Gene Expression: From Gene

to Protein
KEV CONCEPTS
17.1 Gen es specify protei ns via
transcription and translation p. 336
17.2 Transcription is the DNA-directed
symhesis of RNA:A aoser Look p. 342
17.3 Eukaryotic cells modify RNA after
tr.inscription p. 345

17.4 Tran slation Is the RNA-direct ed

syn thesis of a polypeptlde: A Closer
Look p. 347

17,5 Mlftiltions of one or a few

nucleotides can affect protein
str111cture and function p. 357

Study Tip Figure 17.1 A population of albino donkeys grazes on vegetation on the hillsides
of Aslnar.i, an Italian Island. Several centuries ago, a recessive mutation that dls.ibles
Make a visual study guide: Sket ch t he pigment synthesis arose In the DNA of one donkey and was passed down through
process shown below, and add labels the generations. Inbreeding has resulted In a large number of homozygous albino
and details as you read the chapter. donkeys living on the Island today.
(In th is exercise, assume all processes
ta ke p lace i n a eukaryotic cell.)

How can one change in DNA result in such

a dramatic change in appearance?

~ --~--
-...
---
Proteins are the hnk between genotype and phenotype. Gene expression
1s the process by which DNA directs the synthesis of proteins:

Genotype: DNA Genotype: DNA

::J
~ ~

I-
Gene for pigmentation
Gene for pigmentation
-;JI ~ TRANSCRIPTION w1th:mutat1onl

mRNA
f) Go to Mastering Biology TRANSLATION
For Students (in eText and Study Area) Protein: Enzyme Protein: Enzyme
required for pigment required for pigment
• Get Ready for Chapt er 17 synthesis synthesis does not work
• Bioflix~ An imation: Protein Synthesis
• Fig ure 17.27 Walkthrough: Types of
Sma ll-Sca le M utations that Affect mRNA Phenotype: ~
Sequence Brown pigment
For Instructors to Assign (In Item Library)
• BloFlix" Tutorial: Protein Synthesis
(1 of 3): Overview
• Tutorial: CRISPR: A Revolution in
Genome Editing
Ready-to-Go Teaching Module
(in Instructor Resources)
• Gene Expression: M utat ions (Concept 17.5)

335
 organisms studied by Mendel (peas) and T. 1-1. Morgan (frui t
G·Wifaifll files), Neurospom is a haploid species. Because its genome
Genes specify proteins via contains only one copy of each gene, that single copy deter-
mines the tndlvidua l's expressed phenotype. Therefore, when
transcription and translation Beadle and Tatum wanted to discover the function of any
Inherited traits like albinism are determined by genes, which gene, they only needed to mutate and disable that one allele.
have Information content In the form of specific sequences of They chose to study the protein-coding genes requir>ed for a
nucleotides along stretches of DNA, the genetic materla1. The specific nutritional activity. They caused mutations !n genes
DNA inherited by an organism leads tospeciflc traits by dictat- by bombarding Ne11rospora with X-rays and looked among the
ing the synthesis of proteins and of RNA molecules Involved in survivors for mutants that differed In their nutritiona l needs
protein synthesis. In the case of coat and skin color, the gene from the wild-type bread mold.
containing the imformatioo to synthesize an enzyme that makes WUd-type Ncurospora has modest food requirements. It can
pigment allows normal coiocing, and a faulty version of that grow in the labora tory on 111/11i111al med/11111-a simple solution
gene leads to lack of color, or the albino phenotype. Proteins are containing minimal nutrients for growth- Inorganic salts,
the link between genotype and phenotype. Gene expression glucose, and the vitamin biotin- incorporated into agar, a sup-
is the process by which DNA directs the synthesis of proteins (or, port medium. From these basics, wild-type mold cells. use their
in some cases, just RNAs). The expression of genes that code for metabolic pathways to produce all the other nutrient mol-
proteins includes two stages: transcription aod translation. ecules (like amino acids) they need for growth, dividing repeat-
Before going into the details of how genes direct protein edly aod forming visible colooles of genetically identical cells.
synthesis, let's step back aod examine how the fundamental As shown in Figure 17.2, Beadle and Tatum generated cllEferent
relations hip between genes and proteins was discovered. "nutritional mutants" of Ne11rospora cells, each of which bad a
mutation lo one gene aod was unable to synthesize a particular
Evidence from Studying Metabolic Defects
T Flgur-e 17.2 Beadle and Tatum's e,cperimental approach.
In 1902, British physician Archibald Garrod was the first to sug-
To obtain nutritional mutants, Beadle and Ta tum exposed
gest that genes dictate phenotypes through enzymes, proteins Neurospora cells to X-rays, Inducing mu tatlons. then screened for
that catalyze speci6cchemical reactions in the cell. He postu- (tested for) mutants that had new nutritional requlremen ts. such
lated that the symptoms of an Inherited disease reflect an Inabil- as arginine. as shown here.
ity to make a particular enzyme. I le later referred to such diseases 0 Individual Neurospora cells
Neurospo,a -.;::::::::----
as "inborn errors of metabolism." For example, people with a cells were placed on complete
disease called alkaptonuria have black urine because ii contains medium.
a chemical calledl alkapton, which darkens upon exposure to air.
6
Garrod reasoned that these people cannot make an enzyme that
breaks down alkapton, so alkapton is expelled in their urine.
Several decades later, research supported Gar.rod's hypothesis
that a gene dlctat.es the production of a specific enzyme, later
1~ The cells were subjected to
X-rays to induce a mutation
in one gene per cell

€) Each surviving cell

named the one gme--011e mzyme hypothesis. Biochemists teamed formed a colony of
genetically identical cells.
that cells synthesize and degrade most organic molecules via
metabolic pathways, in which each chemical reaction io a
O Cells from each colony were
sequence is catalyzed bya specific enzyme (see Concept 8.1). placed in a v,al Wtth only
No--
Such metabolic pathways lead, for instance, to the synthesis of growth minimal medium. Cells that
did not grow were identified
the pigments lhatgive the brown donkey in Agure 17.1 its fur as nutrrtional mutants.
color or £rult flies (DrosoplTlla) their eye color (see Figure 15.3).
In the 1930s, the American biochemist and geneticist George O Cells from one nuu1bonal mutant
colony were placed ,n a series of
Beadle and his French colleague Boris Ephrussi speculated lhat in v,als. each containing minimal
Drosophila, each mutation affecting eye color blocks pigment syn- medium plus one add,uonal nutrient
thesis at a specific step by preventing production of the enzyme
that catalyzes that step. But neither the chemical reactions nor - Growth
the enzymes that catalyze them were known at the time.

Nutritional M utants in Neurospora: Scientific Inquiry Mln,mal Minimal M,mmal Control: Wild-type cells
medium medium medium growing on
A breakthrough in demonstrating the relations hip between + vallne + lysine + arginine minimal medium
genes and enzymes came a few years later at Stanford O The v,afs were observed for growth. In this example, the mutant
University, where Beadle and Edward Tatum bega.n work- cells grew only on minimal medium + arginine, indicating that this
ing with a bread mold, Neurospomcmssa. Unlike the diploid mutant was missing the enzyme for the synthesis of arginine.

