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4: Many RNA Molecules Are Modified after Transcription in Eukaryotes
H2C P P P
structure called a 5 cap. This capping consists of the addition of an extra nucleotide at the 5Ј end of the mRNA and
methylation by the addition of a methyl group (CH3) to the
base in the newly added nucleotide and to the 2Ј-OH group
of the sugar of one or more nucleotides at the 5Ј end (Figure 10.16). Capping takes place rapidly after the initiation of
transcription and, as will be discussed in more depth in
Chapter 11, the 5Ј cap functions in the initiation of translation. Cap-binding proteins recognize the cap and attach to it;
a ribosome then binds to these proteins and moves downstream along the mRNA until the start codon is reached and
translation begins. The presence of a 5Ј cap also increases the
stability of mRNA and influences the removal of introns.
10.16 Most eukaryotic mRNAs have a 5Ј cap. The cap consists
of a nucleotide with 7-methylguanine attached to the pre-mRNA by a
unique 5Ј–5Ј bond, as well as methyl groups added to the 2Ј position
of the sugar in the second and third nucleotides and sometimes a
methyl group added to the base (N) on the initial nucleotide.
The Addition of the Poly(A) Tail A second type of
is translated. Indeed, eukaryotic mRNA is extensively altered
after transcription. Changes are made to the 5Ј end, the 3Ј
end, and the protein-coding section of the RNA molecule.
Recent research suggests that some translation in eukaryotes
may take place in the nucleus, although these findings are
controversial. If, indeed, translation takes place within the
nucleus, then eukaryotic transcription and translation may
be coupled as in prokaryotes. The significance of this coupling for RNA processing is not yet clear.
The Addition of the 5Ј Cap One type of modification of
eukaryotic pre-mRNA is the addition at its 5Ј end of a
modification to eukaryotic mRNA is the addition of 50 to
250 adenine nucleotides at the 3Ј end, forming a poly(A) tail.
These nucleotides are not encoded in the DNA but are added
after transcription (Figure 10.17) in a process termed
polyadenylation. Many eukaryotic genes are transcribed well
beyond the end of the coding sequence; the extra material at
the 3Ј end is then cleaved and the poly(A) tail is added. For
some pre-mRNA molecules, more than 1000 nucleotides
may be removed from the 3Ј end.
Processing of the 3Ј end of pre-mRNA requires
sequences both upstream and downstream of the cleavage
site. The consensus sequence AAUAAA is usually from 11 to
30 nucleotides upstream of the cleavage site (see Figure
10.17) and determines the point at which cleavage will take
place. A sequence rich in uracil nucleotides (or guanine and
uracil nucleotides) is typically downstream of the cleavage
site. A large number of proteins take part in finding the
Pre-mRNA is cleaved, at a position
from 11 to 30 nucleotides downstream of the consensus sequence,
in the 3’ untranslated region.
The addition of adenine nucleotides
(polyadenylation) takes place at
3’ the 3‘ end of the pre-mRNA,
generating the poly(A) tail.
Poly (A) tail
Conclusion: In pre-mRNA processing, a poly(A) tail
is added through cleavage and polyadenylation.
10.17 Most eukaryotic mRNAs have a 3Ј poly(A) tail.
From DNA to Proteins: Transcription and RNA Processing
cleavage site and removing the 3Ј end. After cleavage has
been completed, adenine nucleotides are added to the new 3Ј
end, creating the poly(A) tail.
The poly(A) tail confers stability on many mRNAs,
increasing the time during which the mRNA remains intact
and available for translation before it is degraded by cellular
enzymes. The stability conferred by the poly(A) tail depends
on the proteins that attached to the tail. The poly(A) tail also
facilitates attachment of the ribosome to the mRNA.
Introns in nuclear genes contain three consensus sequences critical to splicing: a 5Ј splice site, a 3Ј splice site, and a branch point.
Splicing of pre-mRNA takes place within a large complex called
the spliceosome, which consists of snRNAs and proteins.
✔ Concept Check 6
If a splice site were mutated so that splicing did not take place, what
would the effect be on the protein encoded by the mRNA?
a. It would be shorter than normal.
