de novo
4 Where are organelle proteins made? Where are the ribosomes? On Free Cytoplasmic Ribosomes
5 Protein import is post-translational (while folded)
6 Localization Signal #1 on COOH end; probably not removed
7 Additional LS None?
8 Function of organelle Detoxification; fatty acid oxidation (in animals)

2. Another way to Compare Features to those of Mito. & Lysosomes

Features like lysosomes

Features like mito/chloroplasts

Unique Features

Single Membrane

Probably grow and split

Signal (for import) on COOH end of proteins ; prob. not removed


Protein made in cytoplasm on free ribosomes.

Protein crosses membrane in folded state.

Density & Size

Protein enters post-translationally

Sequesters Dangerous Stuff

Some energy metabolism (fatty acid oxidation)

"Dangerous stuff" =  product or substrate, not enzyme 

3. How are peroxisomes distinguished from lysosomes, since both organelles are so similar in structure?  

a. Biochemical Method: Peroxisomes separated from lysosomes biochemically ("grind and find" method) after growing animals on diet with triton (detergent). Details:

  • Lysosomes accumulate detergent.

  • Detergent = mimic of  phospholipid = amphipathic molecule with hydrophobic and hydrophilic ends. 

  • Density of organelles is proportional to protein/lipid ratio. Growth on detergent alters the ratio in lysosomes.

  • Lysosomes with triton (equivalent to extra lipid) are unusually light (low density, because of high lipid/detergent content).

  • Density of peroxisomes is unchanged by growth on detergent.

b. In situ Method: Peroxisomes identified in situ as different from lysosomes by marker enzymes

  •  Marker enzymes = enzymes characteristic of and unique to a particular organelle.

  • Typical marker enzymes for peroxixomes are urate oxidase (function unknown) or catalase

  • Typical marker enzyme for lysosomes is acid phosphatase

    B. Major Function = detoxification (in animal cells). See Becker for other roles, esp. in other organisms.

1. Role of Oxidases: Oxidases catalyze: 

RH2 + O2 R + peroxide (H2O2)

2. Role of Catalase: Catalase catalyzes:

  H2O2 + R'H2 (can be a second molecule of peroxide) R' + 2 H2O

If R'H2  is a second molecule of peroxide, R' is oxygen and overall reaction is: 

   2 H2O2 O2 + 2 H2O

Net Result:

  • Catalase gets rid of peroxide, and

  • Catalase generates oxygen for another go round of oxidation (if R'H2 is peroxide) or detoxifies R'H2 (by oxidizing it)

    C. How do Proteins (& phosopholipids) get into Peroxisomes?

To review how proteins enter mitochondria and peroxisomes, try problems 3-6 & 3-7.

IV. How Proteins Enter Nuclei -- Nuclear Pores and Traffic through Them

    A. Pore structure -- hard to explain; will be demonstrated. See Becker fig. 18-27 & 28 (16-27 & 28) and/or Purves fig. 4.9 (4.8)

    B. Pore Function

1. Acts like (ungated, always open) channel for small molecules (may include small proteins).

2. Acts as active transporter for big molecules. Features of active transport:

a. Transport requires energy (GTP split)

b. Requires NLS (nuclear localization signal) on protein transported into nucleus; signal not removed (may be needed again after mitosis to re-localize protein).

c. Involves binding to pore protein

d. Probably works like SRP/SP/Docking protein system with three components -- Protein with NLS binds to "middle man"  or "ferry proteins" (importins) which bind to pore. See Becker fig. 18-30 (16-30) for a model.

What You Need -- Category

to Get into Nucleus

to Get into ER

Address/Localization Sequence



Middle Man or "ferry protein"

Transporter proteins (importin)*


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.

3. Transport is bidirectional -- mRNA, ribosomal subunits etc., must go out (see below) and proteins must go in. (See Becker fig. 18-29 (16-29)) How things get out is not as well understood as how things get in. Exit required an exit signal (NES) and the transporter protein exportin.

To review nuclear transport, try problem 4-2.