336 UNIT THREE Genetics

essential nutrient. Such cells could not grow on minimal chains, and each polypeptide is specified by its own gene. For
medium buc could grow on completl' med/11111, which contains example, hemoglobin-the oxygen-transporting protein of
all nu trients needed for growth. For Neurospora, the complete vertebrate red blood cells-con ta ins two kinds of polypep-
medium consists of the minimal medium supplemented with tides, and th us two genes code for this protein, one for each
all 20 amino acids and a few other nutrients. Beadle and Tatum type of polypeptide (see Figure 5.18). Beadle and Tatum's
hypothesized that in each nutritional mutant, the gene for idea was therefore restated as the one ge11e--011e polypeptide
the enzyme that synthesizes a particular nutrient had been hypothesis. Even this description is not entirely accurate,
disabled by the mutation. They were able to determine experi- though. Flrst, in many cases, a eukaryotic gene can code for a
mentally which nutrient each mutant strain (original cell and set of closely related polypeptides via a process called alterna-
its descendants) was unable to synthesize. tive splici ng, which you will learn about later in this chapter.
This approach resulted in a valuable collection of mutant Second, quite a few genes code for RNA molecules that have
strains of Ne11rospora, each catalogued by lls defect In a par- Important fun ctions in cell.s even though they are never
ticula r pathway. Two colleagues, Adrian Srb and Norman translated in to protein. For now, we will focus on ge nes that
Horowitz, used a collection of arginine-requiring mutants to do code for polypeptides. (No te that it is common to refer to
investigate the biochemical pathway for arginine synthesis in these gene products as proteins- a practice you will encoun-
Neurospora (Rgure 17.3). Srb and Horowitz pinned down each ter in this book- rather than more precisely as polypeptides.)
mutan t's defect more specifically, using additional tests to dis-
tinguish among three classes of arginine-req uiring mutants.
Mutants In each class required a different set of compounds
Basic Principles of Transcription
along the arginine-synthesizing pathway, which has three and Translation
steps. These results, and those of many similar experiments Genes provide the instructions for maklngspeclBe protl'lns,
done by Beadle and Tatum, suggested that eacl1 class was but a gene does not build a protein directly. The bridge
blocked at a differen t s tep in this pathway because mutants in between DNA and protein synthesis is the nucleic acid RNA.
that class lacked the enzyme that catalyzes the blocked step. RNA is chemically similar to DNA except that it contains ribose
Because Beadle and Tatum set up their experimental con- instead of deoxyribose as its sugar and has the nitrogenous
ditions so that each mutant was defective in a single gene, base uracil rather than thymine (see lligure 5.23). Thus, each
the collected results, taken together, provided strong sup- nucleotide along a DNA strand has A, G, C, orT as its base, and
port for the.one gene-one enzyme hrpothesfs, as they dubbed each nucleotide along an RNA strand has A, G, C, or U as Its
it: that the f1UI1ction of a gene is to dictate the production of base. An RNA molecule usually consists of a single strand.
a specific enzyme. Further support for this hypothesis came We often describe the flow of information from gene to
from experiments that identified the specific enzymes lack- protein in terms of languages.Just as specific sequences of let-
ing in the mutants. Beadle and Tatum shared a Nobel Prize in ters communicate information in a language such as English,
1958 for "their discovery that genes act by regulating definite specific sequences of monomers con vey information in
chemical events" (in the words of the Nobel committee). polymers Like nucleic acids and proteins. In DNA o r RNA, the
Today, we know of countless examples in which a muta- monomers are lhe four types of nucleotides listed previously,
tion in a gene causes a faulty enzyme that in tum leads to an which differ in their nitrogenous bases. Genes are typically
identifiable condition. The albino donkeys in Figure 17.1 lack hundreds or Lhousands of nucleotides long, eaclh gene hav-
a key enzyme called tyrosinase In the metabolic pathway that ing a specific sequence of nucleo tides. Each polypeptide or
produces melanin, a dark pigment. The absence of melanin a protein also has monomers arran ged in a particular linear
causes white fur and other effects throughout the donkey's order (the protein's primary structure; see Figure 5.18), but
body. Its nose, ears, and hooves, as well as its eyes, are pink its monomers are amino acids. Thus, nucleic acids and pro-
because no melanin is present to mask the reddish color of teins contain information wri tten in two different chemical
the blood vessels that ru n through those strnctures. languages. Getting from DNA to protein involves two major
stages: transcription and translation.
The Products of Gene Expression: A Developing Story Transcription is the synthesis (production) of RNA using
As researchers learned more about proteins, th ey made revi- information in the DNA. The two nucleic acids are written in
sions to the one gene-one enzyme hypothesis. First or all, different forms of the same language, and the information is
not all proteins are enzymes. Keratin, the s tructural protein simply transcribed, or "rewritten," from DNA to RNA.Just as
of animal hair, and the hormone insulin are two examples of a DNA strand provides a template for making a new comple-
nonenzyme proteins. Because proteins that are not enzymes mentary strand d uring DNA replication (see Concept 16.2), it
are nevertheless gene products, molecular biologists began to also can serve as a template for assembling a complementary
think in terms of one gene-one protein. However, many pro- sequence of RNA nucleotides. For a protein-codhng gene, the
tei ns are comtructed from two or more diffe rent polypeptide resulting RNA molecule is a faithful transcript of the gene's

CHAPTER 11 Gene E.xpresslon: From Gene to Pcotel n 337

 • Figure 17.3 Inquiry
Do Individual genes specify the enzymes that function In a biochemical pathway?

Experiment Working with the mold Neurospora crassa, Adrian Srb and Norman Horowitz, then Precursor
at Stanford Un lverslty, used Beadle and Tatum's experimental approach (see Figure 17.2) to Isolate
mutants that required arginine In their growth medium. The researchers showed that these mutants
fell Into three classes, each defective In a different gene. From studies by others on mammalian liver
ili@4ts l
cells, they suspected that the metabolic pathway of arginine blosynthiesls Involved a precursor nutri- Ornith1ne
ent and the Intermediate molecules omlthlne and cltrulllne, as shown In the diagram on the right.

Their most famous experiment, shown here, tested both the one gen~ne enzyme hypothesis and
l C1trulline

Fifr, n" l
their postulate.cl arginine-synthesizing pathway. In this experiment. they grew thelrthree classes of
mutants under the four different conditions shown In the results table below. They Included mlnlmal 11
medium (MM} as a comrol, knowing that wlld-type cells could grow on MM but mutant cells could not.
(Se,e test tubes below.) Arginine

Results Tab Cla.sses of Neurospora crassa

Growth: - - No growth:
W1ld-type Mutant cells Wild type Class I mutants Oa.ss U mutants Class ill mutants
cells can grow cannot grow
and divide.
V
Control: M 1n1mal medium
and divide. Minimal
medium
(MM)
(control)
Results As shown In the table
on the right, the wild-type stra in
MM+
was apable of growth under all
ornithine
experimental condltlons, requir-
ing only the minimal medium. The
three classes of mutants each had a
ct-----+--------+--------+-------+----------t
0
:1::
specific set of growth requirements. ] MM+
For example, dass II mutants could 8 cltrulline
not grow when ornlthlne alone was
added but could grow when either
cltrulllne or arginine was added.
MM+
arginine
(control)

Conclusion From the growth re- Summary Can grow with or Can grow on Can grow only on Require arginine
quirements of tihe mutants, Srb and withou t any ormth1ne. o trulhne. otrulhne or to grow
Horowitz deduced that each class of of results supplements or arg1n1ne arginine
mutant was unable to carry out one
step In the pathway for synthesiz-
ing arginine, presumably because
Gene Class I mutants Cass II mutants Class [[( mutants
It lack.eel t he necessary enzyme, as
shown In the table on the right.
(codes for
I (mutation In (mutation m (muta tlon In
Because each of their mutants was
mutated In a single gene, they con-
cluded that each mutated gene must
norma lly dictate the production crf
enzyme)

Gene A
i Wild type

-----@111\hf l
Pre.cursor
gene A)

Precursor

),%1i«f: ®,n11a
gene B)
Precursor

l
gene C)

®fo"'s
!Precursor

l
--~l =-1=l
one enzyme. Their results supported
Ornlthme Ornithine Ornithine Ornithine
the one gene-one enzyme hypoth-
esis, proposed by Beadle and Tatum,
and also confirmed that the arginine
Gen~ - @¼,iil; l LtJ&J,¥1 l &&\SJ
pathway described In the mammalian
I
----- WoiJi l
Cltrulllne Cltrulllne Cltrulllne

l
Citrulline
liver also operates In Neurospora.
(Notice In the results table that a mu- Gene C LU!ilui., ii!Jui*'
tam an grow only If supplied with a
compound maole afterthe defectlve
step because this bypasses the defect.)
I Arginine Arginine Arginine Arginine

Data from A. M. S<-b and N. H, Horowitz, The or- WHAT IF? Suppose the experiment had shown that class I mutants could grow only ,n MM
nlthlnc cycle In ffflJrospo,• ond H• genetic con-
trol, Journal of B,olcgal supplemented by om,thme or arginme and chat class II murantt could grow in MM supplememed by
Ch""'lstry I 54:129- 139 (1944) c111ulline, omirhme, or argmine. Whar conclusions would the researchers have drawn from those results
regard,ng the biochemiCiJI pathway and the defect in class I and class fl mutants?