Eukaryotic pre-mRNAs are processed at their 5Ј and 3Ј ends. A cap,
consisting of a modified nucleotide and several methyl groups, is
added to the 5Ј end. The cap facilitates the binding of a ribosome,
increases the stability of the mRNA, and may affect the removal of
introns. Processing at the 3Ј end includes cleavage downstream of
an AAUAAA consensus sequence and the addition of a poly(A) tail.
c. It would be the same length but would have different amino
b. It would be longer than normal.
Before splicing takes place, an intron lies between an
upstream exon (exon 1) and a downstream exon (exon 2),
as shown in Figure 10.19. Pre-mRNA is spliced in two distinct steps. In the first step of splicing, the pre-mRNA is cut
at the 5Ј splice site. This cut frees exon 1 from the intron,
and the 5Ј end of the intron attaches to the branch point;
that is, the intron folds back on itself, forming a structure
called a lariat. In this reaction, the guanine nucleotide in
the consensus sequence at the 5Ј splice site bonds with the
adenine nucleotide at the branch point through a transesterification reaction. The result is that the 5Ј phosphate
group of the guanine nucleotide is now attached to the
2Ј-OH group of the adenine nucleotide at the branch point
(see Figure 10.19).
In the second step of RNA splicing, a cut is made at the
3Ј splice site and, simultaneously, the 3Ј end of exon 1
becomes covalently attached (spliced) to the 5Ј end of exon
2. The intron is released as a lariat. The intron becomes linear when the bond breaks at the branch point and is then
rapidly degraded by nuclear enzymes. The mature mRNA
consisting of the exons spliced together is exported to the
cytoplasm, where it is translated. These splicing reactions
take place within the spliceosome, which carries out the
Many eukaryotic mRNAs undergo alternative processing, in which a single pre-mRNA is processed in different
ways to produce alternative types of mRNA, resulting in the
production of different proteins from the same DNA
sequence. One type of alternative processing is alternative
splicing, in which the same pre-mRNA can be spliced in
more than one way to yield multiple mRNAs that are
RNA Splicing The other major type of modification of
eukaryotic pre-mRNA is the removal of introns by RNA
splicing. This modification takes place in the nucleus, before
the RNA moves to the cytoplasm. Splicing requires the presence of three sequences in the intron. One end of the intron
is referred to as the 5 splice site, and the other end is the 3
splice site (Figure 10.18); these splice sites possess short
consensus sequences. Most introns in pre-mRNAs begin
with GU and end with AG, indicating that these sequences
play a crucial role in splicing. Indeed, changing a single
nucleotide at either of these sites prevents splicing.
The third sequence important for splicing is at the
branch point, which is an adenine nucleotide that lies from
18 to 40 nucleotides upstream of the 3Ј splice site (see Figure
10.18). The sequence surrounding the branch point does not
have a strong consensus. The deletion or mutation of the
adenine nucleotide at the branch point prevents splicing.
Splicing takes place within a large structure called the
spliceosome, which is one of the largest and most complex of
all molecular complexes. The spliceosome consists of five
RNA molecules and almost 300 proteins. The RNA components are small nuclear RNAs; these snRNAs associate with
proteins to form small ribonucleoprotein particles (snRNPs).
Each snRNP contains a single snRNA molecule and multiple
proteins. The spliceosome is composed of five snRNPs,
named for the snRNAs that they contain (U1, U2, U4, U5,
and U6), and some proteins not associated with an snRNA.
5’ splice site
A AG GU /G AGU
3’ splice site
10.18 Splicing of pre-mRNA requires consensus
3’ sequences. Critical consensus sequences are present
at the 5Ј splice site and the 3Ј splice site. A weak
consensus sequence (not shown) exists at the branch
5’ splice site
Pre-mRNA Exon 1
3’ splice site
1 The mRNA is cut at
the 5’ splice site.
2 The 5’ end of the
intron attaches to
the branch point.
3 A cut is made at
the 3’ splice site.
mRNA Exon 1 Exon 2
6 The bond holding the
lariat is broken, and the
linear intron is degraded.
