Download Protein Synthesis, Processing, and Regulation

Protein Synthesis, Processing, and Regulation
Transcription and RNA processing are followed by translation, the synthesis of proteins as directed by mRNA templates.
Proteins are the active players in most cell processes, implementing the myriad tasks that are directed by the information
encoded in genomic DNA. Protein synthesis is thus the final stage of gene expression. However, the translation of mRNA
is only the first step in the formation of a functional protein. The polypeptide chain must then fold into the appropriate
three-dimensional conformation and, frequently, undergo various processing steps before being converted to its active
form. These processing steps, particularly in eukaryotes, are intimately related to the sorting and transport of different
proteins to their appropriate destinations within the cell.
Although the expression of most genes is regulated primarily at the level of transcription, gene expression can also be
controlled at the level of translation, and this control is an important element of gene regulation in both prokaryotic and
eukaryotic cells. Of even broader significance, however, are the mechanisms that control the activities of proteins within
cells. Once synthesized, most proteins can be regulated in response to extracellular signals by either covalent
modifications or by association with other molecules. In addition, the levels of proteins within cells can be controlled by
differential rates of protein degradation. These multiple controls of both the amounts and activities of intracellular
proteins ultimately regulate all aspects of cell behavior.
Translation of mRNA
Proteins are synthesized from mRNA templates by a process that has been highly conserved throughout evolution. All
mRNAs are read in the 5´ to 3´ direction, and polypeptide chains are synthesized from the amino to the carboxy terminus.
Each amino acid is specified by three bases (a codon) in the mRNA, according to a nearly universal genetic code. The
basic mechanics of protein synthesis are also the same in all cells: Translation is carried out on ribosomes, with tRNAs
serving as adaptors between the mRNA template and the amino acids being incorporated into protein. Protein synthesis
thus involves interactions between three types of RNA molecules (mRNA templates, tRNAs, and rRNAs), as well as
various proteins that are required for translation.
Transfer RNAs
During translation, each of the 20 amino acids must be aligned with their corresponding codons on the mRNA template.
All cells contain a variety of tRNAs that serve as adaptors for this process. As might be expected, given their common
function in protein synthesis, different tRNAs share similar overall
structures. However, they also possess unique identifying sequences
that allow the correct amino acid to be attached and aligned with the
appropriate codon in mRNA.
Transfer RNAs are approximately 70 to 80 nucleotides long and
have characteristic cloverleaf structures that result from
complementary base pairing between different regions of the
molecule (Figure 7.1).
Figure 7.1. Structure of tRNAs The structure of
yeast phenylalanyl tRNA is illustrated in open
"cloverleaf" form (A) to show complementary base pairing. Modified bases are indicated as mG, methylguanosine;
mC, methylcytosine; DHU, dihydrouridine; T, ribothymidine; Y, a modified purine (usually adenosine); and ,
pseudouridine. The folded form of the molecule is shown in (B)
X-ray crystallography studies have further shown that all tRNAs fold into similar compact L
shapes, which are likely required for the tRNAs to fit onto ribosomes during the translation
process. The adaptor function of the tRNAs involves two separated regions of the molecule. All
tRNAs have the sequence CCA at their 3´ terminus, and amino acids are covalently attached to
the ribose of the terminal adenosine. The mRNA template is then recognized by the anticodon
loop, located at the other end of the folded tRNA, which binds to the appropriate codon by
complementary base pairing. The incorporation of the correctly encoded amino acids into proteins
depends on the attachment of each amino acid to an appropriate tRNA, as well as on the
specificity of codon-anticodon base pairing. The attachment of amino acids to specific tRNAs is
mediated by a group of enzymes called aminoacyl tRNA synthetases, which were discovered by
Paul Zamecnik and Mahlon Hoagland in 1957. Each of these enzymes recognizes a single amino
acid, as well as the correct tRNA (or tRNAs) to which that amino acid should be attached. The
reaction proceeds in two steps (Figure 7.2).
Figure 7.2. Attachment of amino acids to tRNAs In the first reaction step, the amino acid is joined to AMP, forming an aminoacyl AMP
intermediate. In the second step, the amino acid is transferred to the 3´ CCA terminus of the acceptor tRNA and AMP is released. Both steps
of the reaction are catalyzed by aminoacyl tRNA synthetases.
First, the amino acid is activated by reaction with ATP to form an
aminoacyl AMP synthetase intermediate. The activated amino acid
is then joined to the 3´ terminus of the tRNA. The aminoacyl tRNA
synthetases must be highly selective enzymes that recognize both
individual amino acids and specific base sequences that identify the
correct acceptor tRNAs. In some cases, the high fidelity of amino
acid recognition results in part from a proofreading function by
which incorrect aminoacyl AMPs are hydrolyzed rather than being
joined to tRNA during the second step of the reaction. Recognition
of the correct tRNA by the aminoacyl tRNA synthetase is also
highly selective; the synthetase recognizes specific nucleotide
sequences (in most cases including the anticodon) that uniquely
identify each species of tRNA.
After being attached to tRNA, an amino acid is aligned on the
mRNA template by complementary base pairing between the mRNA
codon and the anticodon of the tRNA. Codon-anticodon base pairing
is somewhat less stringent than the standard A-U and G-C base
pairing discussed in preceding chapters. The significance of this
unusual base pairing in codon-anticodon recognition relates to the
redundancy of the genetic code. Of the 64 possible codons, three are
stop codons that signal the termination of translation; the other 61
encode amino acids .Thus, most of the amino acids are specified by
more than one codon. In part, this redundancy results from the
attachment of many amino acids to more than one species of tRNA.
E. coli, for example, contain about 40 different tRNAs that serve as
acceptors for the 20 different amino acids. In addition, some tRNAs
are able to recognize more than one codon in mRNA, as a result of
nonstandard base pairing (called wobble) between the tRNA
anticodon and the third position of some complementary codons
(Figure 7.3).
Figure 7.3. Nonstandard codon-anticodon base pairing Base pairing at the third codon
position is relaxed, allowing G to pair with U, and inosine (I) in the anticodon to pair with
U, C, or A. Two examples of abnormal base pairing, allowing phenylalanyl (Phe) tRNA to
recognize either UUC or UUU codons and alanyl (Ala) tRNA to recognize GCU, GCC, or
GCA, are illustrated
Relaxed base pairing at this position results partly from the formation of G-U base pairs and partly from the modification
of guanosine to inosine in the anticodons of several tRNAs during processing. Inosine can base-pair with either C, U, or
A in the third position, so its inclusion in the anticodon allows a single tRNA to recognize three different codons in
mRNA templates.
The Ribosome
Ribosomes are the sites of protein synthesis in both prokaryotic and eukaryotic cells. First characterized as particles
detected by ultracentrifugation of cell lysates, ribosomes are usually designated according to their rates of sedimentation:
70S for bacterial ribosomes and 80S for the somewhat larger ribosomes of eukaryotic cells. Both prokaryotic and
eukaryotic ribosomes are composed of two distinct subunits, each containing characteristic proteins and rRNAs. The fact
that cells typically contain many ribosomes reflects the central importance of protein synthesis in cell metabolism. E. coli,
for example, contain about 20,000 ribosomes, which account for approximately 25% of the dry weight of the cell, and
rapidly growing mammalian cells contain about 10 million ribosomes.
