protein target

Chapter 8

PROTEIN TARGETING

Proteins have intricate higher-order structures that formthrough noncovalent interactions during and immedi-ately after ribosomal protein synthesis. In addition, co-valent structural modifications in most proteins mustbe introduced by specialized enzymes. These reactionsare known collectively as posttranslational processing,which should not be confused with the posttranscrip-tional processing of RNA.

The processed proteins must be sent to their properdestinations in the cell. This requires targeting signalsand transport mechanisms. Finally, aged and partiallydenatured proteins must be destroyed in order to pre-vent toxic effects and protein aggregation. This chaptertraces the fate of eukaryotic proteins from the cradle tothe grave.

A SIGNAL SEQUENCE DIRECTS POLYPEPTIDESTO THE ENDOPLASMIC RETICULUM

Some ribosomes are free-floating in the cytoplasm, andothers are attached to the membrane of the endoplas-mic reticulum (ER). These ribosomes have the samestructure but make different proteins. Free cytoplasmicribosomes synthesize the proteins of cytoplasm, nucleus,and mitochondria. ER-bound ribosomes synthesizesecreted proteins, plasma membrane proteins, and theproteins of ER, Golgi apparatus, and lysosomes.

Ribosomes attach to the ER membrane only whenthey synthesize a polypeptide containing a signalsequence of about 20 to 25 mainly hydrophobic aminoacid residues at the amino end. As soon as it emergesfrom the ribosome, the signal sequence binds to a cyto-plasmic signal recognition particle (SRP), which isformed from a small RNA molecule of about 300nucleotides (the 7SL RNA) and six protein subunits.Binding of the SRP halts translation. Translation isresumed only when the SRP-signal sequence-ribosomecomplex binds to an SRP receptor on the ER membrane(Fig. 8.1).

The SRP receptor brings the ribosome in contactwith a protein translocator, which is a donut-shapedprotein in the ER membrane. The tunnel on the largeribosomal subunit from which the growing polypeptide

emerges is placed on the central hollow of the proteintranslocator while the SRP detaches. A pore opens inthe translocator, through which the polypeptide passesinto the lumen of the rough ER.

The signal sequence is no longer required beyondthis stage. It is cleaved off by a signal peptidase on theinner surface of the ER membrane.

Soluble secreted proteins are ferried from the ER tothe Golgi apparatus in transfer vesicles (Fig. 8.2). TheGolgi apparatus is a sorting station in which secretedproteins are packaged into secretory vesicles. Thesevesicles are destined to fuse with the plasma membraneand release their contents by exocytosis. This system oforganelles forms the secretory pathway, which is usedby all protein-secreting cells in the body (Table 8.1).

Proteins of the plasma membrane are initiallyinserted in the ER membrane and then travel throughthe secretory pathway until they are deposited in theplasma membrane during exocytosis. Proteins of theER membrane and the Golgi membrane are retainedin their respective organelles.

GLYCOPROTEINS ARE PROCESSEDIN THE SECRETORY PATHWAY

This road to the periphery is also an assembly line onwhich the proteins are modified covalently (Table 8.2).Disulfide bonds are formed with the help of a proteindisulfide isomerase enzyme in the ER. However, themost important robots in this assembly line are glycosyltransferases, which build oligosaccharides on the sidechains of serine, threonine, and asparagine in the pro-tein. The precursors for these reactions are nucleotide-activated monosaccharides (Figs. 8.3 and 8.4A, andTable 8.3), whose synthesis is described in Chapter 22.Most proteins that are processed through the secretorypathway are glycoproteins (see Fig. 8.3).

O-linked oligosaccharides are bound to the oxygenin the side chains of serine and threonine. They aresynthesized in the Golgi apparatus by the stepwise addi-tion of monosaccharides.

N-linked oligosaccharides are bound to the nitrogenin the side chain of asparagine. N-linked glycosylation

118

starts with the construction of a mannose-rich oligosac-charide on dolichol phosphate, a lipid in the ER mem-brane. The whole oligosaccharide is then transferredto an asparagine side chain of a newly synthesized poly-peptide (Fig. 8.5).

