the flow of genetic information from dna to rna to protein...190 chapter 10 molecular biology of the...

CHAPTER 10 Molecular Biology of the Gene190

The Flow of Genetic Information from DNA to RNA to Protein10.6 The DNA genotype is expressed as proteins, which provide

the molecular basis for phenotypic traitsWith our knowledge of DNA, we can now define genotype andphenotype more precisely than we did in Chapter 9. An organ-ism’s genotype, its genetic makeup, is the heritable informationcontained in its DNA. The phenotype is the organism’s physicaltraits. So what is the molecular connection between genotypeand phenotype?

The answer is that the DNA inherited by an organism speci-fies traits by dictating the synthesis of proteins. In other words,proteins are the links between the genotype and the phenotype.However, a gene does not build a protein directly. Rather, a genedispatches instructions in the form of RNA, which in turn pro-grams protein synthesis. This fundamental concept in biology,termed the “central dogma” by Francis Crick, is summarized inFigure 10.6A. The molecular “chain of command” is from DNAin the nucleus of the cell to RNA to protein synthesis in the cy-toplasm. The two main stages are transcription, the synthesis ofRNA under the direction of DNA, and translation, the synthe-sis of protein under the direction of RNA.

The relationship between genes and proteins was first pro-posed in 1909, when English physician Archibald Garrod sug-gested that genes dictate phenotypes through enzymes, theproteins that catalyze chemical reactions. Garrod hypothesizedthat an inherited disease reflects a person’s inability to make aparticular enzyme, and he referred to such diseases as “inbornerrors of metabolism.” He gave as one example the hereditarycondition called alkaptonuria, in which the urine is dark becauseit contains a chemical called alkapton. Garrod reasoned that in-dividuals without the disorder have an enzyme that breaks downalkapton, whereas alkaptonuric individuals cannot make the en-zyme. Garrod’s hypothesis was ahead of its time, but researchconducted decades later proved him right. In the intervening

years, biochemists accumulated evidence that cells make andbreak down biologically important molecules via metabolicpathways, as in the synthesis of an amino acid or the breakdownof a sugar. As we described in Unit I (see Module 5.15, for exam-ple), each step in a metabolic pathway is catalyzed by a specificenzyme. Therefore, individuals lacking one of the enzymes for apathway are unable to complete it.

The major breakthrough in demonstrating the relationshipbetween genes and enzymes came in the 1940s from the workof American geneticists George Beadle and Edward Tatumwith the bread mold Neurospora crassa (Figure 10.6B). Beadleand Tatum studied strains of the mold that were unable togrow on a simple growth medium. Each of these so-callednutritional mutants turned out to lack anenzyme in a metabolic pathway thatproduced some molecule the moldneeded, such as an amino acid.Beadle and Tatum also showedthat each mutant was defectivein a single gene. This resultsuggested the one gene–oneenzyme hypothesis—the ideathat the function of a gene is todictate the production of aspecific enzyme.

The one gene–one enzyme hy-pothesis has been amply confirmed,but with important modifica-tions. First, it was extendedbeyond enzymes to includeall types of proteins. For ex-ample, keratin (the structuralprotein of hair) and the hormone insulin are two examples ofproteins that are not enzymes. So biologists began to think interms of one gene–one protein. However, many proteins aremade from two or more polypeptide chains, with eachpolypeptide specified by its own gene. For example, hemoglo-bin, the oxygen-transporting protein in your blood, is builtfrom two kinds of polypeptides, encoded by two differentgenes. Thus, Beadle and Tatum’s hypothesis is now stated asfollows: The function of a gene is to dictate the production ofa polypeptide. Even this description is not entirely accurate,in that the RNA transcribed from some genes is not translated(you’ll learn about two such kinds of RNA in Modules 10.11and 10.12). The flow of information from genotype to pheno-type continues to be an active research area.

What are the functions of transcription and translation??

●Transcription is the transfer of information from DNA to RNA. Translationis the use of the information in RNA to make a polypeptide.

! Figure 10.6A The flow of genetic information in a eukaryotic cell

DNA

Protein

Transcription

Translation

RNA

NUCLEUS

CYTOPLASM

! Figure 10.6B The breadmold Neurospora crassa growingin a culture dish

U U U G G C C G U U U U

Amino acid

DNA

RNA

Polypeptide

Codon

A A A C C G G C A A A A

DNAmolecule

Gene 1

Gene 2

Gene 3

Transcription

Translation

191The Flow of Genetic Information

●300

! Figure 10.7 Transcription and translation of codons

10.7 Genetic information written in codons is translated into amino acid sequencesGenes provide the instructions for making specific proteins.But a gene does not build a protein directly. As you havelearned, the bridge between DNA and protein synthesis is thenucleic acid RNA: DNA is transcribed into RNA, which is thentranslated into protein. Put another way, information withinthe cell flows as DNA RNA protein. This is sometimesstated as: “DNA makes RNA makes protein.”