The general structures of prokaryotic and eukaryotic ribosomes are similar, although they differ in some details (Figure
7.4). The small subunit (designated 30S) of E. coli ribosomes consists of the 16S rRNA and 21 proteins; the large subunit
(50S) is composed of the 23S and 5S rRNAs and 34 proteins. Each ribosome contains one copy of the rRNAs and one
copy of each of the ribosomal proteins, with one exception: One protein of the 50S subunit is present in four copies. The
subunits of eukaryotic ribosomes are larger and contain more proteins than their prokaryotic counterparts have. The small
subunit (40S) of eukaryotic ribosomes is composed of the 18S rRNA and approximately 30 proteins; the large subunit
(60S) contains the 28S, 5.8S, and 5S rRNAs and about 45 proteins.
A noteworthy feature of ribosomes is that they can be formed in vitro by self-assembly of their RNA and protein
constituents. As first described in 1968 by Masayasu Nomura, purified ribosomal proteins and rRNAs can be mixed
together and, under appropriate conditions, will reform a functional ribosome. Although ribosome assembly in vivo
(particularly in eukaryotic cells) is considerably more complicated, the ability of ribosomes to self-assemble in vitro has
provided an important experimental tool, allowing analysis of the roles of individual proteins and rRNAs.
Like tRNAs, rRNAs form characteristic secondary structures by complementary base pairing. In association with
ribosomal proteins the rRNAs fold further, into distinct three-dimensional structures. Initially, rRNAs were thought to
play a structural role, providing a scaffold upon which ribosomal proteins assemble. However, with the discovery of the
catalytic activity of other RNA molecules (e.g., RNase P and the self-splicing introns), the possible catalytic role of
rRNA became widely considered. Consistent with this hypothesis, rRNAs were found to be absolutely required for the in
vitro assembly of functional ribosomes. On the other hand, the omission of many ribosomal proteins resulted in a
decrease, but not a complete loss, of ribosome activity.
Direct evidence for the catalytic activity of rRNA first came from experiments of Harry Noller and his colleagues in 1992.
These investigators demonstrated that the large ribosomal subunit is able to catalyze the formation of peptide bonds (the
peptidyl transferase reaction) even after approximately 95% of the ribosomal proteins have been removed by standard
protein extraction procedures. In contrast, treatment with RNase completely abolishes peptide bond formation, providing
strong support for the hypothesis that the formation of a peptide bond is an RNA-catalyzed reaction. Further studies have
confirmed and extended these results by demonstrating that the peptidyl transferase reaction can be catalyzed by synthetic
fragments of 23S rRNA in the total absence of any ribosomal protein. Thus, the fundamental reaction of protein synthesis
is catalyzed by ribosomal RNA. Rather than being the primary catalytic constituents of ribosomes, ribosomal proteins are
now thought to facilitate proper folding of the rRNA and to enhance ribosome function by properly positioning the
tRNAs.
The direct involvement of rRNA in the peptidyl transferase reaction has important evolutionary implications. RNAs are
thought to have been the first self-replicating macromolecules. This notion is strongly supported by the fact that
ribozymes, such as RNase P and self-splicing introns, can catalyze reactions that involve RNA substrates. The role of
rRNA in the formation of peptide bonds extends the catalytic activities of RNA beyond self-replication to direct
involvement in protein synthesis. Additional studies indicate that the Tetrahymena rRNA ribozyme can catalyze the
attachment of amino acids to RNA, lending credence to the possibility that the original aminoacyl tRNA synthetases were
RNAs rather than proteins. The ability of RNA molecules to catalyze the reactions required for protein synthesis as well
as for self-replication may provide an important link for understanding the early evolution of cells.
The Organization of mRNAs and the Initiation of Translation
Although the mechanisms of protein synthesis in prokaryotic
and eukaryotic cells are similar, there are also differences,
particularly in the signals that determine the positions at which
synthesis of a polypeptide chain is initiated on an mRNA
template (Figure 7.6).
Figure 7.6. Prokaryotic and eukaryotic mRNAs Both prokaryotic and
eukaryotic mRNAs contain untranslated regions (UTRs) at their 5´ and 3´
ends. Eukaryotic mRNAs also contain 5´ 7-methylguanosine (m7G) caps
and 3´ poly-A tails. Prokaryotic mRNAs are frequently polycistronic:
They encode multiple proteins, each of which is translated from an
independent start site. Eukaryotic mRNAs are usually monocistronic,
encoding only a single protein.
Translation does not simply begin at the 5´ end of the mRNA; it starts at
specific initiation sites. The 5´ terminal portions of both prokaryotic and
eukaryotic mRNAs are therefore noncoding sequences, referred to as 5´
untranslated regions. Eukaryotic mRNAs usually encode only a single
polypeptide chain, but many prokaryotic mRNAs encode multiple
polypeptides that are synthesized independently from distinct initiation
sites. For example, the E. coli lac operon consists of three genes that are
translated from the same mRNA (see Figure 6.8).
Figure 6.8. Negative control of the lac operon The i gene encodes a repressor which, in the
absence of lactose (top), binds to the operator (o) and blocks transcription of the three
structural genes (z, -galactosidase; y, permease; and a, transacetylase). Lactose induces
expression of the operon by binding to the repressor (bottom), which prevents the repressor
from binding to the operator. P = promoter; Pol = polymerase.
Messenger RNAs that encode multiple polypeptides are called polycistronic, whereas monocistronic mRNAs encode a
single polypeptide chain. Finally, both prokaryotic and eukaryotic mRNAs end in noncoding 3´ untranslated regions.
In both prokaryotic and eukaryotic cells, translation always initiates with the amino acid methionine, usually encoded by
AUG. Alternative initiation codons, such as GUG, are used occasionally in bacteria, but when they occur at the beginning
of a polypeptide chain, these codons direct the incorporation of methionine rather than of the amino acid they normally
encode (GUG normally encodes valine). In most bacteria, protein synthesis is initiated with a modified methionine
residue (N-formylmethionine), whereas unmodified methionines initiate protein synthesis in eukaryotes (except in
mitochondria and chloroplasts, whose ribosomes resemble those of bacteria).
Figure 7.7. Signals for translation initiation Initiation sites in prokaryotic
mRNAs are characterized by a Shine-Delgarno sequence that precedes the AUG
initiation codon. Base pairing between the Shine-Delgarno sequence and a
complementary sequence near the 3´ terminus of 16S rRNA aligns the mRNA on
the ribosome. In contrast, eukaryotic mRNAs are bound to the 40S ribosomal
subunit by their 5´ 7-methylguanosine caps. The ribosome then scans along the
mRNA until it encounters an AUG initiation codon.
The signals that identify initiation codons are different in
prokaryotic and eukaryotic cells, consistent with the distinct
functions of polycistronic and monocistronic mRNAs (Figure
7.7). Initiation codons in bacterial mRNAs are preceded by a
specific sequence (called a Shine-Delgarno sequence, after its
discoverers) that aligns the mRNA on the ribosome for translation by base-pairing with a complementary sequence near
the 3´ terminus of 16S rRNA. This base-pairing interaction enables bacterial ribosomes to initiate translation not only at
the 5´ end of an mRNA but also at the internal initiation sites of polycistronic messages. In contrast, ribosomes recognize
most eukaryotic mRNAs by binding to the 7-methylguanosine cap at their 5´ terminus (see Figure 6.39).