In the ER andGolgi apparatus, exoglycosidases removethe glucose residues and one or more of the mannoseresidues from the protein-bound oligosaccharide. Theremaining core structure is again extended by glycosyltransferases in the Golgi apparatus.

mRNA

to GolgiProtein

translocator

ER membraneER lumen

SRPreceptor

SRP

5′+ +

Cytoplasm

Signalpeptidase

3′

Figure 8.1 Synthesis of a secreted protein by ribosomes on the rough endoplasmic reticulum (ER). The ribosome forms a tight

seal on the translocator during translocation, to prevent other molecules from diffusing in and out of the ER while the

polypeptide is threaded through the pore. mRNA, Messenger RNA; SRP, signal recognition particle.

3′

Transfervesicle Golgi apparatus

Secretoryvesicle

Rough ER

Extracellularspace

5′

Cytoplasm

Figure 8.2 Secretory pathway. The proteins are transported to the cell periphery through the endoplasmic reticulum (ER),

transfer vesicles, Golgi apparatus, and secretory vesicles. Release from the cell is by exocytosis (fusion of the secretory vesicle

membrane with the plasma membrane).

Table 8.1 Use of the Secretory Pathway by Different Cell Types

Cell Secreted Products Reference Chapter

Pancreatic acinar cells Zymogens (enzyme precursors) 19

Pancreatic b-cells Insulin, C-peptide, amylin 16

Fibroblasts Collagen, elastin, glycoproteins, proteoglycans 14

Goblet cells Glycoproteins (“mucins”), proteoglycans 14

Intestinal mucosal cells Chylomicrons 23

Hepatocytes Serum albumin, other plasma proteins, very-low-density lipoprotein 15

119Protein Targeting

The oligosaccharides of glycoproteins range in sizefrom two sugar residues in the simplest O-linked oligo-saccharides to more than 15 in some of the more complexN-linked oligosaccharides. Most are branched, and inmany cases the terminal positions are occupied by theacidic amino sugar N-acetylneuraminic acid (NANA)(see Fig. 8.3).

The carbohydrate content of glycoproteins varies fromless than 10% to greater than 50%. The oligosaccharidesof glycoproteins affect their biological functions, includ-ing maintenance of their higher-order structure, watersolubility, antigenicity, and regulation of the protein’smetabolic fate.

THE ENDOCYTIC PATHWAY BRINGSPROTEINS INTO THE CELL

Besides being able to secrete proteins, cells can ingestproteins and other extracellular materials. Three pro-cesses can be distinguished.

1. Phagocytosis (“cell eating”) (Fig. 8.6) is the uptakeof solid particles into the cell. The particle first bindsto components of the cell surface. The cytoplasmthen flows around the particle by a mechanism thatinvolves the polymerization and depolymerizationof actin microfilaments, forming a phagocytic vacu-ole. The usual fate of the phagocytic vacuole isfusion with lysosomes and digestion of the engulfedparticle by lysosomal enzymes. Unicellular eukary-otes (e.g., amoeba) use phagocytosis for their ownnutrition. In the human body, however, the processis limited to macrophages, neutrophils, and dendriticcells. These professional phagocytes protect the bodyby eating aberrant cells and microbial invaders.

2. Pinocytosis (“cell drinking”) is the nonselectiveuptake of fluid droplets into the cell. Pinocytic vesi-cles contain dissolved substances according to theirconcentrations in the extracellular medium. Secretorycells use pinocytosis to retrieve the membrane mate-rial that is added to the plasma membrane duringexocytosis.

