Chapter 15 | Genes and Proteins 389

15 | GENES AND
PROTEINS

Figure 15.1 Genes, which are carried on (a) chromosomes, are linearly organized instructions for making the RNA
and protein molecules that are necessary for all of processes of life. The (b) interleukin-2 protein and (c) alpha-2u-
globulin protein are just two examples of the array of different molecular structures that are encoded by genes. (credit
“chromosome: National Human Genome Research Institute; credit “interleukin-2”: Ramin Herati/Created from PDB
1M47 and rendered with Pymol; credit “alpha-2u-globulin”: Darren Logan/rendered with AISMIG)

Chapter Outline
15.1: The Genetic Code
15.2: Prokaryotic Transcription
15.3: Eukaryotic Transcription
15.4: RNA Processing in Eukaryotes
15.5: Ribosomes and Protein Synthesis

Introduction
Since the rediscovery of Mendel’s work in 1900, the definition of the gene has progressed from an abstract unit of heredity
to a tangible molecular entity capable of replication, expression, and mutation (Figure 15.1). Genes are composed of DNA
and are linearly arranged on chromosomes. Genes specify the sequences of amino acids, which are the building blocks of
proteins. In turn, proteins are responsible for orchestrating nearly every function of the cell. Both genes and the proteins
they encode are absolutely essential to life as we know it.

15.1 | The Genetic Code

By the end of this section, you will be able to:
• Explain the “central dogma” of protein synthesis
• Describe the genetic code and how the nucleotide sequence prescribes the amino acid and the protein sequence

The cellular process of transcription generates messenger RNA (mRNA), a mobile molecular copy of one or more
genes with an alphabet of A, C, G, and uracil (U). Translation of the mRNA template converts nucleotide-based genetic
information into a protein product. Protein sequences consist of 20 commonly occurring amino acids; therefore, it can be
said that the protein alphabet consists of 20 letters (Figure 15.2). Each amino acid is defined by a three-nucleotide sequence
390 Chapter 15 | Genes and Proteins

called the triplet codon. Different amino acids have different chemistries (such as acidic versus basic, or polar and nonpolar)
and different structural constraints. Variation in amino acid sequence gives rise to enormous variation in protein structure
and function.

Figure 15.2 Structures of the 20 amino acids found in proteins are shown. Each amino acid is composed of an amino
-
group ( NH+3 ), a carboxyl group (COO ), and a side chain (blue). The side chain may be nonpolar, polar, or charged,
as well as large or small. It is the variety of amino acid side chains that gives rise to the incredible variation of protein
structure and function.

The Central Dogma: DNA Encodes RNA; RNA Encodes Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the Central Dogma (Figure 15.3),
which states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins. The decoding of
one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central
to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis,
while keeping the DNA itself intact and protected. The copying of DNA to RNA is relatively straightforward, with one
nucleotide being added to the mRNA strand for every nucleotide read in the DNA strand. The translation to protein is a bit
more complex because three mRNA nucleotides correspond to one amino acid in the polypeptide sequence. However, the
translation to protein is still systematic and colinear, such that nucleotides 1 to 3 correspond to amino acid 1, nucleotides 4
to 6 correspond to amino acid 2, and so on.

This OpenStax book is available for free at http://cnx.org/content/col11448/1.10

Chapter 15 | Genes and Proteins 391

Figure 15.3 Instructions on DNA are transcribed onto messenger RNA. Ribosomes are able to read the genetic
information inscribed on a strand of messenger RNA and use this information to string amino acids together into a
protein.

The Genetic Code Is Degenerate and Universal

Given the different numbers of “letters” in the mRNA and protein “alphabets,” scientists theorized that combinations of
nucleotides corresponded to single amino acids. Nucleotide doublets would not be sufficient to specify every amino acid
because there are only 16 possible two-nucleotide combinations (42). In contrast, there are 64 possible nucleotide triplets
(43), which is far more than the number of amino acids. Scientists theorized that amino acids were encoded by nucleotide
triplets and that the genetic code was degenerate. In other words, a given amino acid could be encoded by more than one
nucleotide triplet. This was later confirmed experimentally; Francis Crick and Sydney Brenner used the chemical mutagen
proflavin to insert one, two, or three nucleotides into the gene of a virus. When one or two nucleotides were inserted, protein
synthesis was completely abolished. When three nucleotides were inserted, the protein was synthesized and functional. This
demonstrated that three nucleotides specify each amino acid. These nucleotide triplets are called codons. The insertion of
one or two nucleotides completely changed the triplet reading frame, thereby altering the message for every subsequent
amino acid (Figure 15.5). Though insertion of three nucleotides caused an extra amino acid to be inserted during translation,
the integrity of the rest of the protein was maintained.
Scientists painstakingly solved the genetic code by translating synthetic mRNAs in vitro and sequencing the proteins they
specified (Figure 15.4).
392 Chapter 15 | Genes and Proteins

Figure 15.4 This figure shows the genetic code for translating each nucleotide triplet in mRNA into an amino acid or a
termination signal in a nascent protein. (credit: modification of work by NIH)

In addition to instructing the addition of a specific amino acid to a polypeptide chain, three of the 64 codons terminate
protein synthesis and release the polypeptide from the translation machinery. These triplets are called nonsense codons, or
stop codons. Another codon, AUG, also has a special function. In addition to specifying the amino acid methionine, it also
serves as the start codon to initiate translation. The reading frame for translation is set by the AUG start codon near the 5'
end of the mRNA.
The genetic code is universal. With a few exceptions, virtually all species use the same genetic code for protein synthesis.
Conservation of codons means that a purified mRNA encoding the globin protein in horses could be transferred to a tulip
cell, and the tulip would synthesize horse globin. That there is only one genetic code is powerful evidence that all of life
on Earth shares a common origin, especially considering that there are about 1084 possible combinations of 20 amino acids
and 64 triplet codons.

Transcribe a gene and translate it to protein using complementary pairing and the genetic code at this site
(http://openstaxcollege.org/l/create_protein) .

Figure 15.5 The deletion of two nucleotides shifts the reading frame of an mRNA and changes the entire protein
message, creating a nonfunctional protein or terminating protein synthesis altogether.

Degeneracy is believed to be a cellular mechanism to reduce the negative impact of random mutations. Codons that specify
the same amino acid typically only differ by one nucleotide. In addition, amino acids with chemically similar side chains
are encoded by similar codons. This nuance of the genetic code ensures that a single-nucleotide substitution mutation might
either specify the same amino acid but have no effect or specify a similar amino acid, preventing the protein from being
rendered completely nonfunctional.

This OpenStax book is available for free at http://cnx.org/content/col11448/1.10

Chapter 15 | Genes and Proteins 393

Which Has More DNA: A Kiwi or a Strawberry?