7 The spliced mRNA is
exported to the cytoplasm
10.19 The splicing of nuclear introns requires a two-step process.
translated into different amino acid sequences and thus different proteins (Figure 10.20). Alternative processing is an
important source of protein diversity in vertebrates; an estimated 60% of all human genes are alternatively spliced.
3’ cleavage site
5’ Exon 1
3’ cleavage and
5’ Exon 1
Either two introns
are removed to
yield one mRNA…
Exon 3 AAAAA 3’
…or two introns and
exon 2 are removed to
yield a different mRNA.
5’ Exon 1 Exon 2 Exon 3 AAAAA 3’
5’ Exon 1 Exon 3 AAAAA 3’
x on 2
Intron 1, exon 2,
and intron 2
Conclusion: Alternate splicing produces different mRNAs
from a single pre-mRNA.
10.20 Eukaryotic cells have alternative pathways for
5 …and the two exons
are spliced together.
4 The intron is released
as a lariat,…
Intron splicing of nuclear genes is a two-step process: (1) the 5Ј
end of the intron is cleaved and attached to the branch point to
form a lariat and (2) the 3Ј end of the intron is cleaved and the
two ends of the exon are spliced together. These reactions take
place within the spliceosome. Alternative splicing enables exons to
be spliced together in different combinations to yield mRNAs that
encode different proteins.
Eukaryotic Gene Structure and Pre-mRNA Processing
This chapter introduced a number of different components of genes
and RNA molecules, including promoters, 5Ј untranslated regions,
coding sequences, introns, 3Ј untranslated regions, poly(A) tails, and
caps. Let’s see how some of these components are combined to create a typical eukaryotic gene and how a mature mRNA is produced
The promoter, which typically encompasses about 100
nucleotides upstream of the transcription start site, is necessary for
transcription to take place but is itself not usually transcribed when
protein-encoding genes are transcribed by RNA polymerase II
(Figure 10.21a). Farther upstream or downstream of the start site,
there may be enhancers that also regulate transcription.
From DNA to Proteins: Transcription and RNA Processing
Enhancer is typically upstream, but
could be downstream or in an intron
1 Introns, exons, and a long 3’ end
are all transcribed into pre-mRNA.
5 Finally, the introns
2 A 5’ cap is added.
3 Cleavage at the 3’ end is
approximately 10 nucleotides downstream of the
4 Polyadenylation at the
cleavage site produces
the poly(A) tail.
3’ cleavage site
3’ cleavage site
3’ cleavage site
6 …producing the
10.21 Mature eukaryotic mRNA is produced when pre-mRNA is transcribed and undergoes
several types of processing.
In transcription, all the nucleotides between the transcription
start site and the stop site are transcribed into pre-mRNA, including
exons, introns, and a long 3Ј end that is later cleaved from the transcript (Figure 10.21b). Notice that the 5Ј end of the first exon contains the sequence that encodes the 5Ј untranslated region and that
the 3Ј end of the last exon contains the sequence that encodes the
3Ј untranslated region.
The pre-mRNA is then processed to yield a mature mRNA. The
first step in this processing is the addition of a cap to the 5Ј end of
the pre-mRNA (Figure 10.21c). Next, the 3Ј end is cleaved at a site
downstream of the AAUAAA consensus sequence in the last exon
(Figure 10.21d). Immediately after cleavage, a poly(A) tail is added
to the 3Ј end (Figure 10.21e). Finally, the introns are removed to
yield the mature mRNA (Figure 10.21f). The mRNA now contains
5Ј and 3Ј untranslated regions, which are not translated into amino
acids, and the nucleotides that carry the protein-coding sequences.
The Structure and Processing
of Transfer RNAs
Transfer RNA serves as a link between the genetic code in
mRNA and the amino acids that make up a protein. Each
tRNA attaches to a particular amino acid and carries it to the
ribosome, where the tRNA adds its amino acid to the growing polypeptide chain at the position specified by the genetic
instructions in the mRNA.
