The Topological Relationships of Membrane-enclosed
Organelles Can Be Interpreted in Terms of Their
Evolutionary Origins
To understand the relationships between the compartments of the cell, it is helpful to consider
how they might have evolved. The precursors of the first eucaryotic cells are thought to have
been simple organisms that resembled bacteria, which generally have a plasma membrane but no
internal membranes. The plasma membrane in such cells therefore provides all membranedependent functions, including the pumping of ions, ATP synthesis, protein secretion, and lipid
synthesis. Typical present-day eucaryotic cells are 10–30 times larger in linear dimension and
1000–10,000 times greater in volume than a typical bacterium such as E. coli. The profusion of
internal membranes can be seen in part as an adaptation to this increase in size: the eucaryotic
cell has a much smaller ratio of surface area to volume, and its area of plasma membrane is
presumably too small to sustain the many vital functions for which membranes are required. The
extensive internal membrane systems of a eucaryotic cell alleviate this imbalance.
Figure 12-3
Development of plastids
Figure 12-3
.
Development of plastids
(A) Proplastids are inherited with the cytoplasm of plant egg cells. As immature plant cells
differentiate, the proplastids develop according to the needs of the specialized cell: they can
become chloroplasts (in green leaf cells), storage plastids that accumulate starch (e.g., in potato
tubers) or oil and lipid droplets (e.g., in fatty seeds), or chromoplasts that harbor pigments (e.g.,
in flower petals). (B) Development of the thylakoid. As chloroplasts develop, invaginated
patches of specialized membrane from the proplastid inner membrane pinch off to form
thylakoid vesicles, which then develop into the mature thylakoid. The thylakoid membrane forms
a separate compartment, the thylakoid space, which is structurally and functionally distinct from
the rest of the chloroplast. Thylakoids can grow and divide autonomously as chloroplasts
proliferate.
The evolution of internal membranes evidently accompanied the specialization of membrane
function. Consider, for example, the generation of thylakoid vesicles in chloroplasts. These
vesicles form during the development of chloroplasts from proplastids in the green leaves of
plants. Proplastids are small precursor organelles that are present in all immature plant cells.
They are surrounded by a double membrane and develop according to the needs of the
differentiated cells: they develop into chloroplasts in leaf cells, for example, and into organelles
that store starch, fat, or pigments in other cell types (Figure 12-3A
). In the process of differentiating into chloroplasts, specialized membrane patches form and
pinch off from the inner membrane of the proplastid. The vesicles that pinch off form a new
specialized compartment, the thylakoid, that harbors all of the chloroplast's photosynthetic
machinery (Figure 12-3B
).
Figure 12-4
Hypothetical schemes for the evolutionary origins of (more...)
Figure 12-4
.
Hypothetical schemes for the evolutionary origins of some membrane-enclosed organelles
The origins of mitochondria, chloroplasts, ER, and the cell nucleus can explain the topological
relationships of these intra-cellular compartments in eucaryotic cells.
(A) A possible pathway for the evolution of the cell nucleus and the ER. In some bacteria the
single DNA molecule is attached to an invagination of the plasma membrane. Such an
invagination in a very ancient procaryotic cell could have rearranged to form an envelope around
the DNA, while still allowing the DNA access to the cell cytosol (as is required for DNA to
direct protein synthesis). This envelope is presumed to have eventually pinched off completely
from the plasma membrane, producing a nuclear compartment surrounded by a double
membrane.
As illustrated, the nuclear envelope is penetrated by communicating channels called nuclear pore
complexes. Because it is surrounded by two membranes that are in continuity where they are
penetrated by these pores, the nuclear compartment is topologically equivalent to the cytosol; in
fact, during mitosis the nuclear contents mix with the cytosol. The lumen of the ER is continuous
with the space between the inner and outer nuclear membranes and topologically equivalent to
the extracellular space.
(B) Mitochondria (and plastids) are thought to have originated when a bacterium was engulfed
by a larger pre-eucaryotic cell. They retain their autonomy. This may explain why the lumens of
these organelles remain isolated from the membrane traffic that interconnects the lumens of
many other intracellular compartments.
Figure 12-5
Topological relationships between compartments of the (more...)
Figure 12-5
.