Figure 15.6 Do you think that a kiwi or a strawberry has more DNA per fruit? (credit “kiwi”: "Kelbv"/Flickr; credit:
“strawberry”: Alisdair McDiarmid)

Question: Would a kiwifruit and strawberry that are approximately the same size (Figure 15.6) also have
approximately the same amount of DNA?
Background: Genes are carried on chromosomes and are made of DNA. All mammals are diploid, meaning
they have two copies of each chromosome. However, not all plants are diploid. The common strawberry is
octoploid (8n) and the cultivated kiwi is hexaploid (6n). Research the total number of chromosomes in the
cells of each of these fruits and think about how this might correspond to the amount of DNA in these fruits’
cell nuclei. Read about the technique of DNA isolation to understand how each step in the isolation protocol
helps liberate and precipitate DNA.
Hypothesis: Hypothesize whether you would be able to detect a difference in DNA quantity from similarly
sized strawberries and kiwis. Which fruit do you think would yield more DNA?
Test your hypothesis: Isolate the DNA from a strawberry and a kiwi that are similarly sized. Perform the
experiment in at least triplicate for each fruit.
1. Prepare a bottle of DNA extraction buffer from 900 mL water, 50 mL dish detergent, and two teaspoons
of table salt. Mix by inversion (cap it and turn it upside down a few times).
2. Grind a strawberry and a kiwifruit by hand in a plastic bag, or using a mortar and pestle, or with a metal
bowl and the end of a blunt instrument. Grind for at least two minutes per fruit.
3. Add 10 mL of the DNA extraction buffer to each fruit, and mix well for at least one minute.
4. Remove cellular debris by filtering each fruit mixture through cheesecloth or porous cloth and into a
funnel placed in a test tube or an appropriate container.
5. Pour ice-cold ethanol or isopropanol (rubbing alcohol) into the test tube. You should observe white,
precipitated DNA.
6. Gather the DNA from each fruit by winding it around separate glass rods.
Record your observations: Because you are not quantitatively measuring DNA volume, you can record for
each trial whether the two fruits produced the same or different amounts of DNA as observed by eye. If one
or the other fruit produced noticeably more DNA, record this as well. Determine whether your observations
are consistent with several pieces of each fruit.
Analyze your data: Did you notice an obvious difference in the amount of DNA produced by each fruit?
Were your results reproducible?
Draw a conclusion: Given what you know about the number of chromosomes in each fruit, can you
conclude that chromosome number necessarily correlates to DNA amount? Can you identify any drawbacks
to this procedure? If you had access to a laboratory, how could you standardize your comparison and make
it more quantitative?
394 Chapter 15 | Genes and Proteins

15.2 | Prokaryotic Transcription

By the end of this section, you will be able to:
• List the different steps in prokaryotic transcription
• Discuss the role of promoters in prokaryotic transcription
• Describe how and when transcription is terminated

The prokaryotes, which include bacteria and archaea, are mostly single-celled organisms that, by definition, lack membrane-
bound nuclei and other organelles. A bacterial chromosome is a covalently closed circle that, unlike eukaryotic
chromosomes, is not organized around histone proteins. The central region of the cell in which prokaryotic DNA resides is
called the nucleoid. In addition, prokaryotes often have abundant plasmids, which are shorter circular DNA molecules that
may only contain one or a few genes. Plasmids can be transferred independently of the bacterial chromosome during cell
division and often carry traits such as antibiotic resistance.
Transcription in prokaryotes (and in eukaryotes) requires the DNA double helix to partially unwind in the region of mRNA
synthesis. The region of unwinding is called a transcription bubble. Transcription always proceeds from the same DNA
strand for each gene, which is called the template strand. The mRNA product is complementary to the template strand and
is almost identical to the other DNA strand, called the nontemplate strand. The only difference is that in mRNA, all of the
T nucleotides are replaced with U nucleotides. In an RNA double helix, A can bind U via two hydrogen bonds, just as in
A–T pairing in a DNA double helix.
The nucleotide pair in the DNA double helix that corresponds to the site from which the first 5' mRNA nucleotide is
transcribed is called the +1 site, or the initiation site. Nucleotides preceding the initiation site are given negative numbers
and are designated upstream. Conversely, nucleotides following the initiation site are denoted with “+” numbering and are
called downstream nucleotides.

Initiation of Transcription in Prokaryotes

Prokaryotes do not have membrane-enclosed nuclei. Therefore, the processes of transcription, translation, and mRNA
degradation can all occur simultaneously. The intracellular level of a bacterial protein can quickly be amplified by multiple
transcription and translation events occurring concurrently on the same DNA template. Prokaryotic transcription often
covers more than one gene and produces polycistronic mRNAs that specify more than one protein.
Our discussion here will exemplify transcription by describing this process in Escherichia coli, a well-studied bacterial
species. Although some differences exist between transcription in E. coli and transcription in archaea, an understanding of
E. coli transcription can be applied to virtually all bacterial species.
Prokaryotic RNA Polymerase
Prokaryotes use the same RNA polymerase to transcribe all of their genes. In E. coli, the polymerase is composed of five
polypeptide subunits, two of which are identical. Four of these subunits, denoted α, α, β, and β' comprise the polymerase
core enzyme. These subunits assemble every time a gene is transcribed, and they disassemble once transcription is
complete. Each subunit has a unique role; the two α-subunits are necessary to assemble the polymerase on the DNA; the
β-subunit binds to the ribonucleoside triphosphate that will become part of the nascent “recently born” mRNA molecule;
and the β' binds the DNA template strand. The fifth subunit, σ, is involved only in transcription initiation. It confers
transcriptional specificity such that the polymerase begins to synthesize mRNA from an appropriate initiation site. Without
σ, the core enzyme would transcribe from random sites and would produce mRNA molecules that specified protein
gibberish. The polymerase comprised of all five subunits is called the holoenzyme.
Prokaryotic Promoters
A promoter is a DNA sequence onto which the transcription machinery binds and initiates transcription. In most cases,
promoters exist upstream of the genes they regulate. The specific sequence of a promoter is very important because
it determines whether the corresponding gene is transcribed all the time, some of the time, or infrequently. Although
promoters vary among prokaryotic genomes, a few elements are conserved. At the -10 and -35 regions upstream of the
initiation site, there are two promoter consensus sequences, or regions that are similar across all promoters and across
various bacterial species (Figure 15.7). The -10 consensus sequence, called the -10 region, is TATAAT. The -35 sequence,
TTGACA, is recognized and bound by σ. Once this interaction is made, the subunits of the core enzyme bind to the site.
The A–T-rich -10 region facilitates unwinding of the DNA template, and several phosphodiester bonds are made. The

This OpenStax book is available for free at http://cnx.org/content/col11448/1.10

Chapter 15 | Genes and Proteins 395

transcription initiation phase ends with the production of abortive transcripts, which are polymers of approximately 10
nucleotides that are made and released.

Figure 15.7 The σ subunit of prokaryotic RNA polymerase recognizes consensus sequences found in the promoter
region upstream of the transcription start sight. The σ subunit dissociates from the polymerase after transcription has
been initiated.

View this MolecularMovies animation (http://openstaxcollege.org/l/transcription) to see the first part of transcription
and the base sequence repetition of the TATA box.

Elongation and Termination in Prokaryotes

The transcription elongation phase begins with the release of the σ subunit from the polymerase. The dissociation of σ allows
the core enzyme to proceed along the DNA template, synthesizing mRNA in the 5' to 3' direction at a rate of approximately
40 nucleotides per second. As elongation proceeds, the DNA is continuously unwound ahead of the core enzyme and
rewound behind it (Figure 15.8). The base pairing between DNA and RNA is not stable enough to maintain the stability of
the mRNA synthesis components. Instead, the RNA polymerase acts as a stable linker between the DNA template and the
nascent RNA strands to ensure that elongation is not interrupted prematurely.
396 Chapter 15 | Genes and Proteins

Figure 15.8 During elongation, the prokaryotic RNA polymerase tracks along the DNA template, synthesizes mRNA in
the 5' to 3' direction, and unwinds and rewinds the DNA as it is read.