338 UNIT THREE Genetics

protein-building instructions. This type of RNA molecule 1' Agure 17.4 Overview: th e roles of transcription and
ls call ed m essenger .RNA (mRNA) because it carries a translation In the flow of genetic lnfonruitlon. In a cell,
Inherited Information flows from ONA to RNA 10 protein. The two
genetic mes~ge from the DNA to the protein-synthesizing main stages of Information flow are transcription and translation.
machinery of the cell. ( rranscrlption Is the general term for A miniature version of part (a) or (b) accompanies several figures
the synthesis of any kind of RNA on a DNA template. Later, later In the chapter as an orientation diagram to help you see where
you will learn about some other types of RNA produced by a particular figure fits Into the overall scheme of gene expression.

r~
transcription.)
Translation is the synthesis of a polypeptide using the
information in the mRNA. During this stage, there is a change
lo language: The cell must translate the nucleotide sequence
of an mRNA molecule Into the amino acid sequence of a poly-
TRANSCRIPTION l DNA

peptide. The sites of translation are ribosomes, molecular CYTOPLASM I mRNA

complexes that facilitate the orderly linking of amino acids
♦ Rlbosom
into polypeptide chai ns. TRANSLATION
Transcription and translation occur in all organisms.
Because most studies have involved bacteria and eukaryotic Polypepude
cells, they are our main focus in this chapter. Our understand-
ing of transcription and translation in archaea lags behind,
but we do know that archaeal cells share some features of (a) Bacterial cell In a baaenal cell, which lades a nucleus,
mRNA produced by transcription Is ,mmed,ately
gene expression with bacteria and others with eukaryotes. translated without add,tlonal processing.
The basic mechanics of transcription and lranslalion are
sim ilar for bacteria and eukaryotes, but there is an impor-
tant difference in the flow of genetic information within
the cells. Bacteria do no t have nuclei. Therefore, nuclear
membranes do not separate bacterial DNA and mRNA from
ribosomes and the o ther protein-synthesizing equipment
ff'°"~lR!LR'l \.)
---l ....
(Figu re 17.4a). This lack of compartmentalization allows
TRANSCRIPTION DNA
translation of an mRNA to begin while its transcription
is still in progress, as you'll see later. By contrast, eukary- .._
otic cells have nuclei. The presence of a nuclear envelope Pre-mRNA

-
RNA PROCESSING
separates transcription from translation In space and time
(Figure 17.4b). Transcription occurs in the nucleus, but the mRNA::::. ~
mRNA must be transported to the cytop lasm for translation.
In eukaryotes, before RNA transcripts from protein-coding
genes can leave the nucleus, they are modified In various
ways to produce the final, functional mRNA. The transcrip-
tion of a proteio-codlng eukaryotic gene results in pre-mRNA, TRANSLATION
and further RNA processing yields the finish ed mRNA. The
initia.l RNA ittanSCript from any gene, includi.ng those speci-
~~
fying RNA that is not translated into protein (such as tRNA Polypepllde
and rRNA, which will be described in Concept 17.4), is more
genera lly called a primary transcript.
To summarize: Genes program protein synthesis via (b) Eukaryotlc cell. The nucleus provides a separate
genetic messages in the form of messenger RNA. Put another compartment fo< transcnption. The original RNA
transcript, called pre-mRNA, is processed in various
way, cells are governed by a molecular chain of command ways before leavrng the nucleus as mRNA.
with a cllrectional flow of genetic information:
C) Mastering Biology

H·W·◄ -- Ifill@ Animation; Overview of Protein Synthesis in Bacteria

Animation: Overview of Protein Synthesis in Eukaryotes

Th is idea, that the flow of information went only one (see Concep t 19.2). Still, these exceptions do not djscredit
way, was named the ce11tml dogma by Francis Crick ln 1956. Lhe idea that, ln general, genetic Lnformation flows from
In the 1970S, however, scientists were surprised to discover DNA to RNA to protein. In the next section, we discuss how
some enzymes that use RNA molecules as templates for DNA the instructions for assembling amino acids into a specific
synthesis, an example o r Information flow from RNA to DNA order are encoded In nucleic acids.

CHAPTER 11 Gene Expression: From Gene to Protei n 339

The Genetic Code T Figure 17.5 The triplet code. For each gene, DNA
one DNA strand functions as a template for molecule
When biologists !began to suspect that the instructions for pro- transcription of RNAs, such as mRNA. The base-
tein synthesis were encoded in DNA, they recognized a problem: pairing rules for DNA synthesis also guide
There are only four nudeotide bases to specify 20 amino adds. transcription, except that RNA Is made
with uracil (U) instead of thymine (T).
Thus, the genetic code cannot be a language llke Chinese, where During translation, the mRNA Is mad .is
each written symbol corresponds to a word. How many nudeo- Gene2
a sequence of nucleotide irlpleis. called
tldes, then, would turn out to correspond to an amino acid? codons. Each codon specifies an amino
acid to be added to the growing
polypeptide chain The mRNA Is read
Codons: Triplets of Nucleotides In the 5' ..... 3' direction.