Topological relationships between compartments of the secretory and endocytic pathways
in a eucaryotic cell
Topologically equivalent spaces are shown in red. In principle, cycles of membrane budding and
fusion permit the lumen of any of these organelles to communicate with any other and with the
cell exterior by means of transport vesicles. Blue arrows indicate the extensive network of
outbound and inbound traffic routes, which we discuss in Chapter 13. Some organelles, most
notably mitochondria and (in plant cells) plastids do not take part in this communication and are
isolated from the traffic between organelles shown here.
Other compartments in eucaryotic cells may have originated in a conceptually similar way
(Figure 12-4A
).
Pinching off of specialized intracellular membrane structures from the plasma membrane, for
example, would create organelles with an interior that is topologically equivalent to the exterior
of the cell. We shall see that this topological relationship holds for all of the organelles involved
in the secretory and endocytic pathways, including the ER, Golgi apparatus, endosomes, and
lysosomes. We can therefore think of all of these organelles as members of the same family. As
we discuss in detail in the next chapter, their interiors communicate extensively with one another
and with the outside of the cell via transport vesicles that bud off from one organelle and fuse
with another (Figure 12-5
).
As described in Chapter 14, mitochondria and plastids differ from the other membrane-enclosed
organelles in containing their own genomes. The nature of these genomes, and the close
resemblance of the proteins in these organelles to those in some present-day bacteria, strongly
suggest that mitochondria and plastids evolved from bacteria that were engulfed by other cells
with which they initially lived in symbiosis (discussed in Chapters 1 and 14). According to the
hypothetical scheme shown in Figure 12-4B
, the inner membrane of
mitochondria and plastids corresponds to the original plasma membrane of the bacterium, while
the lumen of these organelles evolved from the bacterial cytosol. As might be expected from
such an endocytic origin, these two organelles are surrounded by a double membrane, and they
remain isolated from the extensive vesicular traffic that connects the interiors of most of the
other membrane-enclosed organelles to each other and to the outside of the cell.
The evolutionary scheme described above groups the intracellular compartments in eucaryotic
cells into four distinct families: (1) the nucleus and the cytosol, which communicate through
nuclear pore complexes and are thus topologically continuous (although functionally distinct);
(2) all organelles that function in the secretory and endocytic pathways—including the ER, Golgi
apparatus, endosomes, lysosomes, the numerous classes of transport intermediates such as
transport vesicles, and possibly peroxisomes; (3) the mitochondria; and (4) the plastids (in plants
only).
Proteins Can Move Between Compartments in Different
Ways
All proteins begin being synthesized on ribosomes in the cytosol, except for the few that are
synthesized on the ribosomes of mitochondria and plastids. Their subsequent fate depends on
their amino acid sequence, which can contain sorting signals that direct their delivery to
locations outside the cytosol. Most proteins do not have a sorting signal and consequently remain
in the cytosol as permanent residents. Many others, however, have specific sorting signals that
direct their transport from the cytosol into the nucleus, the ER, mitochondria, plastids, or
peroxisomes; sorting signals can also direct the transport of proteins from the ER to other
destinations in the cell.
Figure 12-6
A simplified “roadmap” of protein traffic (more...)
Figure 12-6
.
A simplified “roadmap” of protein traffic
Proteins can move from one compartment to another by gated transport (red), transmembrane
transport (blue), or vesicular transport (green). The signals that direct a given protein's
movement through the system, and thereby determine its eventual location in the cell, are
contained in each protein's amino acid sequence. The journey begins with the synthesis of a
protein on a ribosome in the cytosol and terminates when the final destination is reached. At each
intermediate station (boxes), a decision is made as to whether the protein is to be retained in that
compartment or transported further. In principle, a signal could be required for either retention in
or exit from a compartment. We shall use this figure repeatedly as a guide throughout this
chapter and the next, highlighting in color the particular pathway being discussed.
To understand the general principles by which sorting signals operate, it is important to
distinguish three fundamentally different ways by which proteins move from one compartment to
another. These three mechanisms are described below, and their sites of action in the cell are
outlined in Figure 12-6
. The first two mechanisms are detailed
in this chapter, while the third (green arrows in Figure 12-6
the subject of Chapter 13.
) is
Figure 12-7
Vesicle budding and fusion during vesicular transport (more...)
Figure 12-7
.
Vesicle budding and fusion during vesicular transport
Transport vesicles bud from one compartment (donor) and fuse with another (target)
compartment. In the process, soluble components (red dots) are transferred from lumen to lumen.