Prokaryotic Termination Signals

Once a gene is transcribed, the prokaryotic polymerase needs to be instructed to dissociate from the DNA template and
liberate the newly made mRNA. Depending on the gene being transcribed, there are two kinds of termination signals. One
is protein-based and the other is RNA-based. Rho-dependent termination is controlled by the rho protein, which tracks

This OpenStax book is available for free at http://cnx.org/content/col11448/1.10

Chapter 15 | Genes and Proteins 397

along behind the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase encounters a run of
G nucleotides on the DNA template and it stalls. As a result, the rho protein collides with the polymerase. The interaction
with rho releases the mRNA from the transcription bubble.
Rho-independent termination is controlled by specific sequences in the DNA template strand. As the polymerase nears
the end of the gene being transcribed, it encounters a region rich in C–G nucleotides. The mRNA folds back on itself, and
the complementary C–G nucleotides bind together. The result is a stable hairpin that causes the polymerase to stall as soon
as it begins to transcribe a region rich in A–T nucleotides. The complementary U–A region of the mRNA transcript forms
only a weak interaction with the template DNA. This, coupled with the stalled polymerase, induces enough instability for
the core enzyme to break away and liberate the new mRNA transcript.
Upon termination, the process of transcription is complete. By the time termination occurs, the prokaryotic transcript would
already have been used to begin synthesis of numerous copies of the encoded protein because these processes can occur
concurrently. The unification of transcription, translation, and even mRNA degradation is possible because all of these
processes occur in the same 5' to 3' direction, and because there is no membranous compartmentalization in the prokaryotic
cell (Figure 15.9). In contrast, the presence of a nucleus in eukaryotic cells precludes simultaneous transcription and
translation.

Figure 15.9 Multiple polymerases can transcribe a single bacterial gene while numerous ribosomes concurrently
translate the mRNA transcripts into polypeptides. In this way, a specific protein can rapidly reach a high concentration
in the bacterial cell.

Visit this BioStudio animation (http://openstaxcollege.org/l/transcription2) to see the process of prokaryotic

transcription.

15.3 | Eukaryotic Transcription

By the end of this section, you will be able to:
• List the steps in eukaryotic transcription
• Discuss the role of RNA polymerases in transcription
• Compare and contrast the three RNA polymerases
• Explain the significance of transcription factors

Prokaryotes and eukaryotes perform fundamentally the same process of transcription, with a few key differences. The most
important difference between prokaryotes and eukaryotes is the latter’s membrane-bound nucleus and organelles. With the
genes bound in a nucleus, the eukaryotic cell must be able to transport its mRNA to the cytoplasm and must protect its
mRNA from degrading before it is translated. Eukaryotes also employ three different polymerases that each transcribe a
different subset of genes. Eukaryotic mRNAs are usually monogenic, meaning that they specify a single protein.
398 Chapter 15 | Genes and Proteins

Initiation of Transcription in Eukaryotes

Unlike the prokaryotic polymerase that can bind to a DNA template on its own, eukaryotes require several other proteins,
called transcription factors, to first bind to the promoter region and then help recruit the appropriate polymerase.
The Three Eukaryotic RNA Polymerases
The features of eukaryotic mRNA synthesis are markedly more complex those of prokaryotes. Instead of a single
polymerase comprising five subunits, the eukaryotes have three polymerases that are each made up of 10 subunits or more.
Each eukaryotic polymerase also requires a distinct set of transcription factors to bring it to the DNA template.
RNA polymerase I is located in the nucleolus, a specialized nuclear substructure in which ribosomal RNA (rRNA) is
transcribed, processed, and assembled into ribosomes (Table 15.1). The rRNA molecules are considered structural RNAs
because they have a cellular role but are not translated into protein. The rRNAs are components of the ribosome and are
essential to the process of translation. RNA polymerase I synthesizes all of the rRNAs except for the 5S rRNA molecule.
The “S” designation applies to “Svedberg” units, a nonadditive value that characterizes the speed at which a particle
sediments during centrifugation.

Locations, Products, and Sensitivities of the Three Eukaryotic RNA Polymerases

RNA Cellular α-Amanitin
Product of Transcription
Polymerase Compartment Sensitivity
I Nucleolus All rRNAs except 5S rRNA Insensitive
All protein-coding nuclear pre-
II Nucleus Extremely sensitive
mRNAs
5S rRNA, tRNAs, and small nuclear
III Nucleus Moderately sensitive
RNAs

Table 15.1

RNA polymerase II is located in the nucleus and synthesizes all protein-coding nuclear pre-mRNAs. Eukaryotic pre-
mRNAs undergo extensive processing after transcription but before translation. For clarity, this module’s discussion of
transcription and translation in eukaryotes will use the term “mRNAs” to describe only the mature, processed molecules
that are ready to be translated. RNA polymerase II is responsible for transcribing the overwhelming majority of eukaryotic
genes.
RNA polymerase III is also located in the nucleus. This polymerase transcribes a variety of structural RNAs that includes the
5S pre-rRNA, transfer pre-RNAs (pre-tRNAs), and small nuclear pre- RNAs. The tRNAs have a critical role in translation;
they serve as the adaptor molecules between the mRNA template and the growing polypeptide chain. Small nuclear RNAs
have a variety of functions, including “splicing” pre-mRNAs and regulating transcription factors.
A scientist characterizing a new gene can determine which polymerase transcribes it by testing whether the gene is
expressed in the presence of a particular mushroom poison, α-amanitin (Table 15.1). Interestingly, α-amanitin produced
by Amanita phalloides, the Death Cap mushroom, affects the three polymerases very differently. RNA polymerase I is
completely insensitive to α-amanitin, meaning that the polymerase can transcribe DNA in vitro in the presence of this
poison. In contrast, RNA polymerase II is extremely sensitive to α-amanitin, and RNA polymerase III is moderately
sensitive. Knowing the transcribing polymerase can clue a researcher into the general function of the gene being studied.
Because RNA polymerase II transcribes the vast majority of genes, we will focus on this polymerase in our subsequent
discussions about eukaryotic transcription factors and promoters.
Structure of an RNA Polymerase II Promoter
Eukaryotic promoters are much larger and more complex than prokaryotic promoters, but both have a TATA box. For
example, in the mouse thymidine kinase gene, the TATA box is located at approximately -30 relative to the initiation (+1)
site (Figure 15.10). For this gene, the exact TATA box sequence is TATAAAA, as read in the 5' to 3' direction on the
nontemplate strand. This sequence is not identical to the E. coli TATA box, but it conserves the A–T rich element. The
thermostability of A–T bonds is low and this helps the DNA template to locally unwind in preparation for transcription.

This OpenStax book is available for free at http://cnx.org/content/col11448/1.10

Chapter 15 | Genes and Proteins 399

Figure 15.10 A generalized promoter of a gene transcribed by RNA polymerase II is shown. Transcription factors
recognize the promoter. RNA polymerase II then binds and forms the transcription initiation complex.

Figure 15.11 Eukaryotic mRNA contains introns that must be spliced out. A 5' cap and 3' poly-A tail are also
added.

A scientist splices a eukaryotic promoter in front of a bacterial gene and inserts the gene in a bacterial
chromosome. Would you expect the bacteria to transcribe the gene?