1£ each kind of nucleotide base were translated In to an amino

add, only four amino acids could be specified, one per nucle- ONA

~~~- JUIIWIIII
otide base. Would a language of two-letter code words suffice?
The two-nucleotide sequence AG, for example, cou ld specify 5'
one amino add, and GT cou ld specify another. Since there
are four possible nucleotide bases in each position, this would
give us 16 (that is, -I x 4,or 4i) possible arrangements-still
not enough to code for all 20 amino acids.
Triplets of nucleotide bases are the smallest units of
uniform length that can code for all the amino acids. If
each arrangement of three consecutive nucleotide bases
specifies an amino add, there can be 6-1 (that is, 43 ) possible
,--
mRNA 5' 11 n I
MIi ld ld.1d ..___.T'-------v---1
'-v-----J~ Mt-1
3'

3'

code words- more than enough to specify all the amino Codon
adds. Experiments have verified that the flow of informa-
tion from gene tto protein is based on a triplet code: The
TRANSLATION
i i i i
genetic instructions for a polypeptide chain are written in Protein ,. Trp • Phe
the DNA as a series of nonoverlapping, three-n ucleotide
words. The series of words in a gene is transcribed in to a Amino acid
VISUAL SKIUS By convenrfon. the nontemplate strand, also called the
complementary series of nonoverlapping, three-nucleotide coding strand, ts used to represent a DNA sequence. Write the sequence
words in mRNA, which is then translated into a chain of of the mRNA strand and the nontemplate strand-in both cases reading
amino acids (Figure 17.5) . from 5' to 3' -and compare them. Why do you thmk th,s convention
was adopted? (Hint Why is this called the coding strand?)
During transcription, the gene determines the sequence
0£ nucleotide bases along the length of the RNA molecule 0 Mastering Biology MP3 Tutor. DNA to RNA to Protein
that Ls being synthesized. For each gene, on ly one of the
two DNA strands is transcribed. This strand is called the the template strand of DNA. (To review what is meant by
template strand because It provides the pattern, or "antiparallel" and the 5' and 3' ends of a nucleic add chain,
template, for the sequence of nucleotides in an RNA tran- see Figure 16.7.) In the example in Figure 17.5, the nucleo-
script. For any g,iven gene, the same stra nd is used as the tide triplet ACC along the DNA template strand (written as
template every ttlme that gene is transcribed. However, far- 3'-ACC-5') provides a template for 5'-UGG-3' in the mRNA
lher along on lhe same ch romosomal ONA molecule, the molecule. The mRNA nucleotide triplets are called codons,
opposite strand may fun ction as the template for a differ- and they are customarily written In the 5' - 3' direction.
ent gene. Particular ONA sequences associated with a gene In our example, UGG is the codon for the amino acid tryp-
determine how the enzyme that transcribes genes is ori- tophan (abbreviated Trp, or W). The term codon Is also used
ented when it binds, and Lhis establishes which strand will for the ONA nucleotide triplets along the 11011/emplat,e strand.
be used as Lhe template. These codons are complementary to the template strand and
An mRNA molecule is complementary rather than thus Identical In sequence to the mRNA (except for T's Instead
identical to its DNA template because RNA nucleotides are of U's). For this reason, the nontemp late ONA strand is often
assembled on the template according to base-pairing rules called the coding strand; by convention, the sequence of
(see Figure 17.5). The pairs are similar to those that form the coding strand is used when a gene's sequence is reported.
during DNA replication, except that U (the RNA substi- During translation, the sequence of codons along an
tute for'J) pa.irs with A and lhe mRNA nucleotides contain mRNA molecu le is decoded, or translated, into a sequence
ribose instead of deoxyribose. Like a new strand or DNA, the of amino acids making up a polypeptide chain. The codons
RNA molecule is synthesized in an anti parallel dlrection to are read by the translation machinery in the 5 ' - 3'

340 UNIT THREE Genetics

direction along the mRNA . Each codon specifies which ., Agure 17.6 The codon table for mRNA. The three nucleotide
one of the 20 amino acids will be incorporated at the cocre- bases of an mRNA codon are designated here as the first, second,
and third bases. reading in the 5 ' - 3' direction along the mRNA
spon ding position alon g a polypeptide. Beca use codons are
The codon AUG not only stands for the amino add methionine
n udeotide triplets, the n umber of nucleotides making up a (Met, or M) bu t also functions as a •start· signal for ri bosomes
genetic message must be three times the n umber of amino to begin translating the mRNA at that point. Three of the 64
acids in the protein product. For example, 300 nucleotides codons function as ·stop· signals, marlclng where ribosomes end
translation. Both one- and three-letter codes are shown for the
along an mRNA strand code for 100 amino acids in the
amino acids; see Figure 5 .1 4 for their full names.
polypeptide it encodes.
Se<ond mRNA base
Cracking the Code
Molecular biologists cracked the genetic code of life in the
early 1960s when a series of elegant experiments disclosed
the amino add translations of each of the mRNA codons. The UAA Stop UGA Stop
EITTt codon was deciphered In 1961 by MarshaU Nirenberg, of
the National institutes of Health, and colleagues. They syn-
thesized an artificial mRNA made up of on ly uracil-bearing
nucleotides, thus contai n ing only one codon (UUU) over
and over. When added to a test-tube mixture that contained
all 20 amino acids, ribosomes, and the other components
c'
0
'0

0
0
V

'0
.,
C

.....,
it,
CCU l
CCC Pro
CCA (Pl
CCG
UAG Stop

CAU l Hls
CAC (H)

CAA lGln
CAG (Q)
CGUJ
CGC Arg
CGA
CGG
(R)
c0
]
....0
'0
.,C
Cl.

~"]
required for protein synthesis, the "poly-U" mRNA was trans- .,
lated Into a polypeptide containing man y units of the phe- :a
.D
AAU lAsn AGU ]Ser .a"'
ACC Tor AAC (Nl AGC (S) <(
nylalanine (Phe, or F) amino adds, strung together as a poly- <(

phenylalanine chain. Th us, Nirenberg determined that the

mRNA codon UUU specifies the amino acid phenylalanine.
z
a:
E
ACA CD
ACG
AAA
AAG
lys
(Kl
AGA lArg
AGG (R)
z
a:
E
1?
E
Soon, the amino acids specified by the codons AAA, GGG, '..: ~
and CCC were simi larly Identified.
Al though more elaborate techniques were required to &Ul
GCC Al.i
GAU1~
GAC (D)
GGUJ
GGC Gty
decode mixed triplets such as AUA and CGA, all 64 codons GCA (A) GAA lGlu GGA (G)
were deciphered by the mid -1960s. As Figure 17.6 shows, 61 GCG GAG (E) GGG
of t he 64 triplets code for amino acids. The other three codons
act as "stop" signals, or terminatio n codons, marking the end VISUAL SKILLS A segmenc in che middle of an mRNA has the
o f translation. Notice that the codon AUG has a dual £unc- sequence 5'-AGAGAACCGCGA-3'. Using the codon cable, translate this
tion: 1t codes for the amino acid methion ine (Met, or M) and sequence, assuming the firsr rhree nucleoc/des are a codon.
also functions as a "start" signal, o r initiation codon. Genetic f) Mastering Biology Animation: Translatlon: The Genetic Code
messages W'llally begin with the mRNA codon AUG, which
signals the protein-synt hesizing machinery to begin translat- will probably be gibberish: for example, " her edd oga tet heb
ing the mRNA at that location. (Because AUG also stands for ug." The reading frame Is also Important in the molecular
meth ionine, polypeptide chains all begin with methionine language of ce lls. The short stretch of polypeptide s hown
w hen they are synthesized. However, an enzyme may subse- in Figure 17.5, for instance, will be made correctly on ly if
quen tly remove this starter amino add from the chain.) the mRNA nucleotides are read from left to right (5' -+ 3 ')
Notice In Figure 17.6 th at there is red undancy in the In the groups of three shown in the figure: UGG UUU GGC
genetic code, but no am biguity. For example, although ,Ug. Although a genetic message is written witln no spaces
codons GAA and GAG both specify glutamic acid (redun- between the codons, the cell's protein-synthesizing m achin-
da ncy), neither of them ever specifies any o ther amjno acid ery reads the message as a series of nonoverlapping th ree-
(no ambiguity). The red un dancy in the code Is not altogether letter words. The message ls 1101 read as a series of overlapping
random . In many cases, codons that are synonyms for a par- words- UGGUUU, and so on- w hich would convey a very
ticular amino add dlffe.r only in the thlrd nucleotide base of different message.
the trip let. We will see wh y this is later in the chapter.
Our ability to extract t he intended message Crom a writ- Evolution of the Genetic Code
ten language depends on reading the symbols in the correct •W•nlHM~• Th e genetic code is nearly universal, shared
g.roupings- that is, in the correct reading &ame. Consider by organisms from the simplest bacteria to the most complex
thls sta tement: "Tbe red dog ate the bug." Group the letters plants and animals. The mRNA codon CCG, for ins tance, is
incorrectly by starting a t t he wTOng point, and the result translated as t he amino acid prolin e in all organisms whose

CHAPTE R 11 Gene Expression: From Gene to Protein 341

'9' Figure 17.7 Evidence for evolution: express ion of genes
from differe•n t sped es. Because diVerse forms of life share a IM#ifa•MI
common genetic code due to their shared ancestry, one species