Figure 6.39. Processing of eukaryotic messenger RNAs The
processing of mRNA involves modification of the 5 terminus by
capping with 7-methylguanosine (m7G), modification of the 3
terminus by polyadenylation, and removal of introns by splicing.
The 5 cap is formed by the addition of a GTP in reverse
orientation to the 5 end of the mRNA, forming a 5 -to-5 linkage.
The added G is then methylated at the N-7 position, and methyl
groups are added to the riboses of the first one or two nucleotides
in the mRNA.
The ribosomes then scan downstream of the 5´
cap until they encounter an AUG initiation codon.
Sequences that surround AUGs affect the
efficiency of initiation, so in many cases the first
AUG in the mRNA is bypassed and translation
initiates at an AUG farther downstream. However,
eukaryotic mRNAs have no sequence equivalent to the Shine-Delgarno sequence of prokaryotic mRNAs. Translation of
eukaryotic mRNAs is instead initiated at a site determined by scanning from the 5´ terminus, consistent with their
functions as monocistronic messages that encode only single polypeptides.
The Process of Translation
Figure 7.8. Overview of translation
Translation is generally divided into three
stages: initiation, elongation, and
termination (Figure 7.8). In both
prokaryotes and eukaryotes the first step
of the initiation stage is the binding of a
specific initiator methionyl tRNA and the
mRNA to the small ribosomal subunit.
The large ribosomal subunit then joins the
complex, forming a functional ribosome on which elongation of the polypeptide chain proceeds. A number of specific
nonribosomal proteins are also required for the various stages of the translation process.
The first translation step in bacteria is the binding of three initiation factors
(IF-1, IF-2, and IF-3) to the 30S ribosomal subunit (Figure 7.9).
Figure 7.9. Initiation of translation in bacteria Three initiation factors (IF-1, IF-2, and IF-3) first
bind to the 30S ribosomal subunit. This step is followed by binding of the mRNA and the initiator Nformylmethionyl (fMet) tRNA, which is recognized by IF-2 bound to GTP. IF-3 is then released, and
a 50S subunit binds to the complex, triggering the hydrolysis of bound GTP, followed by the release
of IF-1 and IF-2 bound to GDP.
The mRNA and initiator N-formylmethionyl tRNA then join the complex,
with IF-2 (which is bound to GTP) specifically recognizing the initiator
tRNA. IF-3 is then released, allowing a 50S ribosomal subunit to associate
with the complex. This association triggers the hydrolysis of GTP bound to
IF-2, which leads to the release of IF-1 and IF-2 (bound to GDP). The result
is the formation of a 70S initiation complex (with mRNA and initiator tRNA
bound to the ribosome) that is ready to begin peptide bond formation during
the elongation stage of translation.
Initiation in eukaryotes is more complicated and requires at least ten proteins
(each consisting of multiple polypeptide chains), which are designated eIFs
(eukaryotic initiation factors;). The factors eIF-1, eIF-1A, and eIF-3
bind to the 40S ribosomal subunit, and eIF-2 (in a complex with GTP)
associates with the initiator methionyl tRNA (Figure 7.10).
Figure 7.10. Initiation of translation in eukaryotic cells Initiation factors eIF-3,
eIF-1, and eIF-1A bind to the 40S ribosomal subunit. The initiator methionyl tRNA
is brought to the ribosome by eIF-2 (complexed to GTP), and the mRNA by eIF-4E
(which binds to the 5´ cap), eIF-4G (which binds to both eIF-4E at the 5' cap and
PABP at the 3' poly-A tail), eIF-4A, and eIF-4B. The ribosome then scans down the
mRNA to identify the first AUG initiation codon. Scanning requires energy and is
accompanied by ATP hydrolysis. When the initiating AUG is identified, eIF-5
triggers the hydrolysis of GTP bound to eIF-2, followed by the release of eIF-2
(complexed to GDP) and other initiation factors. The 60S ribosomal subunit then
joins the 40S complex.
The mRNA is recognized and brought to the ribosome by the eIF-4
group of factors. The 5´ cap of the mRNA is
recognized by eIF-4E. Another factor, eIF4G, binds to both eIF-4E and to a protein
(poly-A binding protein or PABP)
associated with the poly-A tail at the 3' end
of the mRNA. Eukaryotic initiation factors
thus recognize both the 5' and 3' ends of
mRNAs, accounting for the stimulatory
effect of polyadenylation on translation. The initiation factors eIF-4E and eIF-4G, in
association with eIF-4A and eIF-4B, then bring the mRNA to the 40S ribosomal subunit, with
eIF-4G interacting with eIF-3. The 40S ribosomal subunit, in association with the bound
methionyl tRNA and eIFs, then scans the mRNA to identify the AUG initiation codon. When
the AUG codon is reached, eIF-5 triggers the hydrolysis of GTP bound to eIF-2. Initiation
factors (including eIF-2 bound to GDP) are then released, and a 60S subunit binds to the 40S
subunit to form the 80S initiation complex of eukaryotic cells.
After the initiation complex has formed, translation proceeds by elongation of the polypeptide
chain. The mechanism of elongation in prokaryotic and eukaryotic cells is very similar
(Figure 7.11).
Figure 7.11. Elongation stage of translation The ribosome has three tRNA-binding sites, designated P (peptidyl), A
(aminoacyl), and E (exit). The initiating N-formylmethionyl tRNA is positioned in the P site, leaving an empty A site. The
second aminoacyl tRNA (e.g., alanyl tRNA) is then brought to the A site by EF-Tu (complexed with GTP). Following
GTP hydrolysis, EF-Tu (complexed with GDP) leaves the ribosome, with alanyl tRNA inserted into the A site. A peptide
bond is then formed, resulting in the transfer of methionine to the aminoacyl tRNA at the A site. The ribosome then moves
three nucleotides along the mRNA. This movement translocates the peptidyl (Met-Ala) tRNA to the P site and the
uncharged tRNA to the E site, leaving an empty A site ready for addition of the next amino acid. Translocation is mediated
by EF-G, coupled to GTP hydrolysis. The process, illustrated here for prokaryotic cells, is very similar in eukaryotes.
The ribosome has three sites for tRNA binding, designated the P (peptidyl), A (aminoacyl), and E (exit) sites. The
initiator methionyl tRNA is bound at the P site. The first step in elongation is the binding of the next aminoacyl tRNA to
the A site by pairing with the second codon of the mRNA. The aminoacyl tRNA is escorted to the ribosome by an
elongation factor (EF-Tu in prokaryotes, eEF-1 in eukaryotes), which is complexed to GTP. The GTP is hydrolyzed to
GDP as the correct aminoacyl tRNA is inserted into the A site of the ribosome and the elongation factor bound to GDP is
released. The requirement for hydrolysis of GTP before EF-Tu or eEF-1 is released from the ribosome is the ratelimiting step in elongation and provides a time interval during which an incorrect aminoacyl tRNA, which would bind
less strongly to the mRNA codon, can dissociate from the ribosome rather than being used for protein synthesis. Thus, the
expenditure of a high-energy GTP at this step is an important contribution to accurate protein synthesis; it allows time for
proofreading of the codon-anticodon pairing before the peptide bond forms.