The Structure of Transfer RNA Each tRNA is capable of
attaching to only one type of amino acid. The complex of
tRNA plus its amino acid can be written in abbreviated form
by adding a three-letter superscript representing the amino
acid to the term tRNA. For example, a tRNA that attaches to
the amino acid alanine is written as tRNAAla.
This flattened cloverleaf model shows pairing
between complementary nucleotides.
The anticodon comprises
three bases and interacts
with a codon in mRNA.
This icon for tRNA
will be used in
base ( )
CCCC U AGGCC
C G C
This ribbon model emphasizes
the internal regions of base pairing.
This computer-generated space-filling
molecular model shows the threedimensional structure of a tRNA.
10.22 All tRNAs possess a common secondary structure, the cloverleaf structure. The base
sequence in the flattened model is for tRNAAla.
A unique feature of tRNA is the presence of rare modified bases. All RNAs have the four standard bases (adenine,
cytosine, guanine, and uracil) specified by DNA, but tRNAs
have additional bases, including ribothymine, pseudouridine
(which is also occasionally present in snRNAs and rRNA),
and dozens of others.
The structures of all tRNAs are similar, a feature critical
to tRNA function. Some of the nucleotides in a tRNA are
complementary to each other and form intramolecular
hydrogen bonds. As a result, each tRNA has a cloverleaf
structure (Figure 10.22). All tRNAs have the same sequence
(CCA) at the 3Ј end, where the amino acid attaches to the
tRNA. At the other end of the tRNA is a set of three
nucleotides that make up the anticodon, which pairs with
the corresponding codon on the mRNA during protein synthesis to ensure that the amino acids link in the correct order.
Although each tRNA molecule folds into a cloverleaf
owing to the complementary pairing of bases, the cloverleaf
is not the three-dimensional (tertiary) structure of tRNAs
found in the cell. The results of X-ray crystallographic
studies have shown that the cloverleaf folds on itself to form
an L-shaped structure, as illustrated by the space-filling and
ribbon models in Figure 10.22.
Transfer RNA Processing Both bacterial and eukaryotic
tRNAs are extensively modified after transcription. In E. coli,
several tRNAs are usually transcribed together as one large
precursor tRNA, which is then cut up into pieces, each containing a single tRNA. Additional nucleotides may then be
removed one at a time from the 5Ј and 3Ј ends of the tRNA
in a process known as trimming. Base-modifying enzymes
may then change some of the standard bases into modified
bases. The CCA sequence found at the 3Ј of all tRNAs is often
synthesized by a special enzyme that adds these nucleotides
without the use of any template. Eukaryotic tRNAs are
processed in a manner similar to that for bacterial tRNAs:
most are transcribed as larger precursors that are then
cleaved, trimmed, and modified to produce mature tRNAs.
All tRNAs are similar in size and have a common secondary structure known as the cloverleaf. Transfer RNAs contain modified
bases and are extensively processed after transcription in both
bacterial and eukaryotic cells.
The Structure and Processing
of Ribosomal RNA
Within ribosomes, the genetic instructions contained in
mRNA are translated into the amino acid sequences of
polypeptides. Ribosomes are complex organelles, each consisting of more than 50 different proteins and RNA molecules
(Table 10.4). A functional ribosome consists of two subunits,
a large ribosomal subunit and a small ribosomal subunit,
each of which consists of one or more pieces of RNA and a
number of proteins. The sizes of the ribosomes and their
RNA components are given in Svedberg (S) units (a measure
of how rapidly an object sediments in a centrifugal field).
Ribosomal RNA is processed in both bacterial and
eukaryotic cells. A precursor RNA molecule is methylated in
several places and then cleaved and trimmed to produce the
From DNA to Proteins: Transcription and RNA Processing
Composition of ribosomes in bacterial and eukaryotic cells
23S (2900 nucleotides), 5S (120 nucleotides)
16S (1500 nucleotides)
28S (4700 nucleotides), 5.8S (160 nucleotides),
5S (120 nucleotides)
18S (1900 nucleotides)
Note: The letter “S” stands for Svedberg unit.
mature rRNAs that make up the ribosome. In eukaryotes,
small nucleolar RNAs (snoRNAs) help to cleave and modify
rRNA and assemble the processed rRNA into a mature
A ribosome is a complex organelle consisting of several rRNA molecules and many proteins. Each functional ribosome consists of a
large and a small subunit. Ribosomal RNAs in both bacterial and
eukaryotic cells are modified after transcription.