can be programmed to produce proteins characteristic of a second Transcription is the DNA-directed
species by lntrodudng DNA from the second species Into the first.
synthesis of RNA: A Closer Look
Now that we have considered the linguistic logic and evo-

·,• ... lutionary significa nce of Lhe genetic code, we are ready to
reexamine transcription, the ArsL stage of gene expression,
in greater detail.
••
•• Molecular Components of Transcription
•
,, Messenger RNA, the carrier of information from DNA to
>, the cell's protein-synthesizing machinery, is transcribed
from the templatestTand of a gene. An enzyme called an
RNA polym erase pries the two strands of DNA apart and
joins together RNA nucleotides complementary to the DNA
(a) Tobacco plant. expressing a (bl Mosquito larva expressing template stra nd, thus elongating the RNA polynucleotide
firefly gene. The yellow glow Is a jellyfish gene. The gene codes (Figure 17.B). Like the DNA polymerases that function in
produced by a chemical reaction for green ftuor1!5Cenl protein (GA') DNA replication, RNA polymerases can assemble a polynu-
catalyzed by the protein product and is inserted into organisms as
of the firefly gene. a reponer gene so researchers cleotide only In its 5' _. 3' direction, adding onto its 3' end.
can tell ,fa gene of interest rs Unlike DNA polymerases, however, RNA polymerases are able
berng expressed. to start a chain From scratch; they don't need to add the Eirst
0 Mastering Biology Video: GFP Transgenic M ice nucleotide onto a pre-existing primer.
Specific sequences of nucleotides along the DNA mark
genetic code has been examined. In laboratory experiments, where transcription of a gene begins and ends. The DNA
genes can be transcribed and translated aher being trans- sequence where RNA polymerase attaches and initiates tran-
planted from one species to another, sometimes with quite
scription is known as the promoter; in bacteria, the sequence
striking results, as shown in Figure 17.7 . Bacteria can be that signals the end of transcription is called thl' t-ermioator.
programmed by the insertion of human genes to synthesize (fhe termination mechanism in eukaryotes will be described
certain human proteins for medical use, such as insulin. Such
later.) Molecular biologists refer to the direction of transcrip-
applications ha,,e produced many exciting developments in
tion as "downstream" and the other direction as "upstream."
the area of biotechnology (see Concept 20.4).
These terms are also used to describe the positions of nucleo-
The evolutionary slgnlElcance of the code's near universal-
tide sequences withln the DNA or RNA. Tims, the promoter
ity is clear. A language shared by all living things must have
sequence in DNA is said to be upstream from the terminator.
been operating very early in the hlstory of life-early enough The stretch of DNA do\vnstream from the promoter that is tran-
to be present in the common ancestor of aU present-day
scribed into an RNA molecule is called a transcription uni t.
organisms. A shared genetic vocabulary Is a reminder of the Bacteria have a single type of RNA polymerase that synthe-
kinship of all life. sizes not only mRNA but also other types of RNA that fu nc-
CONCEPT CHECK 17 . 1 tion in gene expression, such as ribosomal RNA. In contrast,
, . MAKE CONNECTIONS In a research artlcle about alkap- eukaryotes have at least three types of RNA polymerase in
tonurla published In 1902, Garrod suggested that humans their nuclei; I.he one used for pre-mRNA synthesis is called
Inherit two "characters· (alleles) for a particular enzyme and RNA polymerase II. The other RNA polymerases transcribe
that both parents must contribute a faulty version for the RNA molecules that- are not translated Into protein. In the
offspring to have alkaptonurla. Today, would this disorder
be called domlnant or recessive? (See Concept 14.4.) discussion that follows, we sta rt with the fea tures of mRNA
2. Describe the polypeptide product you would expect from a synthesis common to both bacteria and eukaryotes and then
poly-G mRNA that Is 30 nucleotides long. describe some key differences.
3. DRAW IT The templa1ee strand of a gene contains the
sequence 3'-TTCAGTCGT-5'. Suppose that the non template
sequence was transcribed Instead of the template sequence. Synthesis of an RNA Transcript
Draw the nontemplate sequence In 3' to s• order. Then draw
the mRNA sequence and translate It using Figure 17.6. Predict The three stages of transcription, as shown In Figure 17.8 and
how well the protein synthesized from the nontemplate described next, are initiation, elongation, and termination of
strand would function. if at alI. the RNA chain. Study Figure 17.8 to familiarize yourself with
For suggested answers, see Appendix A the stages and the terms used to describe them.

342 UNIT THR£E Genetics

RNA Polymerase Binding and Initiation extends several dozen or so nucleotide pairs upstream &om
of Tra.nscription the start point (Figure 17.9). Based on interactions with pro-
teins (transcription factors), RNA polymerase binds in a pre-
The promoter sequence of a gene includes within it the cise location and orientation on the promoter. This binding
transcription start point-the nucleotide where RNA poly- determlnes where transcription starts and the direction it will
merase actuaJly begins syn thesizlog the mRNA-and t ypically travel, thus which strand or DNA is used as the template.

T Figure 17 . 8 The stages of tran.Krlptlon: Initiation, T Rgure 17.9 The Initiation of transcription at a eukaryotlc
elongation. and t.e rmlnatlon. ThiS general depiction of promoter. In eukaryotlc cells, proteins called transcrlpllon faaors
transcription applies to both baaerla and eukaryotes, but the mediate the Initiation of transcription by RNA polymerase 11.
details of termination differ, as described In the text. Also. In a
baaerlum, the RNA transcript Is Immediately usable as mRNA; In a
eukaryote. the RNA transcript must first undergo processing.
~
Promo ter Transcription umt ii ti4i3"iltii.PI l
OM

3' 0 A eukaryotlc promoter

5• commonly 111cludes a TATA
l'. ~ . ,,,-m D~ box (a nucleoude sequence
contalnmg TATA) about 25
RNA polymerase nucleondes upstream rrom
O Initiation. After RNA the transcnpttonal start poinL

-·~r,.~;:
l
polymerase binds to the promoter,
the polymerase unwinds the DNA
strands and initiates RNA synthesis
at the start point on the
5'
3•
DNA

;:::::; I
template strand.
Unwound DNA TATA box Start point Template strand
Nomemplate strand of DNA
5• 3' 6 Several transcription
3' 5•
factors, one recognizing
Template strand of DNA the TATA box. nnust bind
Start point transcript

6 Elongation. The polymerase

moves downstream, unwinding
Transcription
factors 1 to the DNA before RNA
polymerase II can bind in
the correct posrtion and
orientat10n. as shown in
step 3.
the DNA and elangaung the RNA

1
transcript 5' -+ 3'. After transcrip- 5' 3'
!Jon has occurred, the DNA 3' 5'
strands re-form a double helot
Rewound
€) Additional transcription
factors (purple) bind to
D~N·!A)
~:
-7--;g;
3' the DNA along with RNA
5•
polymerase II. forming the
transcnptJon lnl Llatlon
complex. RNA polymerase II
transwpt then unwinds the DNA double
hehx., and RNA synthesis
O Termination. Eventually, the

l
begins at the start point an
RNA transcript Is released, and the template strand
the polymerase detaches from
the ONA.

5'
3' s·. -=':f:::::=TI= ~ 3•
3 5•
5' - - - ----
Completed -transcript
RNA -------
Start po1M
Direction of lranscnpt1on ("downstream")
Tr<!11~Qiption !n!t!<!t!Qn ,Qmp!g,i
MAKE CONNECTIONS Compare the use of a template strand during
transcription and repfieation. See Figure 16.18 0 fxpfain how the inreraction of RNA polymerase with the promoter
C) Mastering Biology Animation: Ovecview of Transcription would differ ff the figure shawed transcription initiation for bacteria.
Animation: Ovecview of Transcription in Bacteria

CHAPTER 11 Gene Expression: From Gene to Protein 343

 Certain sections of a promoter sequence are especially 'f Figure 17.10 Transcription e lo ngation. RNA polymerase
importan t for binding RNA polymerase in a way that moves along the DNA template strand. Joining complementary RNA
nucleotides to the 3' end of the growing RNA transcript Behind
ensures that transcription will begin at the correct start the polymerase, the new RNA peels away from the template strand.
point. In bacteria, part of the RNA polymerase Itself specifi- which re-forms a double helix with the nontemplare strarnd.
cally recognizes. and binds to th e promoter. In eukaryotes,
a collection of proteins ca lled transcription factors
(purple proteins in Figure 17.9), help guide the binding of
RNA polymerase and the Initiation of transcr iption. Only
after transcription factors are attached to the promoter
does RNA polymerase II bind to It. The whole complex of
transcription factors and RNA polymerase II bo und to the
promoter is called a traoscri1,tion initiation complex.
Figure 17 .9 shows the role of transcription facto rs and a
crucial promoter DNA sequence caJJed the TATA b ox in
forming the initiation complex at a eukaryotic promoter.
The Interaction between eukaryotic RNA polymerase Il
and transcription factocs is an example of the importance
of protein-protein interactions in controlling eukaryotic
transctiption. Once the appropriate transcription factots are
wmly attached to the promoter DNA and the polymerase is
bound to them in the correct orientation on the DNA, the
enzyme unwinds the two DNA strands and begins transcrib-