Transcription and translation are linguistic terms, and it isuseful to think of nucleic acids and proteins as having lan-guages. To understand how genetic information passes fromgenotype to phenotype, we need to see how the chemical language of DNA is translated into the different chemical lan-guage of proteins.

What, exactly, is the language of nucleic acids? Both DNAand RNA are polymers (long chains) made of nucleotidemonomers (the individual units that make up the polymer). InDNA, there are four types of nucleotides, which differ in theirnitrogenous bases (A, T, C, and G). The same is true for RNA,although it has the base U instead of T.

Figure 10.7 focuses on a small region of one gene (gene 3,shown in light blue) carried by a DNA molecule. DNA’slanguage is written as a linear sequence of nu-cleotide bases on a polynucleotide, a sequencesuch as the one you see on the enlarged DNAsegment in the figure. Specific sequences ofbases, each with a beginning and an end,make up the genes on a DNA strand. A typi-cal gene consists of hundreds or thousandsof nucleotides in a specific sequence.

The pink strand underneath the enlargedDNA segment represents the results of transcrip-tion: an RNA molecule. The process is called tran-scription because the nucleic acid language of DNAhas been rewritten (transcribed) as a sequence of baseson RNA. Notice that the language is still that of nucleicacids, although the nucleotide bases on theRNA molecule are complemen-tary to those on the DNA strand.As we will see in Module 10.9,

this is because the RNA was synthesized using the DNA as atemplate.

The purple chain represents the results of translation, theconversion of the nucleic acid language to the polypeptide lan-guage (recall that proteins consist of one or more polypep-tides). Like nucleic acids, polypeptides are polymers, but themonomers that compose them are the 20 amino acids com-mon to all organisms. Again, the language is written in a linearsequence, and the sequence of nucleotides of the RNA mol-ecule dictates the sequence of amino acids of the polypeptide.

The RNA acts as a messenger carrying genetic infor-mation from DNA.

During translation, there is a change in lan-guage from the nucleotide sequence of theRNA to the amino acid sequence of thepolypeptide. How is this translationachieved? Recall that there are only four dif-ferent kinds of nucleotides in DNA (A, G,C, T) and RNA (A, G, C, U). In translation,these four nucleotides must somehow spec-

ify all 20 amino acids. Consider whethereach single nucleotide base were to specify one

amino acid. In this case, only four of the 20 aminoacids could be accounted for, one for each type of base.

What if the language consisted of two-letter code words?If we read the bases of a gene two at a time—AG, for example,could specify one amino acid, whereas AT could designate adifferent amino acid—then only 16 arrangements would bepossible (42), which is still not enough to specify all 20 aminoacids. However, if the code word in DNA consists of a triplet,

with each arrangement of three consecutive bases specifyingan amino acid—AGT specifies one amino acid, for example,while AGA specifies a different one—then there can be 64(that is, 43) possible code words, more than enough tospecify the 20 amino acids. Indeed, there are enoughtriplets to allow more than one coding for each aminoacid. For example, the base triplets AAT and AAC could

both code for the same amino acid. Thus, triplets of basesare the smallest “words” of uniform length that can specify

all the amino acids (see the brackets below the strand of RNAin Figure 10.7).

Experiments have verified that the flow of informationfrom gene to protein is based on a triplet code: The geneticinstructions for the amino acid sequence of a polypeptidechain are written in DNA and RNA as a series of nonover-lapping three-base “words” called codons. Notice in the fig-ure that three-base codons in the DNA are transcribed intocomplementary three-base codons in the RNA, and then theRNA codons are translated into amino acids that form apolypeptide. We turn to the codons themselves in the nextmodule.

What is the minimum number of nucleotides necessary tocode for 100 amino acids?

?


10.8 The genetic code dictates how codons are translated into amino acidsDuring the 1960s, scientists cracked the genetic code, the set ofrules that relate codons in RNA to amino acids in proteins. Therules were established by a series of elegant experiments that dis-closed the amino acid translations of each of the nucleotide-triplet code words. The first codon was deciphered in 1961 byAmerican biochemist Marshall Nirenberg. He synthesized anartificial RNA molecule by linking together identical RNA nu-cleotides having uracil as their only base. No matter where thismessage started or stopped, it could contain only one type oftriplet codon: UUU. Nirenberg added this “poly-U” to a test-tube mixture containing ribosomes and the other ingredientsrequired for polypeptide synthesis. This mixture translated thepoly-U into a polypeptide containing a single kind of aminoacid, phenylalanine (Phe). Thus, Nirenberg learned that theRNA codon UUU specifies the amino acid phenylalanine. Byvariations on this method, the amino acids specified by all thecodons were soon determined.