Small Interfering RNAs
In 1998, Andrew Fire, Craig Mello, and their colleagues
observed what appeared to be a strange phenomenon. They
were inhibiting the expression of genes in the nematode
Caenorhabditis elegans by putting into the animals singlestranded RNA molecules that were complementary to a
gene’s DNA sequence. Called antisense RNA, such molecules
are known to inhibit gene expression by binding to the
mRNA sequences and inhibiting translation. Fire, Mello, and
their colleagues found that even more potent gene silencing
was triggered when double-stranded RNA was injected into
the animals. This finding was puzzling, because no mechanism by which double-stranded RNA could inhibit translation was known. Several other, previously described types of
gene silencing also were found to be triggered by doublestranded RNA. These studies led to the discovery of an abundant class of very small RNAs, called small interfering RNAs
(siRNAs) or microRNAs (miRNAs), depending on their origin and mode of function. As mentioned earlier, we now
know that siRNAs and miRNAs are found in many eukaryotes and are responsible for regulating gene expression
through a process called RNA interference; microRNAs have
also been implicated in a variety of other phenomena. For
their discovery of RNA interference, Andrew Fire and Craig
Mello were awarded the Nobel Prize in physiology or medicine in 2006.
RNA interference (RNAi) is a powerful and precise
mechanism used by eukaryotic cells to limit the invasion of
foreign genes (from viruses and transposons) and to censor
the expression of their own genes. RNA interference is triggered by double-stranded RNA molecules, which may arise
in several ways (Figure 10.23): by the transcription of
inverted repeats into an RNA molecule that then base pairs
with itself to form double-stranded RNA; by the simultaneous transcription of two different RNA molecules that are
complementary to one another and that pair, forming
double-stranded RNA; or by infection by viruses that make
double-stranded RNA. These double-stranded RNA molecules are chopped up by an enzyme appropriately called
Dicer, resulting in tiny RNA molecules that are unwound to
produce siRNAs and miRNAs (see Figure 10.23).
RNA interference is responsible for regulating a number
of key genetic and developmental processes, including
changes in chromatin structure, translation, cell fate and
proliferation, and cell death. Geneticists also use the RNAi
machinery as an effective tool for blocking the expression of
specific genes (see Chapter 14).
Types of Small RNAs Small interfering RNAs and
microRNAs constitute the two most abundant classes of
RNA molecules in RNA interference. Although these two
types of RNA differ in how they originate (Table 10.5; see
Figure 10.23), they have a number of features in common
and their functions overlap considerably.
Both siRNA and miRNA molecules combine with proteins to form an RNA-induced silencing complex (RISC; see
Figure 10.23). The RISC pairs with an mRNA molecule that
possesses a sequence complementary to RISC’s siRNA or
miRNA component and either cleaves the mRNA, leading to
degradation of the mRNA, or represses translation of the
mRNA. Some siRNAs also serve as guides for the methylation of complementary sequences in DNA, whereas others
alter chromatin structure, both of which affect transcription.
10.23 Small interfering RNAs and microRNAs are produced
from double-stranded RNAs.
(b) Small interfering
The Processing and Function of MicroRNAs MicroR-
through an inverted
repeat in the DNA…
RNA may arise from
RNA viruses or from
2 …produces an RNA
molecule that folds
to produce doublestranded RNA.
3 Double-stranded RNA
is cleaved by the
NAs have been found in all eukaryotic organisms examined
to date, as well as viruses; they control the expression of
genes taking part in many biological processes, including
growth, development, and metabolism.