Table 8.2 Posttranslational Processing in the Secretory

Pathway

Type of Processing Examples

Removal of signal

sequence

All proteins of secretory pathway

Disulfide bond formation Most proteins of secretory

pathway

Glycosylation Collagen, other glycoproteins,

proteoglycans

Amino acid modifications Collagen, elastin

Partial proteolytic cleavage Insulin, other peptide and

protein hormones

H2C—OH

H H

OHHO

HN

OH H

H

O

C O

CH3

H2C—OH

HO H

OHH

OH OH

α-D-Galactose(Gal)

α-D-N-Acetylglucosamine(GlcNAc)

H2C—OH

H

OHH

HO

HN

H

H

OH H

H

O

C O

CH3

α-D-N-Acetylgalactosamine(GalNAc)

H

H H

OHHO

H

H

OH

HO

O

CH3

β-L-Fucose(Fuc)

H

H2C—OH

HC—OH

HC—OH

H3C—C— COO–

OHH

HN

HOH

H H

O

N-Acetylneuraminic acid(NANA)

H

OH H H

O

H2C—OH

HO

H

OH

H

α-D-Glucose(Glc)

H

OH

HH

O

H2C—OH

H H

OHHO

H

HO

α-D-Mannose(Man)

H

OH

H

O

O

Figure 8.3 Structures of some monosaccharides in glycoproteins.

120 GENETIC INFORMATION: DNA, RNA, AND PROTEIN SYNTHESIS

CH2

OHOH

O

O–

O

O–

O

OHOH

O

O–

O

O–

O

CH2OH

HO

HN

OH

O

OHOH

O

O–

O

O–

O

C O

CH3

O OP P

CH2O OP P

CH2O OP P

CH2OH

HO

HN

O

O

C O

CH3

CH2OH

HO

OH

OH

OO CHCH2

CH

CH2OH

HO

OH

UDP-glucoseA

OH

O

UDP

Glucose

Uracil

CH2OH

HO

HN

UDP-N-acetylgalactosamine Serine residue

B

OH

O

Uracil

O C

CH2OH

HO

OH

GDP-mannose

OH

O

GDP

Mannose

Guanine

C O

CH3

NH

O C

NH

+

O C

NH

UDP

UDP

UDP-galactose

O

O

O

HO CH2

O CHCH2

Figure 8.4 Synthesis of O-linked oligosaccharides in glycoproteins. A, Examples of activated monosaccharides used in the

synthesis of oligosaccharides. The nucleotide is generally bound to the anomeric carbon (C-1 in the aldohexoses and their

derivatives). B, Two steps in the synthesis of an O-linked oligosaccharide in a glycoprotein. Each reaction requires a specific

glycosyltransferase in the Golgi apparatus. GDP, Guanosine diphosphate; UDP, uridine diphosphate.

Table 8.3 Monosaccharides Commonly Found in Glycoproteins

Monosaccharide Type

Activated

Form Comments

Galactose (Gal) Aldohexose UDP-Gal Common

Glucose (Glc) Aldohexose UDP-Glc Rare in mature glycoproteins

Mannose (Man) Aldohexose GDP-Man Very common in N-linked oligosaccharides

Fucose (Fuc) 6-Deoxyhexose GDP-Fuc Both in O- and N-linked oligosaccharides

N-Acetylglucosamine (GlcNAc) Amino sugar UDP-GlcNAc Linked to asparagine in N-linked

oligosaccharides

N-Acetylgalactosamine

(GalNAc)

Amino sugar UDP-GalNAc Common

N-Acetylneuraminic acid

(NANA)

A sialic acid (acidic sugar

derivative)

CMP-NANA In terminal positions of many O- and N-linked

oligosaccharides

GDP, Guanosine diphosphate; UDP, uridine diphosphate; CMP, cytidine monophosphate.

3. Receptor-mediated endocytosis (Fig. 8.7) is a mecha-nism for the selective uptake of soluble proteins andother high-molecular-weight materials. Unlike pino-cytosis, it requires a cell surface receptor to whichthe endocytosed product binds selectively. Binding

is followed by the clustering of receptor-ligand com-plexes on the cell surface and the formation of anendocytic vesicle.