As shown in Figure 10.8A, 61 of the 64 triplets code foramino acids. The triplet AUG (green box in the figure) has adual function: It codes for the amino acid methionine (Met)and also can provide a signal for the start of a polypeptidechain. Three codons (red) do not designate amino acids. Theyare the stop codons that mark the end of translation.

Notice in Figure 10.8A that there is redundancy in thecode but no ambiguity. For example, although codons UUUand UUC both specify phenylalanine (redundancy), neitherof them ever represents any other amino acid (no ambiguity).The codons in the figure are the triplets found in RNA. Theyhave a straightforward, complementary relationship to the

codons in DNA, with UUU in the RNA matching AAA in theDNA, for example. The nucleotides making up the codonsoccur in a linear order along the DNA and RNA, with nogaps or “punctuation” separating the codons.

As an exercise in translating the genetic code, consider the 12-nucleotide segment of DNA in Figure 10.8B. Let’s read this as aseries of triplets. Using the base-pairing rules (with U in RNA in-stead of T), we see that the RNA codon corresponding to the firsttranscribed DNA triplet, TAC, is AUG. As you can see in Figure10.8A, AUG specifies, “Place Met as the first amino acid in thepolypeptide.” The second DNA triplet, TTC, dictates RNA codonAAG, which designates lysine (Lys) as the second amino acid.We continue until we reach a stop codon (UAG in this example).

The genetic code is nearly universal, shared by organismsfrom the simplest bacteria to the most complex plants andanimals. As you will learn in Chapter 12, such universality iskey to modern DNA technologies because it allows scientiststo mix and match genes from various species (Figure 10.8C).A language shared by all living things must have evolved earlyenough in the history of life to be present in the common an-cestors of all modern organisms. A shared genetic vocabularyis a reminder of the kinship that connects all life on Earth.

Translate the RNA sequence CCAUUUACG into the correspon-ding amino acid sequence.

?

●Pro-Phe-Thr

UCU

UCC

UCA

UCG

UAU

UAC

UGU

UGC

UGG Trp

UUU

UUC

UUA

UUG

Phe

Leu

Tyr Cys

Ser

CUU

CUC

CUA

CUG

CCU

CCC

CCA

CCG

Pro

CAU

CAC

CAA

CAG

His

Gln

CGU

CGC

CGA

CGG

Arg

Ile

AUU

AUC

AUA

ACU

ACC

ACA

ACG

Thr

AAU

AAC

AAA

AAG

Asn

Lys

AGU

AGC

AGA

AGG

GGU

GGC

GGA

GGG

Gly

Ser

Arg

GAU

GAC

GAA

GAG

Asp

Glu

GCU

GCC

GCA

GCG

AlaVal

GUU

GUC

GUA

GUG

UAA Stop

UAG Stop

UGA Stop

AUG Met orstart

Leu

Firs

t bas

e

Second baseU C A G

U

C

A

G

U

C

A

G

U

C

A

G

U

C

A

G

U

C

A

G

Thir

d b

ase

AT C T T C A A A A T C

A T G A A G T T T T A G

A U G A A G U U U U A G

Startcodon

Stopcodon

Met Lys

Strand to be transcribed

Phe

DNA

RNA

Polypeptide

Transcription

Translation

" Figure 10.8CThe mice to the left andright are engineered toexpress a greenfluorescence proteinobtained from a jelly(jellyfish)

! Figure 10.8B Deciphering the genetic information in DNA

! Figure 10.8A Dictionary of the genetic code (RNA codons)

DNA of gene

RNA polymerase

PromoterDNA

TerminatorDNA

Initiation1

2

3

Elongation

Termination

Completed RNA RNApolymerase

Area shownin Figure 10.9A

GrowingRNA


10.9 Transcription produces genetic messages in the form of RNAIn eukaryotic cells, transcription, the transfer of geneticinformation from DNA to RNA, occurs in the nucleus. (Thenucleus, after all, contains the DNA; see Figure 10.6A for areview.) An RNA molecule is transcribed from a DNA tem-plate by a process that resembles the synthesis of a DNAstrand during DNA replication (see Module 10.4).