Once EF-Tu (or eEF-1) has left the ribosome, a peptide bond can be formed between the initiator methionyl tRNA at
the P site and the second aminoacyl tRNA at the A site. This reaction is catalyzed by the large ribosomal subunit, with the
rRNA playing a critical role (as already discussed). The result is the transfer of methionine to the aminoacyl tRNA at the
A site of the ribosome, forming a peptidyl tRNA at this position and leaving the uncharged initiator tRNA at the P site.
The next step in elongation is translocation, which requires another elongation factor (EF-G in prokaryotes, eEF-2 in
eukaryotes) and is again coupled to GTP hydrolysis. During translocation, the ribosome moves three nucleotides along
the mRNA, positioning the next codon in an empty A site. This step translocates the peptidyl tRNA from the A site to the
P site, and the uncharged tRNA from the P site to the E site. The ribosome is then left with a peptidyl tRNA bound at the
P site, and an empty A site. The binding of a new aminoacyl tRNA to the A site then induces the release of the uncharged
tRNA from the E site, leaving the ribosome ready for insertion of the next amino acid in the growing polypeptide chain.
As elongation continues, the EF-Tu (or eEF-1) that is released from
the ribosome bound to GDP must be reconverted to its GTP form
(Figure 7.12).
Figure 7.12. Regeneration of EF-Tu/GTP EF-Tu complexed to GTP escorts the
aminoacyl tRNA to the ribosome. The bound GTP is hydrolyzed as the correct tRNA is
inserted, so EF-Tu complexed to GDP is released. The EF-Tu/GDP complex is inactive and
unable to bind another tRNA. In order for translation to continue, the active EF-Tu/GTP
complex must be regenerated by another factor, EF-Ts, which stimulates the exchange of
the bound GDP for free GTP.
This conversion requires a third elongation
factor, EF-Ts (eEF-1 in eukaryotes),
which binds to the EF-Tu/GDP complex
and promotes the exchange of bound GDP for GTP. This exchange results in the regeneration
of EF-Tu/GTP, which is now ready to escort a new aminoacyl tRNA to the A site of the
ribosome, beginning a new cycle of elongation. The regulation of EF-Tu by GTP binding and
hydrolysis illustrates a common means of the regulation of protein activities. As will be
discussed in later chapters, similar mechanisms control the activities of a wide variety of
proteins involved in the regulation of cell growth and differentiation, as well as in protein
transport and secretion.
Elongation of the polypeptide chain continues until a stop codon (UAA, UAG, or UGA) is
translocated into the A site of the ribosome. Cells do not contain tRNAs with anticodons
complementary to these termination signals; instead, they have release factors that recognize
the signals and terminate protein synthesis (Figure 7.13).
Figure 7.13. Termination of translation A termination codon (e.g., UAA) at the A site is recognized by a
release factor rather than by a tRNA. The result is the release of the completed polypeptide chain, followed by
the dissociation of tRNA and mRNA from the ribosome.
Prokaryotic cells contain two release factors that recognize termination codons: RF-1
recognizes UAA or UAG, and RF-2 recognizes UAA or UGA.In eukaryotic cells a single
release factor (eRF-1) recognizes all three termination codons. Both prokaryotic and
eukaryotic cells also contain release factors (RF-3 and eRF-3, respectively) that do not
recognize specific termination codons but act together with RF-1 (or eRF-1) and RF-2. The
release factors bind to a termination codon at the A site and stimulate hydrolysis of the bond
between the tRNA and the polypeptide chain at the P site, resulting in release of the completed
polypeptide from the ribosome. The tRNA is then released, and the ribosomal subunits and the
mRNA template dissociate.
Messenger RNAs can be translated simultaneously by several ribosomes in both prokaryotic
and eukaryotic cells. Once one ribosome has moved away from the initiation site, another can
bind to the mRNA and begin synthesis of a new polypeptide chain. Thus, mRNAs are usually translated by a series of
ribosomes, spaced at intervals of about 100 to 200 nucleotides (Figure 7.14). The group of ribosomes bound to an mRNA
molecule is called a polyribosome, or polysome. Each ribosome within the group functions independently to synthesize a
separate polypeptide chain.
Figure 7.14. Polysomes Messenger RNAs are translated by a series of multiple
ribosomes (a polysome) Schematic of a generalized poly-some. Note that the ribosomes
closer to the 3´ end of the mRNA have longer polypeptide chains
Regulation of Translation
Although transcription is the primary level at which gene expression is controlled, the translation of mRNAs is also
regulated in both prokaryotic and eukaryotic cells. One mechanism of translational regulation is the binding of repressor
proteins, which block translation, to specific mRNA sequences. The best understood example of this mechanism in
eukaryotic cells is regulation of the synthesis of ferritin, a protein that stores iron within the cell. The translation of
ferritin mRNA is regulated by the supply of iron: More ferritin is
synthesized if iron is abundant (Figure 7.15).
Figure 7.15. Translational regulation of ferritin The mRNA contains an
iron response element (IRE) near its 5´ cap. In the presence of adequate
supplies of iron, translation of the mRNA proceeds normally. If iron is scarce,
however, a protein (called the iron response element binding protein, or
IRE-BP) binds to the IRE, blocking translation of the mRNA
This regulation is mediated by a protein which (in the absence of iron) binds to a sequence (the iron response element, or
IRE) in the 5´ untranslated region of ferritin mRNA, blocking its translation. In the presence of iron, the repressor no
longer binds to the IRE and ferritin translation is able to proceed.
It is interesting to note
that the regulation of
translation of ferritin
mRNA by iron is similar
to the regulation of
transferrin receptor
mRNA stability, which
was discussed in the
previous chapter (see Figure 6.48).
Figure 6.48. Regulation of transferrin receptor mRNA stability The levels of transferrin receptor mRNA are regulated by the availability of iron. If the
supply of iron is adequate, the mRNA is rapidly degraded as a result of nuclease cleavage near the 3 end. If iron is scarce, however, a regulatory protein (called
the iron response element-binding protein, or IRE-BP) binds to a sequence near the 3 end of the mRNA (the iron response element, or IRE), protecting the
mRNA from nuclease cleavage.
Namely, the stability of transferrin receptor mRNA is regulated by protein binding to an IRE in its 3´ untranslated region.
The same protein binds to the IREs of both ferritin and transferrin receptor mRNAs. However, the consequences of
protein binding to the two IREs are quite different. Protein bound to the transferrin receptor IRE protects the mRNA from
degradation rather than inhibiting its translation. These distinct effects presumably result from the different locations of
the IRE in the two mRNAs. To function as a repressor-binding site, the IRE must be located within 70 nucleotides of the
5´ cap of ferritin mRNA, suggesting that protein binding to the IRE blocks translation by interfering with cap recognition
and binding of the 40S ribosomal subunit. Rather than inhibiting translation, protein binding to the same sequence in the
3´ untranslated region of transferrin receptor mRNA protects the mRNA from nuclease degradation. Binding of the same
regulatory protein to different sites on mRNA molecules can thus have distinct effects on gene expression, in one case
inhibiting translation and in the other stabilizing the mRNA to increase protein synthesis.