The mouse genome includes one gene and two pseudogenes for cytoplasmic thymidine kinase. Pseudogenes are genes that
have lost their protein-coding ability or are no longer expressed by the cell. These pseudogenes are copied from mRNA and
incorporated into the chromosome. For example, the mouse thymidine kinase promoter also has a conserved CAAT box
(GGCCAATCT) at approximately -80. This sequence is essential and is involved in binding transcription factors. Further
upstream of the TATA box, eukaryotic promoters may also contain one or more GC-rich boxes (GGCG) or octamer boxes
(ATTTGCAT). These elements bind cellular factors that increase the efficiency of transcription initiation and are often
identified in more “active” genes that are constantly being expressed by the cell.
400 Chapter 15 | Genes and Proteins

Transcription Factors for RNA Polymerase II

The complexity of eukaryotic transcription does not end with the polymerases and promoters. An army of basal transcription
factors, enhancers, and silencers also help to regulate the frequency with which pre-mRNA is synthesized from a gene.
Enhancers and silencers affect the efficiency of transcription but are not necessary for transcription to proceed. Basal
transcription factors are crucial in the formation of a preinitiation complex on the DNA template that subsequently recruits
RNA polymerase II for transcription initiation.
The names of the basal transcription factors begin with “TFII” (this is the transcription factor for RNA polymerase II) and
are specified with the letters A–J. The transcription factors systematically fall into place on the DNA template, with each
one further stabilizing the preinitiation complex and contributing to the recruitment of RNA polymerase II.
The processes of bringing RNA polymerases I and III to the DNA template involve slightly less complex collections of
transcription factors, but the general theme is the same. Eukaryotic transcription is a tightly regulated process that requires a
variety of proteins to interact with each other and with the DNA strand. Although the process of transcription in eukaryotes
involves a greater metabolic investment than in prokaryotes, it ensures that the cell transcribes precisely the pre-mRNAs
that it needs for protein synthesis.

The Evolution of Promoters

The evolution of genes may be a familiar concept. Mutations can occur in genes during DNA replication, and
the result may or may not be beneficial to the cell. By altering an enzyme, structural protein, or some other
factor, the process of mutation can transform functions or physical features. However, eukaryotic promoters
and other gene regulatory sequences may evolve as well. For instance, consider a gene that, over many
generations, becomes more valuable to the cell. Maybe the gene encodes a structural protein that the cell
needs to synthesize in abundance for a certain function. If this is the case, it would be beneficial to the cell
for that gene’s promoter to recruit transcription factors more efficiently and increase gene expression.
Scientists examining the evolution of promoter sequences have reported varying results. In part, this is
because it is difficult to infer exactly where a eukaryotic promoter begins and ends. Some promoters occur
within genes; others are located very far upstream, or even downstream, of the genes they are regulating.
However, when researchers limited their examination to human core promoter sequences that were defined
experimentally as sequences that bind the preinitiation complex, they found that promoters evolve even
faster than protein-coding genes.
It is still unclear how promoter evolution might correspond to the evolution of humans or other higher
organisms. However, the evolution of a promoter to effectively make more or less of a given gene product
[1]
is an intriguing alternative to the evolution of the genes themselves.

Promoter Structures for RNA Polymerases I and III

In eukaryotes, the conserved promoter elements differ for genes transcribed by RNA polymerases I, II, and III. RNA
polymerase I transcribes genes that have two GC-rich promoter sequences in the -45 to +20 region. These sequences alone
are sufficient for transcription initiation to occur, but promoters with additional sequences in the region from -180 to -105
upstream of the initiation site will further enhance initiation. Genes that are transcribed by RNA polymerase III have
upstream promoters or promoters that occur within the genes themselves.

Eukaryotic Elongation and Termination

Following the formation of the preinitiation complex, the polymerase is released from the other transcription factors, and
elongation is allowed to proceed as it does in prokaryotes with the polymerase synthesizing pre-mRNA in the 5' to 3'
direction. As discussed previously, RNA polymerase II transcribes the major share of eukaryotic genes, so this section will
focus on how this polymerase accomplishes elongation and termination.
Although the enzymatic process of elongation is essentially the same in eukaryotes and prokaryotes, the DNA template
is more complex. When eukaryotic cells are not dividing, their genes exist as a diffuse mass of DNA and proteins
called chromatin. The DNA is tightly packaged around charged histone proteins at repeated intervals. These DNA–histone

1. H Liang et al., “Fast evolution of core promoters in primate genomes,” Molecular Biology and Evolution 25 (2008): 1239–44.

This OpenStax book is available for free at http://cnx.org/content/col11448/1.10

Chapter 15 | Genes and Proteins 401

complexes, collectively called nucleosomes, are regularly spaced and include 146 nucleotides of DNA wound around eight
histones like thread around a spool.
For polynucleotide synthesis to occur, the transcription machinery needs to move histones out of the way every time it
encounters a nucleosome. This is accomplished by a special protein complex called FACT, which stands for “facilitates
chromatin transcription.” This complex pulls histones away from the DNA template as the polymerase moves along it. Once
the pre-mRNA is synthesized, the FACT complex replaces the histones to recreate the nucleosomes.
The termination of transcription is different for the different polymerases. Unlike in prokaryotes, elongation by RNA
polymerase II in eukaryotes takes place 1,000–2,000 nucleotides beyond the end of the gene being transcribed. This pre-
mRNA tail is subsequently removed by cleavage during mRNA processing. On the other hand, RNA polymerases I and
III require termination signals. Genes transcribed by RNA polymerase I contain a specific 18-nucleotide sequence that is
recognized by a termination protein. The process of termination in RNA polymerase III involves an mRNA hairpin similar
to rho-independent termination of transcription in prokaryotes.

15.4 | RNA Processing in Eukaryotes

By the end of this section, you will be able to:
• Describe the different steps in RNA processing
• Understand the significance of exons, introns, and splicing
• Explain how tRNAs and rRNAs are processed

After transcription, eukaryotic pre-mRNAs must undergo several processing steps before they can be translated. Eukaryotic
(and prokaryotic) tRNAs and rRNAs also undergo processing before they can function as components in the protein
synthesis machinery.

mRNA Processing
The eukaryotic pre-mRNA undergoes extensive processing before it is ready to be translated. The additional steps involved
in eukaryotic mRNA maturation create a molecule with a much longer half-life than a prokaryotic mRNA. Eukaryotic
mRNAs last for several hours, whereas the typical E. coli mRNA lasts no more than five seconds.
Pre-mRNAs are first coated in RNA-stabilizing proteins; these protect the pre-mRNA from degradation while it is processed
and exported out of the nucleus. The three most important steps of pre-mRNA processing are the addition of stabilizing
and signaling factors at the 5' and 3' ends of the molecule, and the removal of intervening sequences that do not specify the
appropriate amino acids. In rare cases, the mRNA transcript can be “edited” after it is transcribed.
402 Chapter 15 | Genes and Proteins

RNA Editing in Trypanosomes

The trypanosomes are a group of protozoa that include the pathogen Trypanosoma brucei, which causes
sleeping sickness in humans (Figure 15.12). Trypanosomes, and virtually all other eukaryotes, have
organelles called mitochondria that supply the cell with chemical energy. Mitochondria are organelles that
express their own DNA and are believed to be the remnants of a symbiotic relationship between a eukaryote
and an engulfed prokaryote. The mitochondrial DNA of trypanosomes exhibit an interesting exception to
The Central Dogma: their pre-mRNAs do not have the correct information to specify a functional protein.
Usually, this is because the mRNA is missing several U nucleotides. The cell performs an additional RNA
processing step called RNA editing to remedy this.