Figure 10.9A is a close-up view of the process of transcrip-tion. As with replication, the two DNA strands must first sepa-rate at the place where the process will start. In transcription,however, only one of the DNA strands serves as a template forthe newly forming RNA molecule; the other strand is unused.The nucleotides that make up the new RNA molecule taketheir place one at a time along the DNA template strand byforming hydrogen bonds with the nucleotide bases there. Notice that the RNA nucleotides follow the same base-pairingrules that govern DNA replication, except that U, rather thanT, pairs with A. The RNA nucleotides are linked by the tran-scription enzyme RNA polymerase, symbolized in the figureby the large gray shape.

Figure 10.9B is an overview of the transcription of an en-tire prokaryotic gene. (We focus on prokaryotes here; eukary-otic transcription occurs via a similar but more complexprocess.) Specific sequences of nucleotides along the DNAmark where transcription of a gene begins and ends. The“start transcribing” signal is a nucleotide sequence called apromoter. A promoter is a specific binding site for RNApolymerase and determines which of the two strands of theDNA double helix is used as the template in transcription.

! The first phase of transcription, called initiation, is theattachment of RNA polymerase to the promoter and the startof RNA synthesis. " During a second phase of transcription,elongation, the RNA grows longer. As RNA synthesis contin-ues, the RNA strand peels away from its DNA template,allowing the two separated DNA strands to come back

together in the region already transcribed. # Finally, in thethird phase, termination, the RNA polymerase reaches a se-quence of bases in the DNA template called a terminator.This sequence signals the end of the gene; at that point, thepolymerase molecule detaches from the RNA molecule andthe gene.

In addition to producing RNA that encodes amino acid se-quences, transcription makes two other kinds of RNA thatare involved in building polypeptides. We discuss these threekinds of RNA—messenger RNA, transfer RNA, and riboso-mal RNA—in the next three modules.

What is a promoter? What molecule binds to it??

●A promoter is a specific nucleotide sequence at the start of a gene where RNApolymerase attaches and begins transcription.

A

C C A A TA

C

T

T A G G TG

T

G

C C AUA

U

U

C

Newly made RNA

Free RNA nucleotides

Direction oftranscription

RNApolymerase

Templatestrand of DNA

TA

C

A

C

T

G

! Figure 10.9B The transcription of a gene

! Figure 10.9A A close-up view of transcription


●These genes have introns, noncoding sequences of nucleotides that arespliced out of the initial RNA transcript, to produce mRNA.

10.10 Eukaryotic RNA is processed before leaving the nucleus as mRNAThe kind of RNA that encodes amino acid sequences is calledmessenger RNA (mRNA) because it conveys genetic messagesfrom DNA to the translation machinery of the cell. MessengerRNA is transcribed from DNA, and the information in themRNA is then translated into polypeptides. In prokaryoticcells, which lack nuclei, transcription and translation occur inthe same place: the cytoplasm. In eukaryotic cells, however,mRNA molecules must exit the nucleus via the nuclear poresand enter the cytoplasm, where the machinery for polypeptidesynthesis is located.

Before leaving the nucleus as mRNA, eukaryotic transcriptsare modified, or processed, in several ways (Figure 10.10). Onekind of RNA processing is the addition of extra nucleotides tothe ends of the RNA transcript. These additions include a smallcap (a single G nucleotide) at one end and a long tail (a chainof 50 to 250 A nucleotides) at the other end. The cap and tail(yellow in the figure) facilitate the export of the mRNA fromthe nucleus, protect the mRNA from attack by cellular en-zymes, and help ribosomes bind to the mRNA. The cap andtail themselves are not translated into protein.

Another type of RNA processing is made necessary in eu-karyotes by noncoding stretches of nucleotides that interruptthe nucleotides that actually code for amino acids. It is as if un-intelligible sequences of letters were randomly interspersed inan otherwise intelligible document. Most genes of plants andanimals, it turns out, include such internal noncoding regions,which are called introns (“intervening sequences”). The cod-ing regions—the parts of a gene that are expressed—are calledexons. As Figure 10.10 shows, both exons (darker color) andintrons (lighter color) are transcribed from DNA into RNA.However, before the RNA leaves the nucleus, the introns are removed, and the exons are joined to produce an mRNA molecule with a continuous coding sequence. (The short non-coding regions just inside the cap and tail are considered partsof the first and last exons.) This cutting-and-pasting process iscalled RNA splicing. In most cases, RNA splicing is catalyzedby a complex of proteins and small RNA molecules, but some-times the RNA transcript itself catalyzes the process. In otherwords, RNA can sometimes act as an enzyme that removes itsown introns! As we will see in the next chapter (in Module 11.4),

RNA splicing also provides a means to produce multiplepolypeptides from a single gene.