Note that membrane is also transferred, and that the original orientation of both proteins and
lipids in the donor-compartment membrane is preserved in the target-compartment membrane.
Thus, membrane proteins retain their asymmetric orientation, with the same domains always
facing the cytosol.

1
In gated transport, the protein traffic between the cytosol and nucleus occurs between
topologically equivalent spaces, which are in continuity through the nuclear pore
complexes. The nuclear pore complexes function as selective gates that actively transport
specific macromolecules and macromolecular assemblies, although they also allow free
diffusion of smaller molecules.

2
In transmembrane transport, membrane-bound protein translocators directly transport
specific proteins across a membrane from the cytosol into a space that is topologically
distinct. The transported protein molecule usually must unfold to snake through the
translocator. The initial transport of selected proteins from the cytosol into the ER lumen
or from the cytosol into mitochondria, for example, occurs in this way.

3
In vesicular transport, membrane-enclosed transport intermediates—which may be small,
spherical transport vesicles or larger, irregularly shaped organelle fragments—ferry
proteins from one compartment to another. The transport vesicles and fragments become
loaded with a cargo of molecules derived from the lumen of one compartment as they
pinch off from its membrane; they discharge their cargo into a second compartment by
fusing with that compartment (Figure 12-7
). The
transfer of soluble proteins from the ER to the Golgi apparatus, for example, occurs in
this way. Because the transported proteins do not cross a membrane, vesicular transport
can move proteins only between compartments that are topologically equivalent (see
Figure 12-5
discuss vesicular transport in detail in Chapter 13.
). We
Each of the three modes of protein transfer is usually guided by sorting signals in the transported
protein that are recognized by complementary receptor proteins. If a large protein is to be
imported into the nucleus, for example, it must possess a sorting signal that is recognized by
receptor proteins that guide it through the nuclear pore complex. If a protein is to be transferred
directly across a membrane, it must possess a sorting signal that is recognized by the translocator
in the membrane to be crossed. Likewise, if a protein is to be loaded into a certain type of vesicle
or retained in certain organelles, its sorting signal must be recognized by a complementary
receptor in the appropriate membrane.
Signal Sequences and Signal Patches Direct Proteins to the
Correct Cellular Address
Figure 12-8
Two ways in which a sorting signal can be built into (more...)
Figure 12-8
.
Two ways in which a sorting signal can be built into a protein
(A) The signal resides in a single discrete stretch of amino acid sequence, called a signal
sequence, that is exposed in the folded protein. Signal sequences often occur at the end of the
polypeptide chain (as shown), but they can also be located internally. (B) A signal patch can be
formed by the juxtaposition of amino acids from regions that are physically separated before the
protein folds (as shown). Alternatively, separate patches on the surface of the folded protein that
are spaced a fixed distance apart can form the signal.
There are at least two types of sorting signals in proteins. One type resides in a continuous
stretch of amino acid sequence, typically 15–60 residues long. Some of these signal sequences
are removed from the finished protein by specialized signal peptidases once the sorting process
has been completed. The other type consists of a specific three-dimensional arrangement of
atoms on the protein's surface that forms when the protein folds up. The amino acid residues that
comprise this signal patch can be distant from one another in the linear amino acid sequence, and
they generally persist in the finished protein (Figure 12-8
). Signal sequences
are used to direct proteins from the cytosol into the ER, mitochondria, chloroplasts, and
peroxisomes, and they are also used to transport proteins from the nucleus to the cytosol and
from the Golgi apparatus to the ER. The sorting signals that direct proteins into the nucleus from
the cytosol can be either short signal sequences or longer sequences that are likely to fold into
signal patches. Signal patches also direct newly synthesized degradative enzymes into
lysosomes.
Each signal sequence specifies a particular destination in the cell. Proteins destined for initial
transfer to the ER usually have a signal sequence at their N terminus, which characteristically
includes a sequence composed of about 5–10 hydrophobic amino acids. Many of these proteins
will in turn pass from the ER to the Golgi apparatus, but those with a specific sequence of four
amino acids at their C terminus are recognized as ER residents and are returned to the ER.
Proteins destined for mitochondria have signal sequences of yet another type, in which positively
charged amino acids alternate with hydrophobic ones. Finally, many proteins destined for
peroxisomes have a signal peptide of three characteristic amino acids at their C terminus.