Pinocytic and endocytic vesicles tend to fuse with eachother and with intracellular vesicles to form larger

Glc—Glc—Glc—Man—Man—Man

Man—GlcNAc—GlcNAc—

ManMan—Man

Man—Man

15–18

–O —P—O—CH2—CH2—CH—CH2—CH2—CH C—CH2—CH2—CH C—CH3

CH3O–

O

CH3 CH3

Cytosol

ER lumenAsn

ER membrane

mRNA

Asn

H3N+

P

P

P

P

H3N+

P — P —Dolichol

A

BDolichol

pyrophosphate

C

Dolicholpyrophosphate

Figure 8.5 Synthesis of N-linked oligosaccharides in glycoproteins. A, Structure of dolichol phosphate. This lipid is used

as a carrier of the core oligosaccharide in the endoplasmic reticulum (ER) membrane. B, Structure of the dolichol-bound

precursor oligosaccharide in N-linked glycosylation. This oligosaccharide is synthesized by the stepwise addition of the

monosaccharides from activated precursors. The second phosphate residue in dolichol pyrophosphate is introduced by

UDP-a-D-N-acetylglucosamine (UDP-GlcNAc) during synthesis of the oligosaccharide. C, Transfer of the precursor

oligosaccharide to an asparagine side chain of the polypeptide. This transfer reaction is cotranslational. Asn, Asparagine; Glc, a-D-

Glucose; Man, a-D-mannose; mRNA,messenger RNA; P, phosphate.

Formation ofpseudopods

Formation ofphagocyticvacuole

Fusion ofphagocyticvacuole withlysosomes

L

Figure 8.6 Phagocytosis is triggered by the binding of a solid particle to a protein in the plasma membrane that functions

as a receptor ( ). Pseudopods are formed that flow around the particle. This requires the reversible depolymerization and

repolymerization of actin microfilaments ( ) under the plasma membrane. The phagocytic vacuole fuses with lysosomes (L),

and the particle is digested by lysosomal enzymes.


structures called endosomes, which become acidified toa pH of 5 to 6. Materials can be transferred from theendosome to the Golgi apparatus. More commonly,however, the endosome fuses with a lysosome to forma secondary lysosome in which the endocytosed mate-rial is digested by lysosomal enzymes. In most but notall cases, the receptor is recycled to the cell surface.

The most important uses of receptor-mediated endo-cytosis are as follows:

1. Uptake of nutritive substances. The uptake of low-density lipoprotein (see Chapter 25) and the iron-transferrin complex (see Chapter 29) are the mostprominent examples.

2. Waste disposal. The uptake of “worn-out” plasma pro-teins and hemoglobin-haptoglobin complexes by hepa-tocytes or macrophages (see Chapter 15) is an example.The endocytosed products are digested by lysosomalenzymes.

3. Mucosal transfer. Single-layered epithelia can endo-cytose a protein on one side and exocytose it onthe opposite side. This process is called transcytosis.The secretion of immunoglobulin A (IgA) acrossmucosal surfaces is an example (see Chapter 15).

Receptor-mediated endocytosis is initiated when thecytoplasmic protein adaptin is recruited to the plasmamembrane by the ligand-bound receptor. The structuralprotein clathrin then binds to the adaptin, pulling themembrane into a coated pit. Within seconds, this struc-ture is pinched off as a coated vesicle that is surroundedby a cagelike structure formed from clathrin (Fig. 8.8).

Other coat proteins and many different adaptor pro-teins are used for other types of vesicular transfer. They

regulate the complex trafficking of vesicles and theircontents in the intersecting secretory and endocyticpathways.

CLINICAL EXAMPLE 8.1: I-Cell Disease

I-cell disease is a rare, recessively inherited disease in

which one of the enzymes for the attachment of

mannose-6-phosphate to prospective lysosomal

enzymes is deficient. As a result, lysosomal enzymes are

not sorted into the lysosomes but are secreted. High levels

of lysosomal enzymes circulate in the blood, and

undegraded lipids and polysaccharides accumulate in

the cells.

The accumulation of these products leads to mental

deterioration, skeletal deformities, and death between 5

and 8 years of age. The disease is named after the

inclusions of polysaccharides and glycolipids that are

seen in the cells of these patients. Protein accumulation

is not an important feature because proteins can be

degraded by the proteasome as well as the lysosome.