The genes that encode miRNAs are transcribed into
longer precursors, called primary microRNA (pri-miRNA),
that range from several hundred to several thousand
nucleotides in length (Figure 10.24). The pri-miRNA is then
cleaved into one or more smaller RNA molecules with a
hairpin, which is a secondary structure that forms when
sequences on the same strand are complementary and pair
with one another. Dicer binds to this hairpin structure and
removes the terminal loop. One of the miRNA strands is
incorporated into the RISC; the other strand is released and
Small interfering RNAs and microRNAs are tiny RNAs produced
when larger double-stranded RNA molecules are cleaved by the
enzyme Dicer. Small interfering RNAs and microRNAs participate
in a variety of processes, including mRNA degradation, the inhibition of translation, the methylation of DNA, and chromatin
4 …to produce
5 One strand of the miRNA
or siRNA combines with
proteins to form an
from distinct gene
RNA duplex or singlestranded RNA that
forms long hairpins
from folded RNA
RNA that forms
of mRNA, others
Genes from which
they were transcribed
Genes other than
those from which
6 …which pairs with an
mRNA and inhibits
translation (in the miRNA
case) or degrades the
mRNA (in the siRNA case).
Differences between siRNAs
From DNA to Proteins: Transcription and RNA Processing
Genes for miRNA are transcribed…
…to produce a primary
The pri-miRNA is cleaved
to produce a short RNA
with a hairpin.
Dicer removes the
terminal loop of the
One of the RNA strands
of the miRNA combines
with proteins to form
The other strand
of RNA is degraded.
10.24 MicroRNAs are cleaved from larger precursors
Model Genetic Organism
The Nematode Worm Caenorhabditis
As we have seen, RNA interference was first demonstrated in the nematode Caenorhabditis elegans
when geneticists discovered that they could silence
specific genes in this species by injecting the animals with
double-stranded DNA that was complementary to the genes.
Geneticists were studying gene expression in C. elegans
because this species had proved to be an excellent model
genetic organism, particularly for studies of how genes influence development. For reasons that are not completely
understood, RNAi is particularly effective in this species.
You may be asking, What is a nematode and why is it a
model genetic organism? Although rarely seen, nematodes are
one of the most abundant organisms on Earth, inhabiting soils
throughout the world. Most are free living and cause no harm,
but a few are important parasites of plants and animals,
including humans. Although C. elegans has no economic
importance, it has become widely used in genetic studies
because of its simple body plan, ease of culture, and high
reproductive capacity (Figure 10.25). First introduced to the
study of genetics by Sydney Brenner, who formulated plans in
1962 to use C. elegans for the genetic dissection of behavior,
this species has made important contributions to the study of
development, cell death, aging, and behavior.
Advantages of Caenorhabditis elegans as a model
genetic organism An ideal genetic organism, C. elegans is
small, easy to culture, and produces large numbers of offspring. The adult C. elegans is about 1 mm in length. Most
investigators grow C. elegans on agar-filled petri plates that
are covered with a lawn of bacteria, which the nematodes
devour. Thousands of worms can be easily cultured in a single laboratory. Compared with most multicellular animals,
they have a very short generation time, about 3 days at room
temperature. And they are prolific reproducers, with a single
female producing from 250 to 1000 fertilized eggs in 3 to
Another advantage of C. elegans, particularly for developmental studies, is that the worm is transparent, allowing
easy observation of internal development at all stages. It has
a simple body structure, with a small, invariant number of
somatic cells: 959 cells in a mature hermaphroditic female
and 1031 cells in a mature male.
Life cycle Most mature adults are hermaphrodites, with
the ability to produce both eggs and sperm and undergo selffertilization. A few are male, which produce only sperm and
mate with hermaphrodites. The hermaphrodites have two
sex chromosomes (XX); the males possess a single sex chromosome (XO). Thus, hermaphrodites that self-fertilize produce only females (with the exception of a few males that
result from nondisjunction of the X chromosomes). When
hermaphrodites mate with males, half of the progeny are XX
hermaphrodites and half are XO males.
Eggs are fertilized internally, either from sperm produced by the hermaphrodite or from sperm contributed by
a male (see Figure 10.25). The eggs are then laid, and development is completed externally. Approximately 14 hours
after fertilization, a larva hatches from the egg and goes
through four larval stages—termed L1, L2, L3, and L4—that
are separated by molts. The L4 larva undergoes a final molt
to produce the adult worm. Under normal laboratory conditions, worms will live for 2 to 3 weeks.