Another mechanism of translational regulation in eukaryotic cells, resulting in global effects on overall translational
activity rather than on the translation of specific mRNAs, involves modulation of the activity of initiation factors,
particularly eIF-2. As already discussed, eIF-2 (complexed with GTP) binds to the initiator methionyl tRNA, bringing it
to the ribosome. The subsequent release of eIF-2 is accompanied by GTP hydrolysis, leaving eIF-2 as an inactive GDP
complex. To participate in another cycle of initiation, the eIF-2/GTP complex must be regenerated by the exchange of
bound GDP for GTP. This exchange is mediated by another factor, eIF-2B. The control of eIF-2 activity by GTP binding
and hydrolysis is thus similar to that of EF-Tu (see Figure 7.12). However, the regulation of eIF-2 provides a critical
control point in a variety of eukaryotic cells. In particular, eIF-2 can be phosphorylated by regulatory protein kinases.
This phosphorylation blocks the exchange of bound GDP for GTP, thereby inhibiting initiation of translation. One type of
cell in which such phosphorylation occurs is the reticulocyte,
which is devoted to the synthesis of hemoglobin (Figure 7.16).
Figure 7.16. Regulation of translation by phosphorylation of eIF-2 Translation in
reticulocytes (which is devoted to synthesis of hemoglobin) is controlled by the supply
of heme, which regulates the activity of eIF-2. The active form of eIF-2 (complexed
with GTP) escorts initiator methionyl tRNA to the ribosome (see Figure 7.10). The eIF2 is then released from the ribosome in an inactive GDP-bound form, which must be
reactivated by exchange of GTP for the bound GDP. If adequate heme is available, this
exchange occurs and translation is able to proceed. If heme supplies are inadequate,
however, a protein kinase that phosphorylates eIF-2 is activated. Phosphorylation of
eIF-2 blocks the exchange of GTP for GDP, so eIF-2/GTP cannot be regenerated and
translation is inhibited.
The translation of globin mRNA is controlled by the availability of
heme: The mRNA is translated only if adequate heme is available
to form functional hemoglobin molecules. In the absence of heme,
a protein kinase that phosphorylates eIF-2 is activated, and further
translation is inhibited. Similar mechanisms have been found to
control protein synthesis in other cell types, particularly virusinfected cells in which viral protein synthesis is inhibited by
interferon.
Other studies have implicated eIF-4E, which binds to the 5´ cap of
mRNAs, as a translational regulatory protein. For example, the
hormone insulin stimulates protein synthesis in adipocytes and muscle cells. This effect of insulin is mediated, at least in
part, by phosphorylation of proteins associated with eIF-4E, resulting in stimulation of eIF-4E activity and increased rates
of translational initiation.
Translational regulation is particularly important during early development. As discussed in Chapter 6, a variety of
mRNAs are stored in oocytes in an untranslated form; the translation of these stored mRNAs is activated at fertilization
or later stages of development. One mechanism of such translational regulation is the controlled polyadenylation of
oocyte mRNAs. Many untranslated mRNAs are stored in oocytes with short poly-A tails (approximately 20 nucleotides).
These stored mRNAs are subsequently recruited for translation at the appropriate stage of development by the
lengthening of their poly-A tails to several hundred nucleotides. In addition, the translation of some mRNAs during
development appears to be regulated by repressor proteins that bind to specific sequences in their 3´ untranslated regions.
These regulatory proteins may also direct mRNAs to specific regions of eggs or embryos, allowing localized synthesis of
the encoded proteins during embryonic development.
Protein Folding and Processing
Translation completes the flow of genetic information within the cell. The sequence of nucleotides in DNA has now been
converted to the sequence of amino acids in a polypeptide chain. The synthesis of a polypeptide, however, is not
equivalent to the production of a functional protein. To be useful, polypeptides must fold into distinct three-dimensional
conformations, and in many cases multiple polypeptide chains must assemble into a functional complex. In addition,
many proteins undergo further modifications, including cleavage and the covalent attachment of carbohydrates and lipids,
that are critical for the function and correct localization of proteins within the cell.
Chaperones and Protein Folding
The three-dimensional conformations of
proteins result from interactions between
the side chains of their constituent amino
acids. The classic principle of protein
folding is that all the information required
for a protein to adopt the correct threedimensional conformation is provided by
its amino acid sequence. This was initially
established by Christian Anfinsen's
experiments demonstrating that denatured
RNase can spontaneously refold in vitro to its active conformation (see Figure 2.17).
Figure 2.17. Protein denaturation and refolding Ribonuclease (RNase) is a protein of 124 amino acids (indicated by numbers). The protein is normally
folded into its native conformation, which contains four disulfide bonds (indicated as paired circles representing the cysteine residues).
Protein folding thus appeared to be a self-assembly process that did not require additional cellular factors. More recent
studies, however, have shown that this is not an adequate description of protein folding within the cell. The proper
folding of proteins within cells is mediated by the activities of other proteins.
Proteins that facilitate the folding of other proteins are called molecular chaperones. The term "chaperone" was first used
by Ron Laskey and his colleagues to describe a protein (nucleoplasmin) that is required for the assembly of nucleosomes
from histones and DNA. Nucleoplasmin binds to histones and mediates their assembly into nucleosomes, but
nucleoplasmin itself is not incorporated into the final nucleosome structure. Chaperones thus act as catalysts that facilitate
assembly without being part of the assembled complex. Subsequent studies have extended the concept to include proteins
that mediate a variety of other assembly processes, particularly protein folding.
It is important to note that chaperones do not convey additional information required for the folding of polypeptides into
their correct three-dimensional conformations; the folded conformation of a protein is determined solely by its amino acid
sequence. Rather, chaperones catalyze protein folding by assisting the self-assembly process. They appear to function by
binding to and stabilizing unfolded or partially folded polypeptides that are intermediates along the pathway leading to
the final correctly folded state. In the absence of chaperones, unfolded or partially folded polypeptide chains would be
unstable within the cell, frequently folding incorrectly or aggregating into insoluble complexes. The binding of
chaperones stabilizes these unfolded polypeptides, thereby preventing incorrect folding or aggregation and allowing the
polypeptide chain to fold into its correct conformation.
A good example is provided by chaperones that bind to
nascent polypeptide chains that are still being translated
on ribosomes, thereby preventing incorrect folding or
aggregation of the amino-terminal portion of the
polypeptide before synthesis of the chain is finished
(Figure 7.17).
Figure 7.17. Action of chaperones during translation Chaperones bind
to the amino (N) terminus of the growing polypeptide chain, stabilizing it
in an unfolded configuration until synthesis of the polypeptide is completed.
The completed protein is then released from the ribosome and is able to
fold into its correct three-dimensional conformation.