ing the template strand at the start point.

Elongation of the RNA Strand C) M astering Bio logy BioFllx"' Animation: Tran.S<rlptl on
Animation: Elongation of th& RNA Strand
As RNA polymerase moves along the DNA, it un twists the
double helix, exposing about 10-20 DNA nucleotides at a time
for pairing witJ1 RNA nucleotides (Agure 17.10). The enzyme transcribes a sequence on the DNA called the polyadenyl -
adds nucleotides to the 3 • end of the growing RNA molecule ation signal seq uence, which specifies a polyadenylation
as it moves along the double helix. As transcription proceeds signal (AAUAAA) in the pre-mRNA. This is called a "signal"
forward, the newly synthesized RNA molecule behind the because once Lhls stretch of six RNA nucleotides appears,
RNA polymerase peels away from its DNA templa te, and the it is immediately bound by certain proteins in the nucleus.
DNA double helix re-forms. Transcription progresses at a rate Then, at a point about 10-35 nucleotides downstream from
of about 40 nucleotides per second In eukaryotes. the AAUAAA, these proteins cut the RNA transcript free
Asingle gene can be transcribed simultaneously by sev- from the polymerase, releasing the pre-mRNA. The pre-
eral molecules o:f RNA po lymerase following each other like mRNA then undergoes processing, the topic of the .next sec-
trucks in a convoy. A growing strand of RNA trai.ls off from tion. Although that cleavage marks the end of the mRNA,
each polymerase, with the length of each new strand reflect- the RNA polymerase II continues to transcribe. Enzymes
ing how far along the templa te the enzyme has traveled from begin to degrade the RNA made after cleavage, starting at
the start point (see the mRNA molecules in Figure 17.23). The its newly exposed 5' end. The polymerase continues tran-
congregatloo of many polymerase molecules simultaneously scribing, pursued by the enzymes, untU they catch up to the
transcribing a siogle gene increases the amount of mRNA polymerase and it dissociates Crom the DNA.
transcribed from it, which helps the cell make the encoded
protein In large amounts.
CONCEPT CHECK 17 . 2
Termination of Transcription 1. What Is a promoter? Is It located at t he upnream or down-
Bacteria and eukaryotes differ in the way they terminate stream end of a transcription unit?
transcription. In bacteria, transcription proceeds through 2. what enables RNA polymerase to start transcribing a gene
a terminator sequence in the DNA. The transcribed ter- at the right place on the DNA In a bacterial cell? In a eukary-
otlc cell?
minator (an RNA sequence) functions as the termination
3. WHAT IF? suppme X-rays caused a siiquiince change In the
signal, causing the polymerase to detach from th e DNA and TATA box of a particular gene's promoter. How would that
release the transcript, which requires no further modifica- affect transcription ofthe gene? (See Figure 17.9.)
tion before translation. In eukaryotes, RNA polymerase II For suggested ansv1et1, see Appendix A

344 UNIT THREE Genetics

ii-i~Gfaifll nudeus. Recall that the pre-mRNA is cut and released soon
after the polyadenylation signal, AAUAAA, is transcribed. At
Eukaryotic cells modify RNA the 3' end, an enzyme then adds 50- 250 more adenine (A)
nucleotides, forming a poly-A tail. The 5' cap and poly-A tail
after transcription share several important functions. First, they seem to facilltate
Enzymes in the eukaryotic nucleus modify pre-mRNA in the export of the mature mRl'IA from the nucleus. Second,
specific ways before the genetic message is dispatched to the they help protect the mRNA from degradation by hydrolytic
cytoplasm. During this RNA processing , both ends of the enzymes. And third, they help ribosomes attach to the 5' end
primary transcript are altered. Also, in most cases, certain of the mRNA once it reaches the cytoplasm. In addition to
interior sections of the RNA molecule are cut out and the the cap and ta il on a eukaryotic mRNA molecule, Figme 17.11
remaining parts spliced together. These modifications pro- shows the untranslated regions (UTRs) at the 5' and 3' ends
duce an mRNA molecule ready for translation. of the mRNA (referred to as the 5' UTRand 3' ITTR). The UTRs
are parts of the mRNA that will not be translated into protein,
Alteration of mRNA Ends but they have other functions, such as ribosome binding.
Each end of a pre-mRNA molecule is modified in a particular
way (Figure 17.11). The 3 • end, which is synthesized 0rst, Split Genes and RNA Splicing
recelves a S ' cap, a modi fled form of a guanine (G) nucleotide A remarkable stage of RNA processing in the eukaryotic
added onto the 5' end after transcription of the 6rst20-40 nucleus Is called RNA splicing (Figure 17.12), In whlcl1
nueJeol:ldes have been uanscrlbed. The 3' end of the pre- large portions of lhe RNA primary transcript molecules are
mRNA molecule is also modified before the mRNA exits the removed and the remaining portions are reconnected. This

T Figure 17. 11 RNA proceHlng; addition nucleus. and they help protect the mRNA poly-A tall are not translated Into protein,
of the 5 ' cap and poly-A t a ll. Enzymes from degradation. When the mRNA reaches nor are the regions called the 5' untranslated
modify the two ends of a eukaryotlc pre- the cytoplasm, the modified ends, In conjunc- region (S' UTR) and 3' umranslated region
mRNA molecule. The modified ends may tion with certain cytoplasmic proteins. help (3' UTR). The pink segments are lntrons, which
promote the,export of mRNA from the with ribosome attachment. The s· cap and will be described shortly (see Figure 17 12)

IRAN~CR
~J
: ION ,._ l
°""' added to the s· end
-
A mod1f11.'d guanine nucleotide 50- 250 adenine nucleotides
added to the 3' end
"" ..,,__ Rewoni !hat includes
l,IU IA l•l•ll'ltM 'J""4nRNA , prate n-coding segments ,..,.._.,
Polyadenylauon signal

=1
T'C!< /
G l" -J' •P
....
5

~ " - s t a r t codon
.,.,.,,,.,.
3'UTR
3'~
AAA·AAA
Poly-A tall

C) Mastering Biology Animation: Adding the 5' Cap, and Poly-A Tall

T Figure 17.12 RNA processing: RNA long. The p-globln gene and Its pre-mRNA exons because they remain in the mRNA.)
spiki ng. The RNA molecule shown here transcript have three exons. corresponding During RNA processing, the lntrons are cut
codes for P-globln, one of the polypeptides to sequences that will exit the nucleus out and the exons spliced together. In many
of hemoglobin. The numbers under the RNA as mRNA. (The S' UTR and 3' UTR do not genes, the lntrons are much longer than
refer to codons; p-globln Is 146 amino adds code for proteins, but they are parts of theexons.
5' Cap \ S' Exon lntron Exon lntron Exon 3'

-~
TRAN5CRI
Pre-mRNA ---
l_,j ~ y
Poly-A tail

l
-, Codon numbers: 1-30 31- 104 105-146
i'i,ti4'1tt•~ lnlrons cut out and
exons spliced together
5' Cap
mRNA ~
~ ·-ly-A tail
5' UTR Coding 3' lJTR
segment
DRAW IT On the mRNA, indicate the sites of the start and stop codons. C) Mastering Biology Bioflix® Animation: RNA Processing

CHAPTER 11 Gene Expression: From Gene to Protelo 34S

cut-and-paste jo'b is similar to editing a movie. The average T Figure 17.13 A sp liceosome spliclng a pre-mRNA. The diagram
length of a trans cription unit along a human DNA molecule shows a ponlon of a pre-mRNA transcript, with an lmron (pink)
flanked by two exons (red). Small RNAs within the spllceosome base-
is abou t 27,000 nucleotide pairs, so the primary RNA tran-
palrwlth nudeotldes at specific sites along the lntron Next. small
script Is also that long. How@v@r, lh@ avl!Iag@-slzed prot@ln spllceosome RNAs catalyze cutting of the pre-mRNA and the splicing
of 400 amino acids requires onl y 1,200 nucleotides in RNA together of the exons. releasing the inrron for rapid degraoatlon.
to code for iL (Remember, each amino acid is encoded by a
triplet of nucleotides.) This is because most eukaryotic genes
and their RNA transcripts have long noncoding stretches
of nucleotides, regions that are not translated. Even more
surprising is that most or these noncoding sequences are
interspersed between coding segments of the gene and tJ1us Exon 1 Exon 2
between coding segments of the pre-mRNA. In o ther words,
the sequence of DNA nucleotides that codes for a eukary-
otic polypeptide Is usually not continuous; it is split Into

J !~
segments. The noncoding segments of nucleic acid that lie
between coding regions are called intervening sequences, or S~1ceosome

-------==-
introns. The other regions are called exons, because they are components
eventually expressed, usually by being translated into amino mRNA
Cut-out
acid sequences. (Exceptions Include the UTRs of the exons at s· Exon 1 Exon 2 1ntron
the ends of the RNA, which make up part of the mRNA but C) Mastering Biology Animation: A Spllceosome
are not translated into protein. Because o f these exceptions,
you may prefer to think of exo ns as sequences of RNA that
exi t the nucleus.) The terms l11tro11 and exo11 are used for both a component o f the o rganism's ribosomes. The pre-rRNA
RNA sequences and the DNA sequences that specify them. actually removes Its own introns! TI1e disco\lery of ribozymes
In maklnga primary transcript from a gene, RNA poly- invalidated the idea that all biologica l catalysts are proteins.
merase [I transcribes both intronsand exons from the DNA, but Three properties of RNA enable some RNA molecules to
the mRNA molecule that enters the cytoplasm is an abridged function as enzymes. First, because RNA is single-stranded , a
version. In the process of RNA splicing, the introns are cutout region of an RNA molecule may base-pair, in an antiparallel