Figure 15.12 Trypanosoma brucei is the causative agent of sleeping sickness in humans. The mRNAs of this
pathogen must be modified by the addition of nucleotides before protein synthesis can occur. (credit: modification
of work by Torsten Ochsenreiter)

Other genes in the mitochondrial genome encode 40- to 80-nucleotide guide RNAs. One or more of
these molecules interacts by complementary base pairing with some of the nucleotides in the pre-mRNA
transcript. However, the guide RNA has more A nucleotides than the pre-mRNA has U nucleotides to bind
with. In these regions, the guide RNA loops out. The 3' ends of guide RNAs have a long poly-U tail, and
these U bases are inserted in regions of the pre-mRNA transcript at which the guide RNAs are looped. This
process is entirely mediated by RNA molecules. That is, guide RNAs—rather than proteins—serve as the
catalysts in RNA editing.
RNA editing is not just a phenomenon of trypanosomes. In the mitochondria of some plants, almost all
pre-mRNAs are edited. RNA editing has also been identified in mammals such as rats, rabbits, and even
humans. What could be the evolutionary reason for this additional step in pre-mRNA processing? One
possibility is that the mitochondria, being remnants of ancient prokaryotes, have an equally ancient RNA-
based method for regulating gene expression. In support of this hypothesis, edits made to pre-mRNAs differ
depending on cellular conditions. Although speculative, the process of RNA editing may be a holdover from
a primordial time when RNA molecules, instead of proteins, were responsible for catalyzing reactions.

5' Capping
While the pre-mRNA is still being synthesized, a 7-methylguanosine cap is added to the 5' end of the growing transcript
by a phosphate linkage. This moiety (functional group) protects the nascent mRNA from degradation. In addition, factors
involved in protein synthesis recognize the cap to help initiate translation by ribosomes.

This OpenStax book is available for free at http://cnx.org/content/col11448/1.10

Chapter 15 | Genes and Proteins 403

3' Poly-A Tail

Once elongation is complete, the pre-mRNA is cleaved by an endonuclease between an AAUAAA consensus sequence and
a GU-rich sequence, leaving the AAUAAA sequence on the pre-mRNA. An enzyme called poly-A polymerase then adds
a string of approximately 200 A residues, called the poly-A tail. This modification further protects the pre-mRNA from
degradation and signals the export of the cellular factors that the transcript needs to the cytoplasm.
Pre-mRNA Splicing
Eukaryotic genes are composed of exons, which correspond to protein-coding sequences (ex-on signifies that they are
expressed), and intervening sequences called introns (int-ron denotes their intervening role), which may be involved in gene
regulation but are removed from the pre-mRNA during processing. Intron sequences in mRNA do not encode functional
proteins.
The discovery of introns came as a surprise to researchers in the 1970s who expected that pre-mRNAs would specify protein
sequences without further processing, as they had observed in prokaryotes. The genes of higher eukaryotes very often
contain one or more introns. These regions may correspond to regulatory sequences; however, the biological significance of
having many introns or having very long introns in a gene is unclear. It is possible that introns slow down gene expression
because it takes longer to transcribe pre-mRNAs with lots of introns. Alternatively, introns may be nonfunctional sequence
remnants left over from the fusion of ancient genes throughout evolution. This is supported by the fact that separate exons
often encode separate protein subunits or domains. For the most part, the sequences of introns can be mutated without
ultimately affecting the protein product.
All of a pre-mRNA’s introns must be completely and precisely removed before protein synthesis. If the process errs by even
a single nucleotide, the reading frame of the rejoined exons would shift, and the resulting protein would be dysfunctional.
The process of removing introns and reconnecting exons is called splicing (Figure 15.13). Introns are removed and
degraded while the pre-mRNA is still in the nucleus. Splicing occurs by a sequence-specific mechanism that ensures introns
will be removed and exons rejoined with the accuracy and precision of a single nucleotide. The splicing of pre-mRNAs is
conducted by complexes of proteins and RNA molecules called spliceosomes.

Figure 15.13 Pre-mRNA splicing involves the precise removal of introns from the primary RNA transcript. The
splicing process is catalyzed by protein complexes called spliceosomes that are composed of proteins and RNA
molecules called snRNAs. Spliceosomes recognize sequences at the 5' and 3' end of the intron.

Errors in splicing are implicated in cancers and other human diseases. What kinds of mutations might lead
to splicing errors? Think of different possible outcomes if splicing errors occur.
404 Chapter 15 | Genes and Proteins

Note that more than 70 individual introns can be present, and each has to undergo the process of splicing—in addition to 5'
capping and the addition of a poly-A tail—just to generate a single, translatable mRNA molecule.

See how introns are removed during RNA splicing at this website (http://openstaxcollege.org/l/RNA_splicing) .

Processing of tRNAs and rRNAs

The tRNAs and rRNAs are structural molecules that have roles in protein synthesis; however, these RNAs are not
themselves translated. Pre-rRNAs are transcribed, processed, and assembled into ribosomes in the nucleolus. Pre-tRNAs
are transcribed and processed in the nucleus and then released into the cytoplasm where they are linked to free amino acids
for protein synthesis.
Most of the tRNAs and rRNAs in eukaryotes and prokaryotes are first transcribed as a long precursor molecule that spans
multiple rRNAs or tRNAs. Enzymes then cleave the precursors into subunits corresponding to each structural RNA. Some
of the bases of pre-rRNAs are methylated; that is, a –CH3 moiety (methyl functional group) is added for stability. Pre-
tRNA molecules also undergo methylation. As with pre-mRNAs, subunit excision occurs in eukaryotic pre-RNAs destined
to become tRNAs or rRNAs.
Mature rRNAs make up approximately 50 percent of each ribosome. Some of a ribosome’s RNA molecules are purely
structural, whereas others have catalytic or binding activities. Mature tRNAs take on a three-dimensional structure through
intramolecular hydrogen bonding to position the amino acid binding site at one end and the anticodon at the other end
(Figure 15.14). The anticodon is a three-nucleotide sequence in a tRNA that interacts with an mRNA codon through
complementary base pairing.

This OpenStax book is available for free at http://cnx.org/content/col11448/1.10

Chapter 15 | Genes and Proteins 405

Figure 15.14 This is a space-filling model of a tRNA molecule that adds the amino acid phenylalanine to a growing
polypeptide chain. The anticodon AAG binds the Codon UUC on the mRNA. The amino acid phenylalanine is attached
to the other end of the tRNA.

15.5 | Ribosomes and Protein Synthesis

By the end of this section, you will be able to:
• Describe the different steps in protein synthesis
• Discuss the role of ribosomes in protein synthesis

The synthesis of proteins consumes more of a cell’s energy than any other metabolic process. In turn, proteins account
for more mass than any other component of living organisms (with the exception of water), and proteins perform virtually
every function of a cell. The process of translation, or protein synthesis, involves the decoding of an mRNA message into
a polypeptide product. Amino acids are covalently strung together by interlinking peptide bonds in lengths ranging from
approximately 50 amino acid residues to more than 1,000. Each individual amino acid has an amino group (NH2) and a
carboxyl (COOH) group. Polypeptides are formed when the amino group of one amino acid forms an amide (i.e., peptide)
bond with the carboxyl group of another amino acid (Figure 15.15). This reaction is catalyzed by ribosomes and generates
one water molecule.
406 Chapter 15 | Genes and Proteins

Figure 15.15 A peptide bond links the carboxyl end of one amino acid with the amino end of another, expelling one
water molecule. For simplicity in this image, only the functional groups involved in the peptide bond are shown. The R
and R' designations refer to the rest of each amino acid structure.

The Protein Synthesis Machinery

In addition to the mRNA template, many molecules and macromolecules contribute to the process of translation. The
composition of each component may vary across species; for instance, ribosomes may consist of different numbers of
rRNAs and polypeptides depending on the organism. However, the general structures and functions of the protein synthesis
machinery are comparable from bacteria to human cells. Translation requires the input of an mRNA template, ribosomes,
tRNAs, and various enzymatic factors.

Click through the steps of this PBS interactive (http://openstaxcollege.org/l/prokary_protein) to see protein synthesis
in action.