Table 12-3
Some Typical Signal Sequences
Table 12-3
Some Typical Signal Sequences
Some specific signal sequences are presented in Table 12-3. The importance of each of these
signal sequences for protein targeting has been shown by experiments in which the peptide is
transferred from one protein to another by genetic engineering techniques. Placing the Nterminal ER signal sequence at the beginning of a cytosolic protein, for example, redirects the
protein to the ER. Signal sequences are therefore both necessary and sufficient for protein
targeting. Even though their amino acid sequences can vary greatly, the signal sequences of all
proteins having the same destination are functionally interchangeable, and physical properties,
such as hydrophobicity, often seem to be more important in the signal-recognition process than
the exact amino acid sequence.
Signal patches are far more difficult to analyze than signal sequences, so less is known about
their structure. Because they often result from a complex three-dimensional protein-folding
pattern, they cannot be easily transferred experimentally from one protein to another.
Both types of sorting signals are recognized by complementary sorting receptors that guide
proteins to their appropriate destination, where the receptors unload their cargo. The receptors
function catalytically: after completing one round of targeting, they return to their point of origin
to be reused. Most sorting receptors recognize classes of proteins rather than just an individual
protein species. They therefore can be viewed as public transportation systems dedicated to
delivering groups of components to their correct location in the cell.
Panel 12-1
Approaches to Studying Signal Sequences and Protein
(more...)
The main ways of studying how proteins are directed from the cytosol to a specific compartment
and how they are translocated across membranes are illustrated in Panel 12-1.
Most Membrane-enclosed Organelles Cannot Be
Constructed From Scratch: They Require Information in
the Organelle Itself
When a cell reproduces by division, it has to duplicate its membrane-enclosed organelles. In
general, cells do this by enlarging the existing organelles by incorporating new molecules into
them; the enlarged organelles then divide and are distributed to the two daughter cells. Thus,
each daughter cell inherits from its mother a complete set of specialized cell membranes. This
inheritance is essential because a cell could not make such membranes from scratch. If the ER
were completely removed from a cell, for example, how could the cell reconstruct it? As we shall
discuss later, the membrane proteins that define the ER and perform many of its functions are
themselves products of the ER. A new ER could not be made without an existing ER or, at the
very least, a membrane that specifically contains the protein translocators required to import
selected proteins into the ER from the cytosol (including the ER-specific translocators
themselves). The same is true for mitochondria, plastids, and peroxisomes (see Figure 12-6
).
Thus, it seems that the information required to construct a membrane-enclosed organelle does
not reside exclusively in the DNA that specifies the organelle's proteins. Epigenetic information
in the form of at least one distinct protein that preexists in the organelle membrane is also
required, and this information is passed from parent cell to progeny cell in the form of the
organelle itself. Presumably, such information is essential for the propagation of the cell's
compartmental organization, just as the information in DNA is essential for the propagation of
the cell's nucleotide and amino acid sequences.
As we discuss in more detail in Chapter 13, however, the ER sheds a constant stream of
membrane vesicles that incorporate only specific proteins and therefore have a different
composition from the ER itself. Similarly, the plasma membrane constantly produces specialized
endocytic vesicles. Thus, some membrane-enclosed compartments can form from other
organelles and do not have to be inherited at cell division.
Summary
Eucaryotic cells contain intracellular membranes that enclose nearly half the cell's total volume
in separate intracellular compartments called organelles. The main types of membrane-enclosed
organelles present in all eucaryotic cells are the endoplasmic reticulum, Golgi apparatus,
nucleus, mitochondria, lysosomes, endosomes, and peroxisomes; plant cells also contain plastids,
such as chloroplasts. Each organelle contains a distinct set of proteins that mediate its unique
functions.
Each newly synthesized organelle protein must find its way from a ribosome in the cytosol,
where it is made, to the organelle where it functions. It does so by following a specific pathway,
guided by signals in its amino acid sequence that function as signal sequences or signal patches.
Signal sequences and patches are recognized by complementary sorting receptors that deliver the
protein to the appropriate target organelle. Proteins that function in the cytosol do not contain
sorting signals and therefore remain there after they are synthesized.
During cell division, organelles such as the ER and mitochondria are distributed intact to each
daughter cell. These organelles contain information that is required for their construction so that
they cannot be made from scratch.