Presumably, this interaction is particularly important for proteins in which the carboxy terminus (the last to be
synthesized) is required for correct folding of the amino terminus. In such cases, chaperone binding stabilizes the aminoterminal portion in an unfolded conformation until the rest of the polypeptide chain is synthesized and the completed
protein can fold correctly. Chaperones also stabilize unfolded
polypeptide chains during their transport into subcellular
organelles for example, during the transfer of proteins into
mitochondria from the cytosol (Figure 7.18).
Figure 7.18. Action of chaperones during protein transport A partially
unfolded polypeptide is transported from the cytosol to a mitochondrion.
Cytosolic chaperones stabilize the unfolded configuration. Mitochondrial
chaperones facilitate transport and subsequent folding of the polypeptide
chain within the organelle.
Proteins are transported across the mitochondrial membrane in
partially unfolded conformations that are stabilized by chaperones
in the cytosol. Chaperones within the mitochondrion then
facilitate transfer of the polypeptide chain across the membrane
and its subsequent folding within the organelle. In addition,
chaperones are involved in the assembly of proteins that consist of multiple polypeptide chains, in the assembly of
macromolecular structures (e.g., nucleoplasmin), and (as discussed later in this chapter) in the regulation of protein
degradation.
Many of the proteins now known to function as molecular chaperones were initially identified as heat-shock proteins, a
group of proteins expressed in cells that have been subjected to elevated temperatures or other forms of environmental
stress. The heat-shock proteins (abbreviated Hsp), which are highly conserved in both prokaryotic and eukaryotic cells,
are thought to stabilize and facilitate the refolding of proteins that have been partially denatured as a result of exposure to
elevated temperature. However, many members of the heat-shock protein family are expressed and have essential cellular
functions under normal growth conditions. These proteins serve as molecular chaperones, which are needed for
polypeptide folding and transport under normal conditions as well as in cells subjected to environmental stress.
The Hsp70 and Hsp60 families of heat-shock proteins appear to be particularly important in the general pathways of
protein folding in both prokaryotic and eukaryotic cells. The proteins of both families function by binding to unfolded
regions of polypeptide chains. Members of the Hsp70 family stabilize unfolded polypeptide chains during translation (see,
for example, Figure 7.17) as well as during the transport of polypeptides into a variety of subcellular compartments, such
as mitochondria and the endoplasmic reticulum. These proteins bind to short segments (seven or eight amino acid
residues) of unfolded polypeptides, maintaining the polypeptide chain in an unfolded configuration and preventing
aggregation.
Members of the Hsp60 family (also called chaperonins) facilitate the folding of proteins into their native conformations.
Each chaperonin consists of 14 subunits of approximately 60 kilodaltons (kd) each, arranged in two stacked rings to form
a "double doughnut" structure. Unfolded polypeptide chains are shielded from the cytosol by being bound within the
central cavity of the chaperonin cylinder. In this isolated environment protein folding can proceed while aggregation of
unfolded segments of the polypeptide chain is prevented by their binding to the chaperonin. The binding of unfolded
polypeptides to the chaperonin is a reversible reaction that is coupled to the hydrolysis of ATP as a source of energy.
ATP hydrolysis thus drives multiple rounds of release and rebinding of unfolded regions of the polypeptide chain to the
chaperonin, allowing the polypeptide to fold gradually into the correct conformation.
In some cases, members of the Hsp70 and Hsp60 families have been found to act together in a sequential fashion. For
example, Hsp70 and Hsp60 family members act sequentially during the transport of proteins into mitochondria and
during the folding of newly
synthesized proteins in E. coli
(Figure 7.20).
Figure 7.20. Sequential actions of Hsp70 and
Hsp60 chaperones Chaperones of the Hsp70
family bind to and stabilize unfolded
polypeptide chains during translation. The
unfolded polypeptide is then transferred to
chaperones of the Hsp60 family, within which
protein folding takes place. ATP hydrolysis is
required for release of the unfolded
polypeptide from Hsp70 as well as for folding
within Hsp60.
First, an Hsp70 chaperone stabilizes nascent polypeptide chains until protein synthesis is completed. The unfolded
polypeptide chain is then transferred to an Hsp60 chaperonin, within which protein folding takes place, yielding a protein
correctly folded into its functional three-dimensional conformation. Members of the Hsp70 and Hsp60 families are found
in the cytosol and in subcellular organelles (e.g., mitochondria) of eukaryotic cells, as well as in bacteria, so the
sequential action of Hsp70 and Hsp60 appears to represent a general pathway of protein folding. An alternative pathway
for the folding of some proteins in the cytosol and endoplasmic reticulum may involve the sequential actions of Hsp70
and Hsp90 family members, although the function of Hsp90 is not yet well understood.
Enzymes and Protein Folding
In addition to chaperones, which facilitate protein folding by binding to and stabilizing partially folded intermediates,
cells contain at least two types of enzymes that catalyze
protein folding by breaking and re-forming covalent
bonds. The formation of disulfide bonds between
cysteine residues is important in stabilizing the folded
structures of many proteins (see Figure 2.16).
Figure 2.16. Amino acid sequence of insulin Insulin consists of two
polypeptide chains, one of 21 and the other of 30 amino acids (indicated
here by their one-letter codes). The side chains of three pairs of cysteine
residues are joined by disulfide bonds, two of which connect the
polypeptide chains
Protein disulfide isomerase, which was
discovered by Christian Anfinsen in 1963,
catalyzes the breakage and re-formation of
these bonds (Figure 7.21).
Figure 7.21. The action of protein disulfide
isomerase Protein disulfide isomerase (PDI) catalyzes
the breakage and rejoining of disulfide bonds, resulting in exchanges between paired disulfides in a polypeptide chain. The enzyme forms a disulfide bond with
a cysteine residue of the polypeptide and then exchanges its paired disulfide with another cysteine residue. In this example, PDI catalyzes the conversion of two
incorrect disulfide bonds (1-2 and 3-4) to the correct pairing (1-3 and 2-4).
For proteins that contain multiple cysteine residues, protein disulfide isomerase (PDI) plays an important role by
promoting rapid exchanges between paired disulfides, thereby allowing the protein to attain the pattern of disulfide bonds
that is compatible with its stably folded conformation. Disulfide bonds are generally restricted to secreted proteins and
some membrane proteins because the cytosol contains reducing agents that maintain cysteine residues in their reduced
( SH form), thereby preventing the formation of disulfide (S S) linkages. In eukaryotic cells, disulfide bonds form in
the endoplasmic reticulum, in which an oxidizing environment is maintained. Consistent with the role of disulfide bonds
in stabilizing secreted proteins, the activity of PDI in the endoplasmic reticulum is correlated with the level of protein
secretion in different types of cells.
Figure 7.22. The action of peptidyl prolyl isomerase Peptidyl prolyl isomerase catalyzes the isomerization of
peptide bonds that involve proline between the cis and trans conformations.
The second enzyme that plays a role in protein folding catalyzes the isomerization of
peptide bonds that involve proline residues (Figure 7.22). Proline is an unusual
amino acid in that the equilibrium between the cis and trans conformations of peptide bonds that precede proline residues
is only slightly in favor of the trans form. In contrast, peptide bonds between other amino acids are almost always in the
trans form. Isomerization between the cis and trans configurations of prolyl peptide bonds, which could otherwise
represent a rate-limiting step in protein folding, is catalyzed by the enzyme peptidyl prolyl isomerase. This enzyme is
widely distributed in both prokaryotic and eukaryotic cells and can catalyze the refolding of at least some proteins.