Ribosomes
Even before an mRNA is translated, a cell must invest energy to build each of its ribosomes. In E. coli, there are between
10,000 and 70,000 ribosomes present in each cell at any given time. A ribosome is a complex macromolecule composed of
structural and catalytic rRNAs, and many distinct polypeptides. In eukaryotes, the nucleolus is completely specialized for
the synthesis and assembly of rRNAs.
Ribosomes exist in the cytoplasm in prokaryotes and in the cytoplasm and rough endoplasmic reticulum in eukaryotes.
Mitochondria and chloroplasts also have their own ribosomes in the matrix and stroma, which look more similar to
prokaryotic ribosomes (and have similar drug sensitivities) than the ribosomes just outside their outer membranes in the
cytoplasm. Ribosomes dissociate into large and small subunits when they are not synthesizing proteins and reassociate
during the initiation of translation. In E. coli, the small subunit is described as 30S, and the large subunit is 50S, for a total of
70S (recall that Svedberg units are not additive). Mammalian ribosomes have a small 40S subunit and a large 60S subunit,
for a total of 80S. The small subunit is responsible for binding the mRNA template, whereas the large subunit sequentially
binds tRNAs. Each mRNA molecule is simultaneously translated by many ribosomes, all synthesizing protein in the same
direction: reading the mRNA from 5' to 3' and synthesizing the polypeptide from the N terminus to the C terminus. The
complete mRNA/poly-ribosome structure is called a polysome.
tRNAs
The tRNAs are structural RNA molecules that were transcribed from genes by RNA polymerase III. Depending on the
species, 40 to 60 types of tRNAs exist in the cytoplasm. Serving as adaptors, specific tRNAs bind to sequences on the
mRNA template and add the corresponding amino acid to the polypeptide chain. Therefore, tRNAs are the molecules that
actually “translate” the language of RNA into the language of proteins.

This OpenStax book is available for free at http://cnx.org/content/col11448/1.10

Chapter 15 | Genes and Proteins 407

Of the 64 possible mRNA codons—or triplet combinations of A, U, G, and C—three specify the termination of protein
synthesis and 61 specify the addition of amino acids to the polypeptide chain. Of these 61, one codon (AUG) also encodes
the initiation of translation. Each tRNA anticodon can base pair with one of the mRNA codons and add an amino acid or
terminate translation, according to the genetic code. For instance, if the sequence CUA occurred on an mRNA template in
the proper reading frame, it would bind a tRNA expressing the complementary sequence, GAU, which would be linked to
the amino acid leucine.
As the adaptor molecules of translation, it is surprising that tRNAs can fit so much specificity into such a small package.
Consider that tRNAs need to interact with three factors: 1) they must be recognized by the correct aminoacyl synthetase
(see below); 2) they must be recognized by ribosomes; and 3) they must bind to the correct sequence in mRNA.
Aminoacyl tRNA Synthetases
The process of pre-tRNA synthesis by RNA polymerase III only creates the RNA portion of the adaptor molecule. The
corresponding amino acid must be added later, once the tRNA is processed and exported to the cytoplasm. Through
the process of tRNA “charging,” each tRNA molecule is linked to its correct amino acid by a group of enzymes called
aminoacyl tRNA synthetases. At least one type of aminoacyl tRNA synthetase exists for each of the 20 amino acids; the
exact number of aminoacyl tRNA synthetases varies by species. These enzymes first bind and hydrolyze ATP to catalyze a
high-energy bond between an amino acid and adenosine monophosphate (AMP); a pyrophosphate molecule is expelled in
this reaction. The activated amino acid is then transferred to the tRNA, and AMP is released.

The Mechanism of Protein Synthesis

As with mRNA synthesis, protein synthesis can be divided into three phases: initiation, elongation, and termination. The
process of translation is similar in prokaryotes and eukaryotes. Here we’ll explore how translation occurs in E. coli, a
representative prokaryote, and specify any differences between prokaryotic and eukaryotic translation.
Initiation of Translation
Protein synthesis begins with the formation of an initiation complex. In E. coli, this complex involves the small 30S
ribosome, the mRNA template, three initiation factors (IFs; IF-1, IF-2, and IF-3), and a special initiator tRNA, called
tRNA Met
f . The initiator tRNA interacts with the start codon AUG (or rarely, GUG), links to a formylated methionine

called fMet, and can also bind IF-2. Formylated methionine is inserted by fMet − tRNA Met
f at the beginning of every
polypeptide chain synthesized by E. coli, but it is usually clipped off after translation is complete. When an in-frame AUG
is encountered during translation elongation, a non-formylated methionine is inserted by a regular Met-tRNA Met.
In E. coli mRNA, a sequence upstream of the first AUG codon, called the Shine-Dalgarno sequence (AGGAGG), interacts
with the rRNA molecules that compose the ribosome. This interaction anchors the 30S ribosomal subunit at the correct
location on the mRNA template. Guanosine triphosphate (GTP), which is a purine nucleotide triphosphate, acts as an energy
source during translation—both at the start of elongation and during the ribosome’s translocation.
In eukaryotes, a similar initiation complex forms, comprising mRNA, the 40S small ribosomal subunit, IFs, and nucleoside
triphosphates (GTP and ATP). The charged initiator tRNA, called Met-tRNAi, does not bind fMet in eukaryotes, but is
distinct from other Met-tRNAs in that it can bind IFs.
Instead of depositing at the Shine-Dalgarno sequence, the eukaryotic initiation complex recognizes the 7-methylguanosine
cap at the 5' end of the mRNA. A cap-binding protein (CBP) and several other IFs assist the movement of the ribosome
to the 5' cap. Once at the cap, the initiation complex tracks along the mRNA in the 5' to 3' direction, searching for the
AUG start codon. Many eukaryotic mRNAs are translated from the first AUG, but this is not always the case. According
to Kozak’s rules, the nucleotides around the AUG indicate whether it is the correct start codon. Kozak’s rules state that the
following consensus sequence must appear around the AUG of vertebrate genes: 5'-gccRccAUGG-3'. The R (for purine)
indicates a site that can be either A or G, but cannot be C or U. Essentially, the closer the sequence is to this consensus, the
higher the efficiency of translation.
Once the appropriate AUG is identified, the other proteins and CBP dissociate, and the 60S subunit binds to the complex of
Met-tRNAi, mRNA, and the 40S subunit. This step completes the initiation of translation in eukaryotes.
Translation, Elongation, and Termination
In prokaryotes and eukaryotes, the basics of elongation are the same, so we will review elongation from the perspective
of E. coli. The 50S ribosomal subunit of E. coli consists of three compartments: the A (aminoacyl) site binds incoming
charged aminoacyl tRNAs. The P (peptidyl) site binds charged tRNAs carrying amino acids that have formed peptide bonds
with the growing polypeptide chain but have not yet dissociated from their corresponding tRNA. The E (exit) site releases
dissociated tRNAs so that they can be recharged with free amino acids. There is one exception to this assembly line of
408 Chapter 15 | Genes and Proteins

tRNAs: in E. coli, fMet − tRNA Met

f is capable of entering the P site directly without first entering the A site. Similarly,
the eukaryotic Met-tRNAi, with help from other proteins of the initiation complex, binds directly to the P site. In both cases,
this creates an initiation complex with a free A site ready to accept the tRNA corresponding to the first codon after the
AUG.
During translation elongation, the mRNA template provides specificity. As the ribosome moves along the mRNA, each
mRNA codon comes into register, and specific binding with the corresponding charged tRNA anticodon is ensured. If
mRNA were not present in the elongation complex, the ribosome would bind tRNAs nonspecifically.
Elongation proceeds with charged tRNAs entering the A site and then shifting to the P site followed by the E site with each
single-codon “step” of the ribosome. Ribosomal steps are induced by conformational changes that advance the ribosome by
three bases in the 3' direction. The energy for each step of the ribosome is donated by an elongation factor that hydrolyzes
GTP. Peptide bonds form between the amino group of the amino acid attached to the A-site tRNA and the carboxyl group
of the amino acid attached to the P-site tRNA. The formation of each peptide bond is catalyzed by peptidyl transferase,
an RNA-based enzyme that is integrated into the 50S ribosomal subunit. The energy for each peptide bond formation is
derived from GTP hydrolysis, which is catalyzed by a separate elongation factor. The amino acid bound to the P-site tRNA
is also linked to the growing polypeptide chain. As the ribosome steps across the mRNA, the former P-site tRNA enters the
E site, detaches from the amino acid, and is expelled (Figure 15.16). Amazingly, the E. coli translation apparatus takes only
0.05 seconds to add each amino acid, meaning that a 200-amino acid protein can be translated in just 10 seconds.