LYSOSOMES ARE ORGANELLESOF INTRACELLULAR DIGESTION

Lysosomes are bags that are filled with hydrolyticenzymes, including glycosidases, proteases, phosphatases,and sulfatases. Their job description is the breakdown ofcellular macromolecules, especially of macromoleculesthat are taken up into the cell by phagocytosis, pinocyto-sis, and receptor-mediated endocytosis. The lysosomalenzymes are synthesized at the rough ER and becomeglycosylated in the ER and Golgi apparatus. In the Golgi

Ligandbinds

Patching,formation ofa coated pit Internalization

Formation of anacidified endosome,

receptor-ligand dissociation

H+

Sorting of receptorand ligand into separate vesicles

Receptor returns to the cell surface, endosomefuses with lysosome,ligand is degradedby lysosomal enzymes

Figure 8.7 Receptor-mediated endocytosis is triggered by the binding of a ligand to a receptor in the plasma membrane.

Fusion of the endocytic vesicle with intracellular vesicles creates an acidified endosome.


apparatus they finally acquire a mannose-6-phosphateresidue on some of their N-linked oligosaccharides:

GlycoproteinOHO

O

OH OH

P CH2O

O

O–

–O

Mannose-6-phosphate is a molecular tag that acts like apostal address to route the enzymes to the lysosomes.

Inherited defects of lysosomal enzymes or lysosomalbiogenesis result in lysosomal storage diseases. In mostof these diseases, a single lysosomal enzyme is deficient.The substrate of the missing enzyme accumulates in thecell to a point where it impairs normal cellular func-tion. In some diseases multiple lysosomal enzymes areaffected (see Clinical Example 8.1).

CLINICAL EXAMPLE 8.2: Crohn Disease

Crohn disease is an inflammatory bowel disease that

preferentially affects the terminal ileum. It is fairly

common, with an incidence of about 5 per 100,000

person-years and prevalence between 100 and 150 per

100,000 in many populations. It is a seriously

debilitating chronic condition that is treated with

immune suppression or surgery. Crohn disease has long

been attributed to an aberrant immune response to

components of the normal bacterial flora in the intestine.

Variations in at least a dozen genes have been

associated with risk of Crohn disease. One of the most

consistent associations is with a single-nucleotide

polymorphism (SNP) in the ATG16L1 (autophagy-

related 16-like 1) gene, one of more than 30 genes

involved in autophagy. An A in the ancestral low-risk

allele is replaced by a G in the high-risk allele, replacing

the amino acid threonine with alanine.

Ordinarily, intestinal bacteria that have entered the

cytoplasm of an intestinal mucosal cell are cleared by

macroautophagy. A hypothesized consequence of the

single amino acid substitution in the ATG16L1 protein is

impaired sequestration of at least some kinds of bacteria

in autophagosomes, which allows these bacteria to

survive long enough to trigger an inflammatory response.

CELLULAR PROTEINS AND ORGANELLESARE RECYCLED BY AUTOPHAGY

Lysosomes digest not only materials from outside the cell.They also dispose of worn-out cellular proteins and defec-tive organelles in a process known as autophagy (literally,“self-eating”).

Extracellularspace

Coated vesicle forms

Cytosol

LDLreceptor

Adaptin andclathrin bind,coated pit forms

Adaptin

Clathrin

to lysosomes

LDL binds,

receptors cluster

LDL

Membrane

Figure 8.8 Receptor-mediated endocytosis of low-density lipoprotein (LDL). LDL is the most important source of cholesterol

for most cells.


The most important type ismacroautophagy. It beginswith the formation of a double membrane that enclosesan organelle or a patch of the cytosol. The resulting struc-ture, known as an autophagosome, fuses with a lysosome,and the contents are digested by lysosomal enzymes.

Macroautophagy is used for the disposal of orga-nelles and protein aggregates that are too large to behandled by other mechanisms. It recycles peroxisomesand parts of the ER but is especially important for theremoval of mitochondria. For example, the average life-span of a liver mitochondrion is only 10 days. Macroau-tophagy is thought to contribute to quality control byremoving defective organelles in preference to functionalones, but how the functional status of an organelle isassessed by the system is not known.