As we have discussed, translation is a conversion betweendifferent languages—from the nucleic acid language to the pro-tein language—and it involves more elaborate machinery thantranscription. The first important ingredient required for trans-lation is the processed mRNA. Once it is present, the machineryused to translate mRNA requires enzymes and sources of chem-ical energy, such as ATP. In addition, translation requires twoheavy-duty components: ribosomes and a kind of RNA calledtransfer RNA, the subject of the next module.

Explain why most eukaryotic genes are longer than the mRNAthat leaves the nucleus.

?

DNA

RNAtranscriptwith capand tail

TranscriptionAddition of cap and tail

Introns removed

Exons spliced together

NUCLEUS

CYTOPLASM

mRNA

Coding sequence

Exon Intron Exon Intron Exon

Tail

Cap

10.11 Transfer RNA molecules serve as interpreters during translationTranslation of any language requires an interpreter, someoneor something that can recognize the words of one languageand convert them to another. Translation of a genetic messagecarried in mRNA into the amino acid language of proteinsalso requires an interpreter. To convert the words of nucleicacids (codons) to the amino acid words of proteins, a cellemploys a molecular interpreter, a special type of RNA calledtransfer RNA (tRNA).

A cell that is producing proteins has in its cytoplasm a sup-ply of amino acids, either obtained from food or made from

other chemicals. But amino acids themselves cannot recognizethe codons in the mRNA. The amino acid tryptophan, for ex-ample, is no more attracted by codons for tryptophan than byany other codons. It is up to the cell’s molecular interpreters,tRNA molecules, to match amino acids to the appropriatecodons to form the new polypeptide. To perform this task,tRNA molecules must carry out two functions: (1) picking upthe appropriate amino acids and (2) recognizing the appro-priate codons in the mRNA. The unique structure of tRNAmolecules enables them to perform both tasks.

! Figure 10.10 The production of eukaryotic mRNA

Enzyme

tRNA

ATP

Anticodon

Amino acid attachment site

RNA polynucleotide chain

Hydrogen bond

A tRNA molecule, showing its polynucleotide strand and hydrogen bonding

A simplifiedschematic of a tRNA


●It is the base triplet of a tRNA molecule that couples the tRNA to acomplementary codon in the mRNA. This is a key step in translatingmRNA to polypeptide.

Figure 10.11A shows two representations of a tRNAmolecule. The structure on the left shows the back-bone and bases, with hydrogen bonds between basesshown as dashed magenta lines. The structure on theright is a simplified schematic that emphasizes themost important parts of the structure. Notice from thestructure on the left that a tRNA molecule is made of asingle strand of RNA—one polynucleotide chain—consisting of about 80 nucleotides. By twisting andfolding upon itself, tRNA forms several double-stranded regions in which short stretches of RNA base-pair with other stretches via hydrogen bonds. Asingle-stranded loop at one end of the folded moleculecontains a special triplet of bases called an anticodon.The anticodon triplet is complementary to a codon tripleton mRNA. During translation, the anticodon on tRNArecognizes a particular codon on mRNA by using base-pairing rules. At the other end of the tRNA molecule is asite where one specific kind of amino acid can attach.

In the modules that follow, we represent tRNA with thesimplified shape shown on the right in Figure 10.11A. Thisshape emphasizes the two parts of the molecule—the anticodon and the amino acid attachment site—that givetRNA its ability to match a particular nucleic acid word (a codon in mRNA) with its corresponding protein word (an amino acid). Although all tRNA molecules are similar,there is a slightly different variety of tRNA for each amino acid.

Each amino acid is joined to the correct tRNA by a specificenzyme. There is a family of 20 versions of these enzymes, oneenzyme for each amino acid. Each enzyme specifically bindsone type of amino acid to all tRNA molecules that code for thatamino acid, using a molecule of ATP as energy to drive the re-

action. The resulting amino acid–tRNA complex can thenfurnish its amino acid to a growing polypeptide chain, a

process that we describe in Module 10.12.The computer graphic in Figure 10.11B shows a tRNA

molecule (green) and an ATP molecule (purple) boundto the enzyme molecule (blue). (To help you see the twodistinct molecules, the tRNA molecule is shown with a

stick representation, while the enzyme is shown as space-filling spheres.) In this figure, you can see the proportional

sizes of these three molecules. The amino acid that would at-tach to the tRNA is not shown; it would be less than half thesize of the ATP.

Once an amino acid is attached to its appropriate tRNA,it can be incorporated into a growing polypeptide chain.This is accomplished within ribosomes, the cellular organ-elles directly responsible for the synthesis of protein. Weexamine ribosomes in the next module.