This OpenStax book is available for free at http://cnx.org/content/col11448/1.10

Chapter 15 | Genes and Proteins 409

Figure 15.16 Translation begins when an initiator tRNA anticodon recognizes a codon on mRNA. The large
ribosomal subunit joins the small subunit, and a second tRNA is recruited. As the mRNA moves relative to the
ribosome, the polypeptide chain is formed. Entry of a release factor into the A site terminates translation and the
components dissociate.

Many antibiotics inhibit bacterial protein synthesis. For example, tetracycline blocks the A site on the
bacterial ribosome, and chloramphenicol blocks peptidyl transfer. What specific effect would you expect
each of these antibiotics to have on protein synthesis?
Tetracycline would directly affect:
a. tRNA binding to the ribosome
b. ribosome assembly
c. growth of the protein chain
Chloramphenicol would directly affect
a. tRNA binding to the ribosome
b. ribosome assembly
c. growth of the protein chain

Termination of translation occurs when a nonsense codon (UAA, UAG, or UGA) is encountered. Upon aligning with
the A site, these nonsense codons are recognized by release factors in prokaryotes and eukaryotes that instruct peptidyl
transferase to add a water molecule to the carboxyl end of the P-site amino acid. This reaction forces the P-site amino acid
to detach from its tRNA, and the newly made protein is released. The small and large ribosomal subunits dissociate from the
mRNA and from each other; they are recruited almost immediately into another translation initiation complex. After many
410 Chapter 15 | Genes and Proteins

ribosomes have completed translation, the mRNA is degraded so the nucleotides can be reused in another transcription
reaction.

Protein Folding, Modification, and Targeting

During and after translation, individual amino acids may be chemically modified, signal sequences may be appended,
and the new protein “folds” into a distinct three-dimensional structure as a result of intramolecular interactions. A signal
sequence is a short tail of amino acids that directs a protein to a specific cellular compartment. These sequences at the
amino end or the carboxyl end of the protein can be thought of as the protein’s “train ticket” to its ultimate destination. Other
cellular factors recognize each signal sequence and help transport the protein from the cytoplasm to its correct compartment.
For instance, a specific sequence at the amino terminus will direct a protein to the mitochondria or chloroplasts (in plants).
Once the protein reaches its cellular destination, the signal sequence is usually clipped off.
Many proteins fold spontaneously, but some proteins require helper molecules, called chaperones, to prevent them from
aggregating during the complicated process of folding. Even if a protein is properly specified by its corresponding mRNA, it
could take on a completely dysfunctional shape if abnormal temperature or pH conditions prevent it from folding correctly.

This OpenStax book is available for free at http://cnx.org/content/col11448/1.10

Chapter 15 | Genes and Proteins 411

KEY TERMS
7-methylguanosine cap modification added to the 5' end of pre-mRNAs to protect mRNA from degradation and assist
translation

aminoacyl tRNA synthetase enzyme that “charges” tRNA molecules by catalyzing a bond between the tRNA and a
corresponding amino acid

anticodon three-nucleotide sequence in a tRNA molecule that corresponds to an mRNA codon

CAAT box (GGCCAATCT) essential eukaryotic promoter sequence involved in binding transcription factors

Central Dogma states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins

codon three consecutive nucleotides in mRNA that specify the insertion of an amino acid or the release of a polypeptide
chain during translation

colinear in terms of RNA and protein, three “units” of RNA (nucleotides) specify one “unit” of protein (amino acid) in a
consecutive fashion

consensus DNA sequence that is used by many species to perform the same or similar functions

core enzyme prokaryotic RNA polymerase consisting of α, α, β, and β' but missing σ; this complex performs elongation

degeneracy (of the genetic code) describes that a given amino acid can be encoded by more than one nucleotide triplet;
the code is degenerate, but not ambiguous

downstream nucleotides following the initiation site in the direction of mRNA transcription; in general, sequences that
are toward the 3' end relative to a site on the mRNA

exon sequence present in protein-coding mRNA after completion of pre-mRNA splicing

FACT complex that “facilitates chromatin transcription” by disassembling nucleosomes ahead of a transcribing RNA
polymerase II and reassembling them after the polymerase passes by

GC-rich box (GGCG) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of
transcription; may be present several times in a promoter

hairpin structure of RNA when it folds back on itself and forms intramolecular hydrogen bonds between complementary
nucleotides

holoenzyme prokaryotic RNA polymerase consisting of α, α, β, β', and σ; this complex is responsible for transcription
initiation

initiation site nucleotide from which mRNA synthesis proceeds in the 5' to 3' direction; denoted with a “+1”

initiator tRNA in prokaryotes, called U3/ " .FU ; in eukaryotes, called tRNAi; a tRNA that interacts with a start codon,
G
binds directly to the ribosome P site, and links to a special methionine to begin a polypeptide chain

intron non–protein-coding intervening sequences that are spliced from mRNA during processing

Kozak’s rules determines the correct initiation AUG in a eukaryotic mRNA; the following consensus sequence must
appear around the AUG: 5’-GCC(purine)CCAUGG-3’; the bolded bases are most important

nonsense codon one of the three mRNA codons that specifies termination of translation

nontemplate strand strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except that
T nucleotides in the DNA are replaced by U nucleotides in the mRNA

Octamer box (ATTTGCAT) nonessential eukaryotic promoter sequence that binds cellular factors to increase the
efficiency of transcription; may be present several times in a promoter
412 Chapter 15 | Genes and Proteins

peptidyl transferase RNA-based enzyme that is integrated into the 50S ribosomal subunit and catalyzes the formation
of peptide bonds

plasmid extrachromosomal, covalently closed, circular DNA molecule that may only contain one or a few genes; common
in prokaryotes

poly-A tail modification added to the 3' end of pre-mRNAs to protect mRNA from degradation and assist mRNA export
from the nucleus

polysome mRNA molecule simultaneously being translated by many ribosomes all going in the same direction

preinitiation complex cluster of transcription factors and other proteins that recruit RNA polymerase II for transcription
of a DNA template

promoter DNA sequence to which RNA polymerase and associated factors bind and initiate transcription

reading frame sequence of triplet codons in mRNA that specify a particular protein; a ribosome shift of one or two
nucleotides in either direction completely abolishes synthesis of that protein

Rho-dependent termination in prokaryotes, termination of transcription by an interaction between RNA polymerase

and the rho protein at a run of G nucleotides on the DNA template

Rho-independent termination sequence-dependent termination of prokaryotic mRNA synthesis; caused by hairpin

formation in the mRNA that stalls the polymerase

RNA editing direct alteration of one or more nucleotides in an mRNA that has already been synthesized