from the molecule and the exons joined together, forming an arrangement, with a complementary region elsewhere in the
mRNA molecule with a continuous coding sequence. same molecule; this gives the molecu le a particular tlhree-
How is pre-m RNA splJctng carried out? The removal of dimensional structure. A speciOc structure Is essentia l to the
introns is accomplished by a large complex made of proteins catalytic functio n of ribozymes, just as it ls for enzymatic
and small RNAs called a spliceosome. This complex binds to proteins. Second, like certain amino adds in a n enzymatic
several short nucleotide seq uences along an intron, including protein, some of the bases In RNA contain functional groups
key sequences at each end (Figure 17.13). The ln tron is then that can participate in catalysis. Third, the ability of RNA to
released (and rapidly degraded), and the spliceosome joins h ydrogen-bond with other nucleic add molecules (ei ther RNA
together the two exons that Oanked the intron. The small or DNA) adds specificity to its catalytic activity. For example,
RNAs in the spliceosome not only participate in spliceosome complementary base pairing between the RNA of tbe spli-
assembly and splice site recognition, but also catalyze the ceosome and the RNA of a primary RNA transcript precisely
splldng reaction; like proteins, RNAs can act as catalysts. locates the region where the clbozyme catalyzes splicing. Later
in this chapter, you wiU see how these properties of RNA also
C) M astering Biology allow it to perform important no ncatalyt:lc roles in the cell ,
Interview with Joan Steitz: such as recognition or the three-nucleotide codons o,n mRNA.
Studying RNA. her "favorite molecule"
The Functional and Evolutionary Importan ce
Ribozymes of Intrans
The idea of a catalytic role for the RNAs in the spliceosome H!J•nlUMa Whether or not RNA spHdng and the pres-
arose from the discovery of ribozymes, RNA molecules that ence of introns have provided selective advantages during
function as enzymes. In some organlsms, RNA splicing can evolutionary history is a matter of some debate. In any case,
occur without proteins or even addltional RNA molecules: it is Informative to consider their possible adaptive benefits.
The intron RNA functio ns as a rlbozym e and catalyzes its own Specific functions have not been ldentiEled for m ost introns,
removal. For example, in the ci liate protist Tetmhy111e11a, self- but at least some contain sequences that regu late gene expres-
splicing occurs in the production of ribosomal RNA (rRNA), sion, and many affect gene products.

346 UNIT THREE Genetics

 One important consequence of the presence of introas in CONCEPT CHECK 17 . 3
genes is that a single gene can encode more than one kind 1. Given that there are about 20,000 human proteln-c:odlng genes,
of polypeptide. Many genes are known to give rise to two or how can human cells make 75,000-100,000 different proteins?
more different polypeptides, depending on which segments 2. Compare RNA spllclng to how you would watch a pre-
are treated as exons during RNA processing; thjs is called recorded television show. What would lntrons correspond
alternativ.e RNA splicing (see Figure 18.14). Results from to In this analogy?
the Human Genome Project (discussed in Concept 21.1) sug- 3. WHAT IF? What would be the effect of treating cells with an
agent that removed the 5' cap from mRNAs?
gest that alternative RNA splicing is one reason humans can
For suggested answe,s, see Appendix A
get along with about the same number of genes as a nema-
tode (roundworm). Because of alternative splicing, the num-
ber of different protei n products an orga nism produces can be li-i#3faif¥1
much greater than its number of genes.
Proteins often have a modular architecture consisting of Translation is the RNA-directed
discrete structural and functional regions called dom ains. synthesis of a polypeptide:
One domain of an enzyme, for example, might include the
active site, while anot her might allow the enzyme to bind to a A Closer Look
cellular membrane. In quite a few cases, differen t exons code We will now examine how genetic information £lows from
for the diffe.rent doma ins of a protein (Figure 17.14). mRNA to protein-the process of trarulation (Figure 17.15).
The presence of lntrons In a gene may faci litate the evolu- We'll focus on the basic steps of translation that occur In both
tion or new and potentially beneficial proteins as a result or bacteria and eukaryotes, while pointing out key differences.
a process known as exo11 slwffling (see Figure 21.16). lntrons
Increase the probability of crossing over between the exons T Rgure 17.15 Translation: the basic concept. AS a molecule
of mRNA Is moved through a ribosome, codons are translated Into
of alleles of a gene-simply by providing more terrain for amino acids, one by one. The translatars. or Interpreters, are tRNA
crossovers without interrup ting coding sequences. This molecules, each type with a specific antlcodon at one end and a
might result in new combin ations of exons and proteins with corresponding amino acid at the other end. A tRNA adds Its amino
altered structure and function . We can also imagine the occa- acid cargo to a growing polypeptide chain when the antlcodon
hydrogen-bonds to the complementary codon on the mRNA.
sional milting and matching of exons between completely
different (no nallelic) genes. Exon shuffling of either sort
could lead to new proteins with novel combinations offunc-
tions. While most of the shuffling wou ld result In nonbenefl-
cial changes, occasionall y a beneficial variant might arise.

Amino
~ Figure 17.14 Correspondence between exons and protein acids
domains.
Gene • ~
ONA
'-"''"'
W:--=-
IElllll
- 1_ ,,_
lntroo
~ Exoo 2 lntroo Exon 3 ~ • tRNA with
attached
l
Transcription

RNA processing l
Ribosome

,
C) Mastering Biology BioAix~ Animation: Translation
Polypeptide Animation: Overview of Translation

CHAPTER 11 Gene Expression; From Gene to Protein 347

Molecular Components of Translation ""Figure 17.16 The .tructure of transfer RNA (tRNA).
In the process of translation, a cell "reads" a genetic message 3'
and builds a polypeptide accordingly. The message is a series
Amino acid
of codons a.long an mRNA molecule, and the translator is attachment site
ca.I.led a transfer RNA (tRNA). The function of a tRNA is to
transrer a n amlno acid from the cytoplasmlc pool of amino
acids to a growing polypeptide in a ribosome. A cell keeps
its cytoplasm stocked with all 20 amino acids, el Lher by syn-
thesizing them from other compounds or by ta king them
up from the surrounding solution. The ribosome, a structure
made of proteins and RNAs, adds each amino acid brought to
it by a tRNA to the growing end of a polypeptide chain (see
Figure 17.15).
Trans lation is simple in principle but complex in its bio-
chemistry and mechanics, especially in the euka ryotic cell. In
dissecting translation, we' ll focus on the slightly less compli-
cated version or the process th at occurs in bacteria. We'll first
look at the major players in this process.
~
An!JCOdon
The Structure ,and Function of Transfer RNA (a) Two-dimensional S11Ucture. The four base-paired regions and
The key to translating a genetic message into a specific amino three loops are charactenstJC of all tRNAs, as is the base sequence
of the amino acid attachment site at the 3' end The anticodon
acid sequence Is the fact that each tRNA molecu le enables tnplet Is unique to each tRNA type, as are some sequences In the
translation of a given mRNA codon Into a certa in amino acid. other two loops. (The astensks mark bases that have been
This is possible because a tRNA bears a speciric amino acid at chemically modified, a charaaenstic or tRNA. The modified bases
contribute to tRNA funcnon in a way that 1s not yet understood.)
one end of its tluee-dimensional structure, while at the other
end is a nucleotide triplet that can base-pair witl1 the comple- Amino acid
mentary codon on mRNA. attachment site
A tRNA molecule consists of a single RNA strand tllat is
only about 80 nucleotides lo ng (compared to hundreds of
nucleotides for most mRNA molecules). The presence of com-
plementary stretches of nucleotide bases that ca n hydrogen-
bond to each other allows th Is single s trand to fold back on
itse.1£ and roan a molecule with a particular 3-0 structure.
Flattened into one plane to clarify this base pairing, a tRNA
molecule looks file a cloverleaf (Figure 17.16a). The tRNA
actually twists and folds in to a compact 3-0 structure that ls
rough ly L-shaped (Figure 17.16b), with the 5' and 3' ends
or the linear tRNA both located near one end of the struc-
ture. The protruding 3' end acts as the attachment si te for an
amino acid. The loop extending from the other end of the (c) Symbol used
(b) Three-dimensional structure in thJs book
L includes the anticodon, tile particular nucleotide triplet
that base-pairs to a specific mRNA codon. Thus, the structure VISUAL SKJLLS Look at the tRNA shown in this figure. Based on its
of a tRNA molecule fits its function. anticodon, identify the codon it would bind to, as well as the ammo acid
that it would carry.
Anticodons ue conventionally written 3' -+ 5 • to align ...,,
properly with codons written 5' .... 3' (see Figure 17 .15). (For
base pairing, RNA strands must be antlpara llel, like DNA.) As
C) Mastering Biology HHM I Video: RNA Folding !!,~!!!.
an example of how tRNAs work, consider the mRNA codon