Genetic techniques Geneticists began developing plans
in 1989 to sequence the genome of C. elegans, and the complete genome sequence was obtained in 1998. Compared
with the genomes of most multicellular animals, that of
C. elegans, at 103 million base pairs of DNA, is small, which
The Nematode Worm
• Small size
• Short generation time of 3 days
• Each female can produce
• Easy to culture in laboratory
• Simple body plan
reproduces in soil
• Capable of self-fertilization or
Amount of DNA:
Number of genes:
Percentage of genes in
common with humans:
Average gene size:
5 pairs of autosomes
plus 2 X chromosomes
in females (hermaphrodites) or 1 X chromosome in males
103 million base pairs
5000 base pairs
CONTRIBUTIONS TO GENETICS
• Genetics of development
• Genetic control of behavior
• Apoptosis (programmed cell death)
10.25 The worm Caenorhabditis elegans is a model genetic organism. [Micrograph: courtesy of
William Goodyer and Monique Zetka.]
facilitates genomic analysis. The availability of the complete
genome sequence provides a great deal of information about
gene structure, function, and organization in this species.
Chemical mutagens are routinely used to generate
mutations in C. elegans, which are easy to identify and isolate. The ability of hermaphrodites to self-fertilize means
that progeny homozygous for recessive mutations can be
obtained in a single generation; the existence of males means
that genetic crosses can be carried out.
Developmental studies are facilitated by the transparent
body of the worms. As mentioned earlier, C. elegans has a
small and exact number of somatic cells. Researchers
studying the development of C. elegans have meticulously
mapped the entire cell lineage of the species, and so the
From DNA to Proteins: Transcription and RNA Processing
10.26 The developmental history of every cell in adult C. elegans has been determined.
Shown here are the divisions that lead to adult cells in C. elegans.
developmental fate of every cell in the adult body can be
traced back to the original single-celled fertilized egg (Figure
10.26). Developmental biologists often use lasers to destroy
(ablate) specific cells in a developing worm and then study
the effects on physiology, development, and behavior.
RNA interference has proved to be an effective tool for
turning off genes in C. elegans. Geneticists inject doublestranded copies of RNA that is complementary to specific
genes; the double-stranded RNA then silences the expression
of these genes through the RNAi process. The worms can
even be fed bacteria that have been genetically engineered to
express the double-stranded RNA, thus avoiding the difficulties of microinjection.
Transgenic worms can be produced by injecting DNA
into the ovary, where the DNA becomes incorporated into
the oocytes. Geneticists have created a special reporter gene
that produces the jellyfish green fluorescent protein (GFP).
When this reporter gene is injected into the ovary and
becomes inserted into the worm genome, its expression produces GFP, which fluoresces green, allowing the expression
of the gene to be easily observed (Figure 10.27).
10.27 A sequence for the green fluorescent protein (GFP)
has been used to visually determine the expression of genes
inserted into C. elegans (lower photograph). The gene for GFP is
injected into the ovary of a worm and becomes incorporated into the
worm genome. The expression of this transgene produces GFP, which
fluoresces green (upper photograph). [Huaqi Jiang, Rong Guo, and Jo
Anne Powell-Coffman, The Caenorhabditis elegans hif-1 gene encodes a
bHLH-PAS protein that is required for adaptation to hypoxia. PNAS
98:7916–7921, 2001. © 2001 National Academy of Sciences, U.S.A.]
• RNA is a polymer, consisting of nucleotides joined together by
phosphodiester bonds. Each RNA nucleotide consists of a
ribose sugar, a phosphate, and a base. RNA contains the base
uracil and is usually single stranded.
Cells possess a number of different classes of RNA. Ribosomal
RNA is a component of the ribosome, messenger RNA carries
coding instructions for proteins, and transfer RNA helps
incorporate the amino acids into a polypeptide chain.