However, its physiologically important substrates and role within cells have not yet been determined.
Protein Cleavage
Cleavage of the polypeptide chain (proteolysis) is an important step in the maturation of many proteins. A simple
example is removal of the initiator methionine from the amino terminus of many polypeptides, which occurs soon after
the amino terminus of the growing polypeptide chain emerges from the ribosome. Additional chemical groups, such as
acetyl groups or fatty acid chains (discussed shortly), are then frequently added to the amino-terminal residues.
Proteolytic modifications of the amino terminus also play a part in the translocation of many proteins across membranes,
including secreted proteins in both bacteria and eukaryotes as well as proteins destined for incorporation into the plasma
membrane, lysosomes, mitochondria, and chloroplasts of eukaryotic cells. These proteins are targeted for transport to
their destinations by amino-terminal sequences that are removed by proteolytic cleavage as the protein crosses the
membrane. For example, amino-terminal signal sequences, usually about 20 amino acids long, target secreted proteins to
the plasma membrane of bacteria or to the endoplasmic reticulum of eukaryotic cells while translation is still in progress
(Figure 7.23).
Figure 7.23. The role of signal sequences in
membrane translocation Signal se-quences
target the translocation of polypeptide chains
across the plasma membrane of bacteria or into
the endoplasmic reticulum of eukaryotic cells
(shown here). The signal sequence, a stretch of
hydrophobic amino acids at the amino terminus of
the polypeptide chain, inserts into a membrane
channel as it emerges from the ribosome. The rest
of the polypeptide is then translocated through the
channel and the signal sequence is cleaved by the
action of signal peptidase, releasing the mature
translocated protein.
The signal sequence, which consists predominantly of hydrophobic amino acids, is inserted into the membrane as it
emerges from the ribosome. The remainder of the polypeptide chain passes through a channel in the membrane as
translation proceeds. The signal sequence is then cleaved by a specific membrane protease (signal peptidase), and the
mature protein is released. In eukaryotic cells, the translocation of growing polypeptide chains into the endoplasmic
reticulum is the first step in targeting proteins for secretion, incorporation into the plasma membrane, or incorporation
into lysosomes. The mechanisms that direct the transport of proteins to these destinations, as well as the role of other
targeting sequences in directing the import of proteins into mitochondria and chloroplasts, will be discussed in detail in
Chapters 9 and 10.
In other important instances of proteolytic processing, active enzymes or hormones form via cleavage of larger precursors.
Insulin, which is synthesized as a longer precursor polypeptide, is a good example. Insulin forms by two cleavages. The
initial precursor (preproinsulin) contains an amino-terminal signal sequence that targets the polypeptide chain to the
endoplasmic reticulum (Figure 7.24).
Figure 7.24. Proteolytic processing of insulin The mature insulin molecule
consists of two polypeptide chains (A and B) joined by disulfide bonds. It is
synthesized as a precursor polypeptide (preproinsulin) containing an
aminoterminal signal sequence that is cleaved during transfer of the growing
polypeptide chain to the endoplasmic reticulum. This cleavage yields a second
precursor (proinsulin), which is converted to insulin by further proteolysis,
removing the internal connecting polypeptide.
Removal of the signal sequence during transfer to the endoplasmic
reticulum yields a second precursor, called proinsulin. This
precursor is then converted to insulin, which consists of two chains
held together by disulfide bonds, by proteolytic removal of an
internal peptide. Other proteins activated by similar cleavage
processes include digestive enzymes and the proteins involved in blood clotting.
It is interesting to note that the proteins of many animal viruses are derived from the cleavage of larger precursors. One
particularly important example of the role of proteolysis in virus replication is provided by HIV. In the replication of HIV,
a virus-encoded protease cleaves precursor polypeptides to form the viral structural proteins. Because of its central role in
virus replication, the HIV protease (in addition to reverse transcriptase) is an important target for the development of
drugs used for treating AIDS. Indeed, such protease inhibitors are now among the most effective agents available for
combating this disease.
Glycosylation
Many proteins, particularly in eukaryotic cells, are modified by the addition of carbohydrates, a process called
glycosylation. The proteins to which carbohydrate chains have been added (called glycoproteins) are usually secreted or
localized to the cell surface, although some nuclear and cytosolic proteins are also glycosylated. The carbohydrate
moieties of glycoproteins play important roles in protein folding in the endoplasmic reticulum, in the targeting of proteins
for delivery to the appropriate intracellular compartments, and as recognition sites in cellcell interactions.
Figure 7.25. Linkage of carbohydrate side chains to glycoproteins The carbohydrate chains of N-linked
glycoproteins are attached to asparagine; those of O-linked glycoproteins are attached to either serine
(shown) or threonine. The sugars joined to the amino acids are usually either N-acetylglucosamine (Nlinked) or N-acetylgalactosamine (O-linked).
Glycoproteins are classified as either N-linked or O-linked, depending on the site of
attachment of the carbohydrate side chain (Figure 7.25). In N-linked glycoproteins, the
carbohydrate is attached to the nitrogen atom in the side chain of asparagine. In O-linked
glycoproteins, the oxygen atom in the side chain of serine or threonine is the site of
carbohydrate attachment. The sugars directly attached to these positions are usually either
N-acetylglucosamine or N-acetylgalactosamine, respectively.
Most glycoproteins in eukaryotic cells are destined either for secretion or for incorporation
into the plasma membrane. These proteins are usually transferred into the endoplasmic reticulum (with the cleavage of a
signal sequence) while their translation is still
in progress. Glycosylation is also initiated in
the endoplasmic reticulum before translation is
complete. The first step is the transfer of a
common oligosaccharide consisting of 14
sugar residues (2 N-acetylglucosamine, 3
glucose, and 9 mannose) to an asparagine
residue of the growing polypeptide chain
(Figure 7.26). The oligosaccharide is
assembled within the endoplasmic reticulum
on a lipid carrier (dolichol phosphate). It is
then transferred as an intact unit to an acceptor
asparagine (Asn) residue within the sequence
Asn-X-Ser or Asn-X-Thr (where X is any
amino acid other than proline).
Figure 7.26. Synthesis of N-linked glycoproteins The first step in glycosylation is the addition of an oligosaccharide consisting of 14 sugar residues to a
growing polypeptide chain in the endoplasmic reticulum (ER). The oligosaccharide (which consists of two N-acetylglucosamine, nine mannose, and three
glucose residues) is assembled on a lipid carrier (dolichol phosphate) in the ER membrane. It is then transferred as a unit to an acceptor asparagine residue of
the polypeptide.
In further processing, the common N-linked oligosaccharide is
modified. Three glucose residues and one mannose are removed while
the glycoprotein is in the endoplasmic reticulum. The oligosaccharide
is then further modified in the Golgi apparatus, to which glycoproteins
are transferred from the endoplasmic reticulum. These modifications
include both the removal and addition of carbohydrate residues as the
glycoprotein is transported through the compartments of the Golgi
(Figure 7.27).