5'-GGC3', which is translated as the amino acid glycine. a ribosome, glydne will be added to the polypeptide dlain
Tbe tRNA tllat b.ase-pairs with this codon by hydrogen bond- whenever the codon 5 '-GGC-3' is presented for translation.
ing has 3 '-CCG-5' as its anticodon and carries glycine at its Codon by codon, the genetic message is translated a:s tRNAs
other end (see the incomlng tRNA approaching the ribosome position each amino acid in the order prescribed, and th e
in Figure 17.15). As an mRNA molecule is moved Lhrough ribosome adds that amino acid on to Lhe growing polypeptide

348 UNITTHREE Genetics

chain. The tRNA molecule is a translator in the sense that, in 'f Figure 17.17 Aminoacyl-tRNA synthetases provide
the coo text of the ribosome, it can read a n udeic add word specificity in joining amino acids to their tRNAs. Linkage of a
tRNA to its amino acid is an endergonlc process that occurs at the
(the mRNA codon) and interpret it as a protein word (the
expense of ATP, which loses two phosphate groups. becoming AMP.
amino acid).
Like mRNA and other types of cellular RNA, transfer 0 The amino acid
and the appropriate
RNA molecules are transcribed from DNA templates. lo a tRNA enter the active
eukaryoticcell, tRNA, like mRNA, is made in the nucleus site of the specific
synthetase.
and then travels to the cytoplasm, where it will participate
in the process of translation. lo both bacterial and eukary- Tyrosyl-tRNA
otic cells, each tRNA molecule is used repeatedly, picking syn the lase (enzyme),
up its designated amino acid in the cytosol, depositing this which can only bind
tyrosine and Tyr-tRNA
ca1go onto a polypeptide chain at the ribosome, and then
leaving the ribosome, ready to pick up another of the same
amino add.
The accurate translation of a genetic message requires

~
two instances of molecular recognition. First, a tRNA that
binds to an mRNA codon specifying a particular amino acid
Amlnoacyl-tRNA
must ca1ry that amino add, and no other, to the ribosome. synthetase
The correct matching up of tRNA and amino acid Is carried
Anllcodon on tRNA
out by a family of related enzymes that are aplly named complementary Lo the
anuooacyl-tRNA syothetascs (Figure 17.17). The actlve Tyr codon on mRNA
site or each type of ami noacyl-tRNA synthetase fits only a
specific combination of amino acid and tRNA. (Regions of f) Using ATP,
the synthetase
both the amino add attachment e nd and the anticodon end catalyzes the
of the tRNA ensure the specific fit.) There are 20 different covalent bonding
of the amino acid
synthetases, one for each amino add. A syn thetase joins a to tts specific tRNA.
given amino acid lo an appropriate tRNA; one synthetase
is able to bind to a ll lhe different tRNAs for ltS particular
amino acid. The synthetase catalyzes the covalent attach-
ment of the amino acid to Its t1U11A in a process driven by the €) The tRNA,~
charged with
hydro lysis of ATP. The resulting aminoacyl tRNA, also called its amino acid, Computer model
a charged tRNA , is released from the enzyme and is then is released by
the synthetasc. i
avai lable to deliver its amino acid to a growing polypeptide
chain on a ribosome. C) Mastering Bio logy Ani mation: Transfer RNA
The second instance of molecular recognition is the
pairi ng of the tRNA antlcodon with the appropriate mRNA
codon. If one tRNA type existed for each mRNA codon The Structure and Function of Ribosomes
specifying an amino acid, there would be 61 tRNAs (see Although the ribosomes of bacteria and eukaryotes are very
Figure 17.6). In bacteria, however, there are only about 45 similar in structure and functlon, eukaryotic ribosomes
tRNAs, signifying that some tRNAs must be able to bind to are slightly larger and differ somewhat from bacterial ribo-
more than one codon. Th is is possible because the rules for somes in lhel r mo lecular composilion. The differences
base pairing between the third nucleotide base of a codon are medica lly significant. Certain antibiotic dmgs ca n
and the corresponding base of a tRNA anticodon are relaxed inactlvate bacterial ribosomes without affecting the abil-
compared to those at other codon positions. For example, ity of eukaryotic ribosomes to make proteins. These drugs,
the nucleotide base U at the S' end of a tRNA anticodon can including tetracycline and strep tomycin, are us,ed to combat
pai r with either A or Gin the third position (at the 3 ' end) bacterial infections.
of a n mRNA codon. The flexible base pairing at this codon Ribosomes facilitate the specific coupling of tRNA anti co-
position is called wobble. Wobble explains why the syn- dons with mRNA codons during protein synthes.is. A ribosome
onymous codons for a given amino acid most often differ consists of a large subunit and a small subunit, each made up
in their third nucleotide base. Accordingly, a tRNA with the of proteins and one or more ribosomal RNAs, or rRNAs
anticodon 3 '-UCU-5' ca n base-pair with either the rnRl"lA (Figure 17.18). ln eukaryotes, the subunits are made in the
codon S'-AGA-3 ' or 5 '-AGG -3', both of which code for argi- nucleolus. Ribosomal RNA genes are transcribed, a nd the RNA
nine (see Figure 17.6). is processed and assembled with proteins imported from the

CHAPTER 11 Gene Expression: From Gene to Protein 349

Y Figure 17.18 The anatomy of a functioning ribosome. cytoplasm. Completed ribosomal subunits are then exported
via nuclear pores to the cytoplasm. ln both bacteria and
eukaryotes, a large and a small subunit join to form a func-
tional ribosome only when attached to an mRNA molecu le.
Exit tunnel About one-third or the mass of a ribosome is made up of pro-
Milillil\11-ili ~ ; for growing teins; the rest consists of three rRNA molecules (in bacteria) or
polypeptide
four (in eukaryotes). Because most cells contain thousands of
ribosomes, rRNA is the most abundant type of cellular RNA.
The structure of a ribosome renects Hs function of bringing
Large an mRNA molecule together with tRNAs carrying am lno acids.
subunit
} 111e mRNA Itself has a binding site fo r the ribosome. (In the
Scientific Skllls Exercise, you can work with DNA sequences
tRNA representing this binding site in a group of Escherid1ia coli
molecules Small
} subunit genes.) The cibosome, in turn, has a binding site for mRNA,
as well as three bincling sites fortRNA (see Figure 17.18). The
s· P she (peptidyl-tRNA binding site) holds the tRNA carrying
mRNA ]' the growing polypeptide chain, while the A site (aminoacyl-
(a} Computer model of functioning ribosome. This is a model of
tRNA binding site) holds the tRNA carrying the next amino
a bacterial ribosome, showing •ts overall shape. The eukaryobc acid to be added to the chain. Discharged tRNAs leave the ribo-
ribosome •s roughly similar. A ribosomal subunit •s a complex some &om the E site (exit site). The ribosome holds the tRNA
of ribosomal RNA molecul~ and protl!fns.
and mRNA in close proximity and positions the new amino

ro p site {peptidyl-tRNA
acid so that it can be added to thecarboxyl end of the growing
binding site) polypeptide. It then catalyzes the fom1atlon of the peptide
bond. As the polypeptide becomes longer, it passes through an
2!!!--Ex•t tunnel
exit t111111el in the ribosome's large subun it. When the polypep-
Asi te (2_1'mnoacyt- tide is complete, It ls released through the exit tunneE.
Esite--- tRNA binding site)
(~xit site) The widely accepted model is that rRNAs, rather than
Large ribosomal proteins, are primarily responsible for both the
subunit
structure and the function of the ribosome. The proteins,
mRNA ----=iii!
binding srte Small which are largely on the exterior, support the shape changes
subunit of the rRNA molecu les as they carry out catalysis during trans-
lation. Ribosomal RNA is the main constituent of the A and
(b} Schematic model showing binding sites. A ribosome has an P sites and of the Interface between the two subunits; it also
mRNA bmd•ng site and three tRNA bmdmg sttes, known as the acts as the catalyst of peptide bond formation. Thus, a ribo-
A, P. and E SI tes. This schematic ribosome w•II appear m later
diagrams. some could actually be considered one colossal Jibozyme!

Building a Polypeptide
We can divide tran.slation, the synthesis of a polypeptide, into
three stages: initiation, elongation, and termination. AU three
require protein "factors" that aid lo the translation process.
Some steps of initiation and elongation also require energy,
provided by the hydrolysis of guanosine tripbosphate (GTP).
mRNA

\ Ribosome Association and Initiation of Translation

The initiation stage of translation brings together an mRNA, a
5'
tRNA bearing the £1rst amino add of the polypeptide, and the
two subunits of a ribosome. First, a small ribosomal subunit
(c) Schematic model with mRNA and tRNA. A tRNA fits into binds to both the mRNA and a specific Initiator tRNA, which
the Asite when ,ts antlcodon base-pairs with an mRNA codon.
The Psite holds the tRNA attached to the growing polypepude. carries the amino acid methionine. In bacteria, the small subunit
The A site holds the tRNA carrying the next amino acid to be added can bind lhl! two In eilhl!r order; It binds I.he mRNA at a speclBc
to the polypepude chain. Discharged tRNAs leave from the RNA sequence, just upstream of the AUG start codon. lo eukary-
Esite. The polypepude grows at Its carboxyl end.
otes, the small subunit, with the initiator tRNA already bound,
C) Mastering Biology Animation: Ribosomes binds to the 5 • cap of the rnRNA and then moves, or scans,

350 UNIT THREE Genetics