Another function of macroautophagy is the disposalof large protein aggregates. Finally, it is a mechanismfor the elimination of bacteria and viruses that haveinvaded the cell (see Clinical Example 8.2).

POORLY FOLDED PROTEINS ARE EITHERREPAIRED OR DESTROYED

Formation of a protein’s higher-order structure is nomean feat. Protein maturation can go awry, leadingto misfolded proteins that are toxic to the cell orform obnoxious aggregates. According to one estimate,about one third of native proteins fail to fold properlyand are degraded before they ever achieve a functionalstate.

Protein folding is assisted by helper proteins calledchaperones, which bind to exposed hydrophobicpatches on partly folded proteins. Repeated bindingand dissociation of the chaperone, which is fueled byATP hydrolysis, prevents aggregation and abnormalfolding and gives the protein time to fold into its properconformation.

Chaperones are abundant proteins in the cell, andtheir synthesis is further stimulated when the cell isexposed to elevated temperature. Therefore these cha-perones are also called heat shock proteins. HSP70(heat shock protein-70) is a type of chaperone that isconcerned mainly with the education of young proteinsthat have just been synthesized or are still in the processof ribosomal synthesis. The HSP60 chaperones are adifferent type that specializes in the reconditioning ofaging proteins.

If the efforts of the chaperones are to no avail, themisfolded protein is marked for destruction by ubiqui-tin, a small protein with 76 amino acids that, as its nameimplies, is ubiquitous in all eukaryotic cells (Fig. 8.9).First, a ubiquitin-conjugating enzyme (E1) activatesubiquitin and transfers it to the E2 component of a ubi-quitin ligase (E2-E3 complex).

The E3 component of the ubiquitin ligase recognizesthe target protein and transfers the ubiquitin from E2 tothe target protein. This process is repeated until a chainof four or more ubiquitins is attached to the target pro-tein, which makes it eligible for degradation by theproteasome.

Humans have about 30 different E2 subunits andhundreds of E3 subunits. Each ubiquitin ligase targets adifferent kind of structurally aberrant protein. Some rec-ognize the presence of oxidized amino acids in the pro-tein, others recognize abnormal hydrophobic patches onthe surface of partially denatured proteins, and still othersrecognize sequence motifs that are normally buried in thecenter of the protein but become exposed in misfoldedproteins.

Some ubiquitin ligases recognize intact proteins thatare naturally short lived in the cell, and some evenrespond to regulatory signals. This means that thecell can regulate the lifespans of distinct classes ofproteins.

Ubiquitin binds toubiquitin ligase

Target proteinbinds

SH

Targetprotein

E2/E3 E1

S

E2/E3

C

O

S C

O

Ubiquitin transferredto target protein

E2/E3

SH

E2/E3

Additional ubiquitins added

Figure 8.9 Ubiquitination of

proteins. The multiubiquitin

chain attached by ubiquitin

ligase (E2/E3 complex) directs

the target protein to the

proteasome.


CLINICAL EXAMPLE 8.3: Proteasome Inhibitorsas Anticancer Drugs

Drugs that inhibit the proteasome are highly toxic, but,

like many other poisons, they can be useful in some

situations. One such drug is Bortezomib:

Bortezomib

N

N

OHO

O

NH

HN

OH

B

This boron-containing tripeptide analog inhibits the

proteasome by binding with high affinity to its proteolytic

sites. It was found to be effective in the treatment

of multiple myeloma, an incurable malignancy of

antibody-secreting plasma cells. The reason for its

somewhat selective toxicity to cancer cells is not fully

known. Its effectiveness is attributed to the accumulation

of misfolded immunoglobulin chains in the cancer cells

and to the accumulation of proteins that promote

programmed cell death (apoptosis).

THE PROTEASOME DEGRADES UBIQUITINATEDPROTEINS

Whereas the ubiquitin ligases are the judges that con-demn a protein to death, the proteasome is the

executioner. The proteasome is a hollow cylinder whoseinner surface is lined with proteases, covered with alarge cap on both sides (Fig. 8.10). The cap capturesubiquitinated proteins, denatures them with the helpof ATP hydrolysis, and feeds them into the hollow cyl-inder for degradation.