V. Summary of Transport, Localization signals, etc.

    A. FYI: Issues to keep in mind --  (See table below)

1. What type of localization signal (or localization sequence = LS) required? Where is it?

2. Is signal removed after membrane is crossed?

3. How many membranes must be crossed?

4. What is localization signal or sequence called?

5. When does translocation (crossing of membrane) occur -- during protein synthesis (co-translational) or after (post-translational)?

    B. Summary Table of Signal*** & Localization Sequences -- For Reference.

Post Translational Import Co-translational
Import Into: Mito/Chloro Peroxisomes Nuclei ER**
Signal: NH2 End * COOH end anywhere usually--NH2 end
Signal removed: Yes No No usually--yes
Enter or Cross: 2 membranes at contact point matrix 1 membrane pores 1 membrane
Name of Signal*** Transit Peptide (TP) Peroxisomal  Localization Signal Nuclear Localization Signal (NLS) Signal Peptide (SP)

*This is the signal needed to enter the matrix. Different and/or additional signals are needed to enter the outer membrane, inner membrane, or intramembrane space.

** Once protein enters ER, additional signals may be needed to direct protein to correct part of endomembrane system

*** The term "signal peptide" or "signal sequence" is sometimes used in a general sense to mean any of the localization signals listed here. It is used in a more specific way to mean only the localization signal used to enter the ER.

To review localization and transport, try problems 3-14 & 3-15.  By this point you should be able to do all the problems in Set 3 (except for protein (5) in 3-14 ).

VI. Nuclear Structure & Role of nucleolus

    A. Lamins A, B, C & Nuclear lamina

1. Lamins = IF's of nucleus (No MT or MF in nucleus)

2. Not to be confused with Laminin -- a glycoprotein in the extracellular matrix (ECM) found primarily in the basal lamina

3. Form nuclear cortex or lamina = web supporting the nuclear envelope -- see Becker fig.  18-31(b) [16-31 (b)]. Similar function to ankryin/spectrin/actin web under plasma membrane.

4. State of Phosphorylation and function change during cell cycle

a. Phosphorylated at G2 M (prophase); de-polymerize; due to rise in protein kinase activity

b. Dephosphorylated at M G1 (anaphase); re-polymerize; due to rise in protein phosphatase activity

c. This is another example of using addition/removal of phosphate to control protein conformation & activity.

  • Kinases & phosphatases here are separate from their target proteins (as vs. case of Na+/K+ pump).

  • Same kinase or phosphatase can modify multiple target proteins at critical points in cell cycle.

5. May help organize chromatin; may provide attachment sites for chromosomes and nuclear pore complexes.

    B. Nucleolus

1. Nucleolus has no membrane (see Becker fig. 18-33 (16-32)). 

2. Nucleolus is site of rRNA synthesis and assembly of ribosomal subunits -- production of ribosomes requires extensive traffic in and out of nucleus

a. rRNA is made in the nucleolus (see Becker fig. 18-34 (16-33)) using polymerase I (see below)

b. Ribosomal proteins are NOT made in the nucleolus.

  • Ribo proteins are made in the cytoplasm, but imported into the nucleus for assembly into subunits.

  • Messenger RNA for ribosomal proteins is made in the nucleus and exported to the cytoplasm, as for any other mRNA.

  • After the mRNA is translated, the proteins are imported back into the nucleus for assembly with rRNA.

c. Ribosomal subunits are assembled in the nucleolus from ribosomal proteins (made in cytoplasm) and rRNA. 

d. Completed ribosomal subunits are shipped out to the cytoplasm to be used in protein synthesis. Export out of the nucleus through the pores requires an NES (nuclear export signal). NES allows transport out of nucleus; NLS allows transport in to nucleus. Mechanism of transport through nuclear pores is thought to be similar, but not identical, in both directions.