Shine-Dalgarno sequence (AGGAGG); initiates prokaryotic translation by interacting with rRNA molecules
comprising the 30S ribosome

signal sequence short tail of amino acids that directs a protein to a specific cellular compartment

small nuclear RNA molecules synthesized by RNA polymerase III that have a variety of functions, including splicing
pre-mRNAs and regulating transcription factors

splicing process of removing introns and reconnecting exons in a pre-mRNA

start codon AUG (or rarely, GUG) on an mRNA from which translation begins; always specifies methionine

TATA box conserved promoter sequence in eukaryotes and prokaryotes that helps to establish the initiation site for
transcription

template strand strand of DNA that specifies the complementary mRNA molecule

transcription bubble region of locally unwound DNA that allows for transcription of mRNA

upstream nucleotides preceding the initiation site; in general, sequences toward the 5' end relative to a site on the mRNA

CHAPTER SUMMARY
15.1 The Genetic Code

The genetic code refers to the DNA alphabet (A, T, C, G), the RNA alphabet (A, U, C, G), and the polypeptide alphabet
(20 amino acids). The Central Dogma describes the flow of genetic information in the cell from genes to mRNA to
proteins. Genes are used to make mRNA by the process of transcription; mRNA is used to synthesize proteins by the
process of translation. The genetic code is degenerate because 64 triplet codons in mRNA specify only 20 amino acids and
three nonsense codons. Almost every species on the planet uses the same genetic code.

15.2 Prokaryotic Transcription

In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template comprising two consensus
sequences that recruit RNA polymerase. The prokaryotic polymerase consists of a core enzyme of four protein subunits

This OpenStax book is available for free at http://cnx.org/content/col11448/1.10

Chapter 15 | Genes and Proteins 413

and a σ protein that assists only with initiation. Elongation synthesizes mRNA in the 5' to 3' direction at a rate of 40
nucleotides per second. Termination liberates the mRNA and occurs either by rho protein interaction or by the formation
of an mRNA hairpin.

15.3 Eukaryotic Transcription

Transcription in eukaryotes involves one of three types of polymerases, depending on the gene being transcribed. RNA
polymerase II transcribes all of the protein-coding genes, whereas RNA polymerase I transcribes rRNA genes, and RNA
polymerase III transcribes rRNA, tRNA, and small nuclear RNA genes. The initiation of transcription in eukaryotes
involves the binding of several transcription factors to complex promoter sequences that are usually located upstream of
the gene being copied. The mRNA is synthesized in the 5' to 3' direction, and the FACT complex moves and reassembles
nucleosomes as the polymerase passes by. Whereas RNA polymerases I and III terminate transcription by protein- or RNA
hairpin-dependent methods, RNA polymerase II transcribes for 1,000 or more nucleotides beyond the gene template and
cleaves the excess during pre-mRNA processing.

15.4 RNA Processing in Eukaryotes

Eukaryotic pre-mRNAs are modified with a 5' methylguanosine cap and a poly-A tail. These structures protect the mature
mRNA from degradation and help export it from the nucleus. Pre-mRNAs also undergo splicing, in which introns are
removed and exons are reconnected with single-nucleotide accuracy. Only finished mRNAs that have undergone 5'
capping, 3' polyadenylation, and intron splicing are exported from the nucleus to the cytoplasm. Pre-rRNAs and pre-
tRNAs may be processed by intramolecular cleavage, splicing, methylation, and chemical conversion of nucleotides.
Rarely, RNA editing is also performed to insert missing bases after an mRNA has been synthesized.

15.5 Ribosomes and Protein Synthesis

The players in translation include the mRNA template, ribosomes, tRNAs, and various enzymatic factors. The small
ribosomal subunit forms on the mRNA template either at the Shine-Dalgarno sequence (prokaryotes) or the 5' cap
(eukaryotes). Translation begins at the initiating AUG on the mRNA, specifying methionine. The formation of peptide
bonds occurs between sequential amino acids specified by the mRNA template according to the genetic code. Charged
tRNAs enter the ribosomal A site, and their amino acid bonds with the amino acid at the P site. The entire mRNA is
translated in three-nucleotide “steps” of the ribosome. When a nonsense codon is encountered, a release factor binds and
dissociates the components and frees the new protein. Folding of the protein occurs during and after translation.

ART CONNECTION QUESTIONS

1. Figure 15.11 A scientist splices a eukaryotic promoter Tetracycline would directly affect:
in front of a bacterial gene and inserts the gene in a
bacterial chromosome. Would you expect the bacteria to a. tRNA binding to the ribosome
transcribe the gene? b. ribosome assembly
2. Figure 15.13 Errors in splicing are implicated in c. growth of the protein chain
cancers and other human diseases. What kinds of Chloramphenicol would directly affect
mutations might lead to splicing errors? Think of different
possible outcomes if splicing errors occur.
a. tRNA binding to the ribosome
3. Figure 15.16 Many antibiotics inhibit bacterial protein b. ribosome assembly
synthesis. For example, tetracycline blocks the A site on c. growth of the protein chain
the bacterial ribosome, and chloramphenicol blocks
peptidyl transfer. What specific effect would you expect
each of these antibiotics to have on protein synthesis?

REVIEW QUESTIONS
4. The AUC and AUA codons in mRNA both specify d. degeneracy
isoleucine. What feature of the genetic code explains this? 5. How many nucleotides are in 12 mRNA codons?
a. complementarity a. 12
b. nonsense codons b. 24
c. universality c. 36
414 Chapter 15 | Genes and Proteins

d. 48 10. Which pre-mRNA processing step is important for

initiating translation?
6. Which subunit of the E. coli polymerase confers
a. poly-A tail
specificity to transcription?
b. RNA editing
a. α
c. splicing
b. β
d. 7-methylguanosine cap
c. β'
d. σ 11. What processing step enhances the stability of pre-
tRNAs and pre-rRNAs?
7. The -10 and -35 regions of prokaryotic promoters are
a. methylation
called consensus sequences because ________.
b. nucleotide modification
a. they are identical in all bacterial species
c. cleavage
b. they are similar in all bacterial species
d. splicing
c. they exist in all organisms
d. they have the same function in all organisms 12. The RNA components of ribosomes are synthesized in
the ________.
8. Which feature of promoters can be found in both
a. cytoplasm
prokaryotes and eukaryotes?
b. nucleus
a. GC box
c. nucleolus
b. TATA box
d. endoplasmic reticulum
c. octamer box
d. -10 and -35 sequences 13. In any given species, there are at least how many types
of aminoacyl tRNA synthetases?
9. What transcripts will be most affected by low levels of
a. 20
α-amanitin?
b. 40
a. 18S and 28S rRNAs
c. 100
b. pre-mRNAs
d. 200
c. 5S rRNAs and tRNAs
d. other small nuclear RNAs

CRITICAL THINKING QUESTIONS

14. Imagine if there were 200 commonly occurring amino of mRNA and the DNA nontemplate strand not identical?
acids instead of 20. Given what you know about the Could they ever be?
genetic code, what would be the shortest possible codon 17. In your own words, describe the difference between
length? Explain. rho-dependent and rho-independent termination of
15. Discuss how degeneracy of the genetic code makes transcription in prokaryotes.
cells more robust to mutations. 18. Transcribe and translate the following DNA sequence
16. If mRNA is complementary to the DNA template (nontemplate strand): 5'-ATGGCCGGTTATTAAGCA-3'
strand and the DNA template strand is complementary to 19. Explain how single nucleotide changes can have
the DNA nontemplate strand, then why are base sequences vastly different effects on protein function.

This OpenStax book is available for free at http://cnx.org/content/col11448/1.10