Figure 7.27. Examples of N-linked oligosaccharides Various oligosaccharides form from
further modifications of the common 14-sugar unit initially added in the endoplasmic
reticulum (see Figure 7.26). In high-mannose oligosaccharides, the glucose residues and
some mannose residues are removed, but no other sugars are added. In the synthesis of
complex oligosaccharides, more mannose residues are removed and other sugars are added.
Hybrid oligosaccharides are intermediate between high-mannose and complex
oligosaccharides. The structures shown are representative examples.
The N-linked oligosaccharides of different glycoproteins are processed to different extents, depending on both the
enzymes present in different cells and on the accessibility of the oligosaccharide to the enzymes that catalyze its
modification. Glycoproteins with inaccessible oligosaccharides do not have new sugars added to them in the Golgi. The
relatively simple oligosaccharides of these glycoproteins are called high-mannose oligosaccharides because they contain
a high proportion of mannose residues, similar to the common oligosaccharide originally added in the endoplasmic
reticulum. In contrast, glycoproteins with accessible oligosaccharides are processed more extensively, resulting in the
formation of a variety of complex oligosaccharides.
O-linked oligosaccharides are also added within the Golgi apparatus. In contrast to the Nlinked oligosaccharides, O-linked oligosaccharides are formed by the addition of one sugar
at a time and usually consist of only a few residues (Figure 7.28). Many cytoplasmic and
nuclear proteins, including a variety of transcription factors, are also modified by the
addition of single O-linked N-acetylglucosamine residues, catalyzed by a different enzyme
system. However, the roles of carbohydrates in the function of these cytoplasmic and
nuclear glycoproteins are not yet understood.
Figure 7.28. Examples of O-linked oligosaccharides O-linked oligosaccharides usually consist of only a
few carbohydrate residues, which are added one sugar at a time.
Attachment of Lipids
Some proteins in eukaryotic cells are modified by the attachment of lipids to the polypeptide chain. Such modifications
frequently target and anchor these proteins to the plasma membrane, with which the hydrophobic lipid is able to
interact.Three general types of lipid additions N-myristoylation, prenylation, and palmitoylation are common in
eukaryotic proteins associated with the cytosolic face of the plasma membrane. A fourth type of modification, the
addition of glycolipids, plays an important role in anchoring some cell surface proteins to the extracellular face of the
plasma membrane.
In some proteins, a fatty acid is attached to the amino terminus of
the growing polypeptide chain during translation. In this process,
called N-myristoylation, myristic acid (a 14-carbon fatty acid) is
attached to an N-terminal glycine residue (Figure 7.29).
Figure 7.29. Addition of a fatty acid by N-myristoylation The initiating methionine is
removed, leaving glycine at the N terminus of the polypeptide chain. Myristic acid (a 14carbon fatty acid) is then added.
The glycine is usually the second amino acid incorporated into the
polypeptide chain; the initiator methionine is removed by proteolysis before fatty acid addition. Many proteins that are
modified by N-myristoylation are associated with the inner face of the plasma membrane, and the role of the fatty acid in
this association has been clearly demonstrated by analysis of mutant proteins in which the N-terminal glycine is changed
to an alanine. This substitution prevents myristoylation and blocks the function of the mutant proteins by inhibiting their
membrane association.
Lipids can also be attached to the side chains of cysteine, serine, and threonine residues. One important example of this
type of modification is prenylation, in which specific types of lipids (prenyl groups) are attached to the sulfur atoms in the
side chains of cysteine residues located near the C terminus of the polypeptide chain (Figure 7.30). Many plasma
membrane associated proteins involved in the control of cell growth and differentiation are modified in this way,
including the Ras oncogene proteins, which are responsible for the uncontrolled growth of many human cancers.
Prenylation of these proteins proceeds by three steps. First, the prenyl group is added to a cysteine located three amino
acids from the carboxy terminus of the polypeptide chain. The prenyl groups added in this reaction are either farnesyl (15
carbons, as shown in Figure 7.30) or geranylgeranyl (20 carbons). The amino acids following the cysteine residue are
then removed, leaving cysteine at the carboxy terminus. Finally, a methyl
group is added to the carboxyl group of the C-terminal cysteine residue.
Figure 7.30. Prenylation of a C-terminal cysteine residue The type of prenylation shown affects Ras
proteins and proteins of the nuclear envelope (nuclear lamins). These proteins terminate with a cysteine
residue (Cys) followed by two aliphatic amino acids (A) and any other amino acid (X) at the C
terminus. The first step in their modification is addition of the 15-carbon farnesyl group to the side
chain of cysteine (farnesylation). This step is followed by proteolytic removal of the three C-terminal
amino acids and methylation of the cysteine, which is now at the C terminus.
The biological significance of prenylation is indicated by the fact that
mutations of the critical cysteine block the membrane association and function
of Ras proteins. Because farnesylation is a relatively rare modification of
cellular proteins, interest in this reaction has been stimulated by the possibility
that inhibitors of the key enzyme (farnesyl transferase) might prove useful as
drugs for the treatment of cancers that involve Ras proteins. Such inhibitors of farnesylation have been found to interfere
with the growth of cancer cells in experimental models and are undergoing evaluation of their efficacy against human
tumors in clinical trials.
In the third type of fatty acid modification, palmitoylation, palmitic acid (a 16-carbon fatty
acid) is added to sulfur atoms of the side chains of internal cysteine residues (Figure 7.31).
Like N-myristoylation and prenylation, palmitoylation plays an important role in the
association of some proteins with the cytosolic face of the plasma membrane.
Figure 7.31. Palmitoylation Palmitate (a 16-carbon fatty acid) is added to the side chain of an internal
cysteine residue.
Finally, lipids linked to oligosaccharides (glycolipids) are added to the C-terminal
carboxyl groups of some proteins, where they serve as anchors that attach the proteins to
the external face of the plasma membrane. Because the glycolipids attached to these
proteins contain phosphatidylinositol, they are usually called
glycosylphosphatidylinositol, or GPI, anchors (Figure 7.32). The oligosaccharide
portions of GPI anchors are attached to the terminal carboxyl group of polypeptide
chains. The inositol head group of phosphatidylinositol is in turn attached to the
oligosaccharide, so the carbohydrate serves as a bridge between the protein and the
fatty acid chains of the phospholipid. The GPI anchors are synthesized and added to
proteins as a preassembled unit within the endoplasmic reticulum. Their addition is
accompanied by cleavage of a peptide consisting of about 20 amino acids from the C
terminus of the polypeptide chain. The modified protein is then transported to the cell
surface, where the fatty acid chains of the GPI anchor mediate its attachment to the
plasma membrane.
Figure 7.32. Structure of a GPI anchor The GPI anchor, attached to the C terminus, anchors the
protein in the plasma membrane. The anchor is joined to the C-terminal amino acid by an
ethanolamine, which is linked to an oligosaccharide that consists of mannose, N-acetylgalactosamine,
and glucosamine residues. The oligosaccharide is in turn joined to the inositol head group of
phosphatidylinositol. The two fatty acid chains of the lipid are embedded in the plasma membrane.
The GPI anchor shown here is that of a rat protein, Thy-1.