3. Nucleolus (but not NOR, see below) disappears during meiosis/mitosis since genes for rRNA inactive then (no rRNA made or ribosomal subunits assembled)

4. Relationship of nucleolus to NOR (= nucleolar organizer region of DNA)

a. NOR =  DNA coding for rRNA = rDNA = genes for rRNA. NOR is permanent -- is part of DNA.

b. Nucleolus forms  at location of one or more NOR's. Several NOR's can cluster together to form one nucleolus. Nucleoli are only visible when NOR is transcribed and ribosomes are being assembled.

c. There are multiple copies of genes for rRNA; often many tandem copies per NOR. Multiple copies are needed because rRNA is made directly off the DNA -- no intermediate such as mRNA to allow for amplification. (Q to think about: Do you need multiple copies of the genes for tRNA?)

    C. RNA polymerases

1. In Prokaryotes -- there is only one.

2. In eukaryotes -- there are three. Differ in sensitivity to drugs, location in nucleus, & what RNA's they make. (See Becker table. 21-1 (19-1) for details; for reference only.)

a. RNA pol I big ribosomal RNAs. This is the polymerase found in the nucleolus.  

b. RNA pol II mRNA (We'll focus primarily on this one when we discuss regulation of transcription.)

c. RNA pol III small RNA's like tRNA, 5S RNA (small ribosomal RNA)

To review nuclear structure, try problem 4-5, parts A & C.

    D. Chromatin. DNA in eukaryotes is not "naked" as it is in bacteria. It is in the form of chromatin = DNA complexed with proteins. So how do polymerases and regulatory proteins (generally called transcription factors or TFs in eukaryotes) get to the DNA and how do they manage to carry out (& regulate)  transcription with all those proteins stuck to the DNA? To answer these questions, we need to look first at chromatin structure.  

VII. General Chromatin Structure -- Euchromatin & Heterochromatin   

    A. Composition of chromatin = DNA + associated proteins

1. Associated proteins are mostly histones (small, basic; more details to follow)

2. Associated proteins includes some (nonhistone) regulatory proteins

    B. States of chromatin

1. In all states, DNA has proteins attached

2. Usually differences are due to different states of folding after histones added, not removal of histones (there are some exceptions which will be discussed later).

3. Two Basic States of Chromatin (visible in the light microscope)

a. Heterochromatin

(1). Darkly stained, relatively condensed, genetically inactive 

(2). Two kinds of (interphase) heterochromatin

(a). Constitutive heterochromatin -- always heterochromatic (ex: chromatin at centromeres, telomeres). Usually repeating in sequence, non coding.

(b). Facultative heterochromatin-- sometimes heterochromatic in interphase, sometimes not (depends on tissue, time etc.). Example: inactive X. Same X is not inactive in all cells. Whichever X is inactive is heterochromatic.

 Note: Most of the DNA that is inactive during interphase (in a particular cell type) is NOT heterochromatic.

(3). All DNA (chromatin) is heterochromatic during mitosis.

b. Euchromatin

(1). Stains more lightly, less condensed.

(2) Capable of genetic activity (transcription) as vs. heterochromatin. Normal state of most DNA during interphase. (Most interphase DNA is euchromatic, whether it is transcribed or not.) DNA must be euchromatic to be active, but not all euchromatin is active. 

(3). Not all euchromatin is folded equally tightly

(a). Tighter vs looser. Euchromatin is often divided into several distinct states of folding,  although tightness of folding is probably really continuous from relatively loose relatively tight.

(b). Different states of (eu)chromatin look about the same in the light microscope.  Therefore indirect methods (such as DNase treatment) are necessary to test state of folding.

(c). Use of DNases. States of folding of (eu)chromatin are often distinguished by effects of treatment with various types of DNase. State of (eu)chromatin will determine relative sensitivity of DNA (while still in chromatin) to degradation by various DNases. DNA that is in tighter areas of chromatin will be more protected from degradation. (Some examples of this will be discussed next time and are in problem sets.)  

(d). Correlation between folding and function. In general, more active (transcribed) chromatin is looser, but the situation is complex -- details to follow.

Next Time: Structure of Chromatin & Regulation of Gene Expression.