! Figure 10.11A The structure of tRNA

" Figure 10.11B A moleculeof tRNA binding to an enzymemolecule (blue)

What is an anticodon, and what is its function??

Psite

Asite

Growingpolypeptide

Smallsubunit

Largesubunit

Ribosome

tRNA binding sites

mRNA binding site

Growing polypeptide

tRNAmolecules

mRNAtRNA

The next amino acid to be added to the polypeptide

Codons


●A ribosome holds mRNA and tRNAs together and connects amino acids fromthe tRNAs to the growing polypeptide chain.

We have now looked at many of thecomponents a cell needs to carry outtranslation: instructions in the formof mRNA molecules, tRNA to in-terpret the instructions, a supplyof amino acids and enzymes (forattaching amino acids to tRNA),and ATP for energy. The finalcomponents are the ribosomes,structures in the cytoplasm thatposition mRNA and tRNA closetogether and catalyze the synthe-sis of polypeptides.

A ribosome consists of two sub-units, each made up of proteins and akind of RNA called ribosomal RNA(rRNA). In Figure 10.12A, you can see the actual shapes and relative sizes of the ribosomal subunits. You can also see where mRNA, tRNA, and thegrowing polypeptide are located during translation.

The ribosomes of prokaryotes and eukaryotes are very simi-lar in function, but those of eukaryotes are slightly larger anddifferent in composition. The differences are medically signifi-cant. Certain antibiotic drugs can inactivate prokaryotic ribo-somes while leaving eukaryotic ribosomes unaffected. Thesedrugs, such as tetracycline and streptomycin, are used to com-bat bacterial infections.

The simplified drawings in Figures 10.12B and 10.12C indi-cate how tRNA anticodons and mRNA codons fit together on ri-bosomes. As Figure 10.12B shows, each ribosome has a bindingsite for mRNA and the two main binding sites (P and A) fortRNA. Figure 10.12C shows tRNA molecules occupying thesetwo sites. The subunits of the ribosome act like a vise, holdingthe tRNA and mRNA molecules close together, allowing the

amino acids carried by the tRNA molecules to be connected intoa polypeptide chain. In the next two modules, we examine thesteps of translation in detail.

How does a ribosome facilitate protein synthesis??

10.13 An initiation codon marks the start of an mRNA messageTranslation can be divided into the same three phases as tran-scription: initiation, elongation,and termination. Theprocess of polypeptideinitiation brings to-gether the mRNA, atRNA bearing the firstamino acid, and the two subunits of a ribosome.

As shown in Figure 10.13A, an mRNA molecule islonger than the genetic message it carries. The lightpink nucleotides at either end of the molecule arenot part of the message, but help the mRNA to bindto the ribosome. The initiation process establishes

exactly where translation will begin, ensuring that the mRNAcodons are translated into the correct sequence of amino acids.

Initiation occurs in two steps (Figure 10.13B). ! An mRNAmolecule binds to a small ribosomal subunit. A special initiator

tRNA binds to the specific codon, called the start codon,where translation is to begin on the mRNA molecule.The initiator tRNA carries the amino acid methion-ine (Met); its anticodon, UAC, binds to the start

codon, AUG. " Next, a large ribosomal subunit bindsto the small one, creating a functional ribosome. The ini-

tiator tRNA fits into one of the two tRNA binding

Start of genetic message

End

Cap

Tail

10.12 Ribosomes build polypeptides

! Figure 10.12A The trueshape of a functioning ribosome

# Figure 10.13A A molecule of eukaryotic mRNA

! Figure 10.12B A ribosomewith empty binding sites

! Figure 10.12C A ribosome with occupiedbinding sites


●The messenger RNA transcribed from the mutated gene would benonfunctional because ribosomes could not initiate translation correctly.

U A C U A C

mRNA

Initiator tRNA

Small ribosomalsubunit

A U G A U G

Psite

Largeribosomalsubunit

Asite

Startcodon

Met Met

! "

Polypeptide

AnticodonCodons

mRNAmovement

Stopcodon

Newpeptidebond

mRNA

Aminoacid

Peptide bondformation

Translocation

Codon recognition

Psite

Asite

!

"

#

10.14 Elongation adds amino acids to the polypeptide chain until a stop codonterminates translation

Once initiation is complete, amino acids are added one by oneto the first amino acid. Each addition occurs in a three-stepelongation process (Figure 10.14):

! Codon recognition. The anticodon of an incomingtRNA molecule, carrying its amino acid, pairs with themRNA codon in the A site of the ribosome.