The template for RNA synthesis is single-stranded DNA. In
transcription, RNA synthesis is complementary and antiparallel
to the DNA template strand. A transcription unit consists of a
promoter, an RNA-coding region, and a terminator.
• The substrates for RNA synthesis are ribonucleoside
RNA polymerase in bacterial cells consists of a core enzyme,
which catalyzes the addition of nucleotides to an RNA
molecule, and other subunits. The sigma factor controls the
binding of the core enzyme to the promoter. Eukaryotic cells
contain three different RNA polymerases.
Transcription begins at the start site, which is determined by
consensus sequences. RNA is synthesized from a single strand
of DNA as a template. RNA synthesis ceases after a terminator
sequence has been transcribed.
Introns—noncoding sequences that interrupt the coding
sequences (exons) of genes—are common in eukaryotic cells
but rare in bacterial cells.
An mRNA molecule has three primary parts: a 5Ј untranslated
region, a protein-coding sequence, and a 3Ј untranslated
• The pre-mRNA of a eukaryotic protein-encoding gene is
extensively processed: a modified nucleotide and methyl
groups, collectively termed the cap, are added to the 5Ј end of
pre-mRNA; the 3Ј end is cleaved and a poly(A) tail is added;
and introns are removed.
Transfer RNAs, which attach to amino acids, are short
molecules that assume a common secondary structure and
contain modified bases. Ribosomes, the sites of protein
synthesis, are composed of several ribosomal RNA molecules
and numerous proteins.
Small interfering RNAs and microRNAs are produced by
cleavage of double-stranded RNA and play important roles in
gene silencing and in a number of other phenonmena.
Caenorhabditis elegans is a nematode that is widely used as a
model genetic organism.
ribozyme (p. 243)
ribosomal RNA (rRNA) (p. 245)
messenger RNA (mRNA) (p. 245)
pre-messenger RNA (pre-mRNA) (p. 245)
transfer RNA (tRNA) (p. 245)
small nuclear RNA (snRNA) (p. 245)
small nuclear ribonucleoprotein (snRNP)
small nucleolar RNA (snoRNA) (p. 245)
microRNA (miRNA) (p. 245)
small interfering RNA (siRNA) (p. 245)
template strand (p. 247)
nontemplate strand (p. 247)
transcription unit (p. 247)
promoter (p. 247)
RNA-coding region (p. 247)
terminator (p. 247)
(rNTP) (p. 248)
RNA polymerase (p. 248)
core enzyme (p. 249)
sigma () factor (p. 249)
holoenzyme (p. 249)
RNA polymerase I (p. 249)
RNA polymerase II (p. 249)
RNA polymerase III (p. 249)
RNA polymerase IV (p. 249)
consensus sequence (p. 250)
–10 consensus sequence (Pribnow box)
–35 consensus sequence (p. 250)
rho-dependent terminator (p. 252)
rho factor (p. 252)
rho-independent terminator (p. 252)
polycistronic RNA (p. 252)
colinearity (p. 253)
exon (p. 254)
intron (p. 254)
codon (p. 255)
5Ј untranslated region (p. 255)
Shine–Dalgarno sequence (p. 255)
protein-coding region (p. 255)
3Ј untranslated region (p. 255)
5Ј cap (p. 256)
poly(A) tail (p. 256)
RNA splicing (p. 257)
5Ј splice site (p. 257)
3Ј splice site (p. 257)
branch point (p. 257)
spliceosome (p. 257)
lariat (p. 257)
alternative processing (p. 257)
alternative splicing (p. 257)
modified base (p. 260)
cloverleaf structure (p. 260)
anticodon (p. 260)
large ribosomal subunit (p. 260)
small ribosomal subunit (p. 260)
RNA interference (RNAi) (p. 261)
RNA-induced silencing complex (RISC)
hairpin (p. 262)
Answers to Concept Checks
2. The template strand is the DNA strand that is transcribed
into an RNA molecule, whereas the nontemplate strand is not
3. The sigma factor recognizes the promoter and controls the
binding of RNA polymerase to the promoter.
4. When DNA was hybridized to the mRNA transcribed from it,
regions of DNA that did not correspond to RNA looped out.