Proteasomes are abundant in both the cytoplasm andthe nucleus, and they constitute about 1% of the totalcellular protein. The ER contains no proteasomes.However, misfolded and damaged proteins can be ret-rotranslocated from the ER lumen to the cytoplasm,where they are degraded by the ubiquitin-proteasomesystem.

SUMMARY

Peptide bond formation by the ribosome is only thefirst step in protein synthesis. The newly synthesizedproteins have to fold themselves into their properhigher-order structure during translation. This is fol-lowed by posttranslational modifications such asdisulfide bond formation and glycosylation.

Secreted proteins and proteins of the ER, Golgiapparatus, plasma membrane, and lysosomes havea signal sequence at their amino end that directsthem to the rough ER. Their posttranslational pro-cessing takes place mainly in the ER and Golgiapparatus.

Cellular proteins are marked for destruction by theattachment of the small protein ubiquitin. The ubi-quitinated proteins are then fed into the proteasome.This mechanism preferentially removes abnormalproteins and those that are naturally short lived inthe cell.

Protein gets fedinto the central

cylinder

Ubiquitinatedprotein binds

“Mouth” of theproteasome

“Gut” of theproteasome

Figure 8.10 Proteasome. The cover on the hollow cylinder recognizes ubiquitinated proteins, denatures them, and feeds

them into the central cavity, where they are degraded by proteases.


QUESTIONS

1. A signal sequence has to be expected in theprecursors of all the following proteins except

A. Ribosomal proteinsB. The sodium-potassium ATPase in the plasma

membraneC. Collagen in the extracellular matrix of connective

tissuesD. Signal peptidaseE. Acid maltase, a lysosomal hydrolase

2. The deficiency of a ubiquitin ligase canpotentially result in

A. Abnormal accumulation of ubiquitin in the cellB. Failure to direct lysosomal proteins to the

lysosomesC. Excessive breakdown of some classes of proteinsD.Buildup of abnormal proteins in the cellsE. Increased mutation rate

Further Reading

Budarf ML, Labbe C, David G, et al: GWA studies: rewritingthe story of IBD, Trends Genet 25:137–146, 2009.

Chang Y-Y, Juhasz G, Goraksha-Hicks P, et al: Nutrient-dependent regulation of autophagy through the targetof rapamycin pathway, Biochem Soc Trans 37:232–236,2009.

Collard F: The therapeutic potential of deubiquitinatingenzyme inhibitors, Biochem Soc Trans 38:137–143, 2010.

Doherty GJ, McMahon HT: Mechanisms of endocytosis,Annu Rev Biochem 78:857–902, 2009.

Hatakeyama S, Nakayama KI: Ubiquitylation as a quality con-trol system for intracellular proteins, J Biochem 134:1–8,2003.

Mizushima N, Klionsky DJ: Protein turnover via autophagy:implications for metabolism, Annu Rev Nutr 27:19–40,2007.

Navon A, Ciechanover A: The 26 S proteasome: frombasic mechanisms to drug targeting, J Biol Chem 284:33713–33718, 2009.

Rapoport TA: Protein translocation across the eukaryoticendoplasmic reticulum and bacterial plasma membranes,Nature 450:663–669, 2007.

Rappoport JZ: Focusing on clathrin-mediated endocytosis,Biochem J 412:415–423, 2008.

Stipanuk MH: Macroautophagy and its role in nutrienthomeostasis, Nutr Rev 67:677–689, 2009.

Turk B, Turk V: Lysosomes as “suicide bags” in cell death:myth or reality? J Biol Chem 284:21783–21787, 2009.

Van Wijk SJL, Timmers HTM: The family of ubiquitin-conjugating enzymes (E2s): deciding between life and deathof proteins, FASEB J 24:981–993, 2010.

Wandinger SK, Richter K, Buchner J: The Hsp90 chaperonemachinery, J Biol Chem 283:18473–18477, 2008.


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