" Peptide bond formation. The polypeptide sepa-rates from the tRNA in the P site and attaches by a newpeptide bond to the amino acid carried by the tRNAin the A site. The ribosome catalyzes formation of thepeptide bond, adding one more amino acid to thegrowing polypeptide chain.

# Translocation. The P site tRNA now leaves theribosome, and the ribosome translocates (moves) the re-maining tRNA in the A site, with the growing polypeptide,to the P site. The codon and anticodon remain hydrogen-bonded, and the mRNA and tRNA move as a unit. This move-ment brings into the A site the next mRNA codon to betranslated, and the process can start again with step 1.

Elongation continues until a stop codon reaches the ribo-some’s A site. Stop codons—UAA, UAG, and UGA—do notcode for amino acids but instead act as signals to stop transla-tion. This is the termination stage of translation. The com-pleted polypeptide is freed from the last tRNA, and theribosome splits back into its separate subunits.

What happens as a tRNA passes through the A and P bindingsites on the ribosome?

?

●In the A site, its amino acid receives the growing polypeptide from thetRNA that precedes it. In the P site, it gives up the polypeptide to the tRNA thatfollows it.

sites on the ribosome. This site, called the P site, will hold the growing polypeptide. The other tRNA binding site, called the A site, is vacant and ready for the next amino-acid-bearing tRNA.

What would happen if a genetic mutation changed a startcodon to some other codon?

?

! Figure 10.13B The initiation of translation

! Figure 10.14 Polypeptide elongation; the small green arrowsindicate movement


10.15 Review: The flow of genetic information in the cell is DNA : RNA : proteinFigure 10.15 summarizes the main stages inthe flow of genetic information from DNA toRNA to protein. ! In transcription (DNA :RNA), the mRNA is synthesized on a DNAtemplate. In eukaryotic cells, transcription oc-curs in the nucleus, and the messenger RNAmust travel from the nucleus to the cytoplasm.In prokaryotes, transcription occurs in the cytoplasm.

"–$ Translation (RNA : protein) can bedivided into four steps, all of which occur inthe cytoplasm in eukaryotic cells. When thepolypeptide is complete at the end of step 5,the two ribosomal subunits come apart, andthe tRNA and mRNA are released (not shownin this figure). Translation is rapid; a single ri-bosome can make an average-sized polypep-tide in less than a minute. Typically, an mRNAmolecule is translated simultaneously by anumber of ribosomes. Once the start codonemerges from the first ribosome, a second ri-bosome can attach to it; thus, several ribo-somes may trail along on the same mRNAmolecule.

As it is made, a polypeptide coils and folds,assuming a three-dimensional shape, its terti-ary structure. Several polypeptides may cometogether, forming a protein with quaternarystructure (see Module 3.13).

What is the overall significance of transcrip-tion and translation? These are the mainprocesses whereby genes control the structuresand activities of cells—or, more broadly, theway the genotype produces the phenotype. Thechain of command originates with the informa-tion in a gene, a specific linear sequence of nu-cleotides in DNA. The gene serves as atemplate, dictating transcription of a comple-mentary sequence of nucleotides in mRNA. In turn, mRNA dictates the linear sequence in which amino acids assemble to form a specific polypeptide. Finally, the proteins thatform from the polypeptides determine the appearance and the capabilities of the cell andorganism.

Which of the following molecules or structures does not participate directly intranslation: ribosomes, transfer RNA, messenger RNA, DNA?

?

●DNA

1

U A C

DNA

mRNA

Transcription

RNApolymerase

Transcription mRNA is transcribed from a DNA template.

Anticodon

Start Codon

mRNA

Amino acid

Translation

Enzyme

tRNA

InitiatortRNA Large

ribosomalsubunit

Smallribosomalsubunit

New peptidebond forming

Initiation of polypeptide synthesis

The mRNA, the first tRNA, and the ribosomal subunits come together.

Growingpolypeptide

Codons

Stop codon

Polypeptide

mRNA

Termination

The ribosome recognizes a stop codon. The polypeptide is terminatedand released.

Elongation

A succession of tRNAsadd their amino acids to the polypeptide chain as the mRNA is moved through the ribosome, one codon at a time.

A U G

ATP

Amino acid attacment Each amino acid attaches to its proper tRNA with the help of a specific enzyme and ATP.

CYTOPLASM

!

"

#

%

$

! Figure 10.15 A summary of transcription and translation

A AG

Glu

C T T

Normal hemoglobin DNA

Normal hemoglobin

U AG

Val

C T

Mutant hemoglobin DNA

Sickle-cell hemoglobin

mRNAmRNA

A


10.16 Mutations can change the meaning of genesMany inherited traits can be understood in molecular terms. Forinstance, sickle-cell disease (see Module 9.13) can be tracedthrough a difference in a protein to one tiny change in a gene. Inone of the two kinds of polypeptides in the hemoglobin protein,an individual with sickle-cell disease has a single different aminoacid—valine (Val) instead of glutamate (Glu). This difference iscaused by the change of a single nucleotide in the coding strandof DNA (Figure 10.16A). In the double helix, one nucleotide pairis changed.

Any change in the nucleotide sequence of DNA is called amutation. Mutations can involve large regions of a chromo-some or just a single nucleotide pair, as in sickle-cell disease.Here we consider how mutations involving only one or a fewnucleotide pairs can affect gene translation.

Mutations within a gene can be divided into two generalcategories: nucleotide substitutions, and nucleotide insertionsor deletions (Figure 10.16B). A nucleotide substitution is thereplacement of one nucleotide and its base-pairing partnerwith another pair of nucleotides. For example, in the secondrow in Figure 10.16B, A replaces G in the fourth codon of themRNA. What effect can a substitution have? Because the ge-netic code is redundant, some substitution mutations have noeffect at all. For example, if a mutation causes an mRNA codonto change from GAA to GAG, no change in the protein prod-uct would result because GAA and GAG both code for thesame amino acid (Glu; see Figure 10.8A). Such a change iscalled a silent mutation.

Other substitutions, called missense mutations, do changethe amino acid coding. For example, if a mutation causes anmRNA codon to change from GGC to AGC, as in the secondrow of Figure 10.16B. The resulting protein will have a serine(Ser) instead of a glycine (Gly) at this position. Some missensemutations have little or no effect on the shape or function of theresulting protein, but others, as in the case of sickle-cell disease,prevent the protein from performing its normal function.

Occasionally, a nucleotide substitution leads to an im-proved protein that enhances the success of the mutant or-ganism and its descendants. Much more often, though,mutations are harmful. Some substitutions, called nonsensemutations, change an amino acid codon into a stop codon.For example, if an AGA (Arg) codon is mutated to a UGA(stop) codon, the result will be a prematurely terminated pro-tein, which probably will not function properly.

Mutations involving the insertion or deletion of one or morenucleotides in a gene often have disastrous effects. BecausemRNA is read as a series of nucleotide triplets (codons) duringtranslation, adding or subtracting nucleotides may alter thereading frame (triplet grouping) of the message. All the nu-cleotides that are “downstream” of the insertion or deletion willbe regrouped into different codons (Figure 10.16B, bottom tworows). The result will most likely be a nonfunctional polypeptide.

The production of mutations, called mutagenesis, canoccur in a number of ways. Spontaneous mutations are due toerrors that occur during DNA replication or recombination.Other mutations are caused by physical or chemical agents,called mutagens. High-energy radiation, such as X-rays or ul-traviolet light, is a physical mutagen. One class of chemicalmutagens consists of chemicals that are similar to normal DNAbases but pair incorrectly or are otherwise disruptive when in-corporated into DNA. For example, the anti-AIDS drug AZTworks because its structure is similar enough to thymine thatviral polymerases incorporate it into newly synthesized DNA,but different enough that the drug blocks further replication.

Although mutations are often harmful, they are also ex-tremely useful, both in nature and in the laboratory. It is be-cause of mutations that there is such a rich diversity of genes inthe living world, a diversity that makes evolution by natural se-lection possible. Mutations are also essential tools for geneti-cists. Whether naturally occurring (as in Mendel’s peas) orcreated in the laboratory (Morgan used X-rays to make most ofhis fruit fly mutants; see Module 9.18), mutations create thedifferent alleles needed for genetic research.

How could a single nucleotide substitution result in ashortened protein product?

?

! Figure 10.16A The molecular basis of sickle-cell disease

! Figure 10.16B Types of mutations and their effects

G

Deleted

G G C A UCA U G A A G U U

Met Lys Leu Ala His

A U G A A G U U G G

Met Lys Phe Ser Ala

U CC A

A U G A A G U U U G G C G C A

Met Lys Phe Gly AlamRNAProtein

Normalgene

Nucleotidesubstitution

Nucleotidedeletion

A

U

G

Inserted

G G GC CUA U G A A G U U

Met Lys Leu Ala His

Nucleotideinsertion

●A substitution that changed an amino acid codon into a stop codon wouldproduce a prematurely terminated polypeptide.

the flow of genetic information from dna to rna to protein...190 chapter 10 molecular biology of the...

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