CHAPTER 12

HOW GENES WORK

THE CENTRAL DOGMA

• The path of information is often referred to as the central dogma.

DNA RNA protein

THE CENTRAL DOGMA

• The use of information in DNA to direct the production of particular proteins is called gene expression, which takes place in two stages.• Transcription is the process when a

messenger RNA (mRNA) is made from a gene within the DNA.

• Translation is the process of using the mRNA to direct the production of a protein.

TRANSCRIPTION

• The information contained in DNA is stored in blocks called genes.• The genes code for proteins.• The proteins determine what a cell will be like.

TRANSCRIPTION

• The DNA stores this information safely in the nucleus where it never leaves.• Instructions are

copied from the DNA into messages comprised of RNA.

• These messages are sent out into the cell to direct the assembly of proteins.

Transcription

TranslationNuclearenvelope

Protein

Cytoplasm

mRNA

Nucleus

DNA

TRANSCRIPTION

• A protein called RNA polymerase produces the mRNA copy of DNA during transcription.• It first binds to one strand of the DNA at a

site called the promoter and then moves down the DNA molecule and assembles a complementary copy of RNA

• RNA uses uracil (U) instead of thymine (T)

A

C

U

G

A

GC

G

CA

TAGCA

T

A

T

AT G C T A C G A

T

G

C T

AG

C

A

TA

TC

GG

C

A

T

G

CA

TTA

U G C U

5′

5′

3′

3′

5′

3′

DNA

Unwinding Templatestrand

Coding strand

Rewinding

mRNARNA

polymeraseRNA-DNAhybrid helix

TRANSCRIPTION

http://www.dnalc.org/resources/3d/12-transcription-basic.html

GENE EXPRESSION

• The prokaryotic gene is an uninterrupted stretch of DNA nucleotides that corresponds to proteins.

• In eukaryotes, the coding portions of the DNA nucleotide sequence are interrupted by noncoding sections of DNA.• The coding portions are known as exons while

the noncoding portions are known as introns.

GENE EXPRESSION

• When a eukaryotic cell first transcribes a gene, it produces a primary RNA transcript of the entire gene.• The primary transcript is then processed in the

nucleus.• Enzyme-RNA complexes cut out the introns

and join together the exons to form a shorter mRNA transcript.

• The sequences of the introns (90% of typical human gene) are not translated.

• A 5’ cap and a 3’ poly-A tail are also added.

1 2 3 4 5 6 7

3′ poly-A tail5′ cap

PrimaryRNAtranscript

Mature mRNAtranscript

DNA

Introns are cut out andcoding regions are

spliced together

Exon(coding region)

Intron(noncoding region)

Transcription

GENE EXPRESSION

http://www.dnalc.org/resources/3d/rna-splicing.html

TRANSLATION

• To correctly read a gene, a cell must translate the information encoded in the DNA (nucleotides) into the language of proteins (amino acids).• Translation follows rules set out by the genetic code.

• The mRNA is “read” in three-nucleotide units called codons.• Each codon corresponds to a particular

amino acid.

TRANSLATION

• The genetic code was determined from trial-and-error experiments to work out which codons matched with which amino acids.

• The genetic code is universal and employed by all living things.

THE GENETIC CODE (RNA CODONS)

There are 64 different codons in the genetic code.

UCAG

A GThirdLetter

Second Letter

Cysteine

Stop

Tryptophan

GGG

UGU

UGC

UGAUGG

CGC

CGACGG

CGU

AGU

AGCAGA

AGG

GGUGGC

GGA

UCAG

UCAG

UCAG

Glycine

Arginine

Serine

Arginine

GAG

GAA

UAU

UACUAA

UAG

CAU

GACGAU

Tyrosine

Stop

Stop

Glutamate

Aspartate

Lysine

Asparagine

Histidine

GlutamineCAACAG

CAC

AAU

AAC

AAG

AAA

C

Alanine

Threonine

Serine

Proline

GCG

GCC

GCA

GCU

ACA

ACG

ACC

ACU

CCGCCA

CCU

CCC

UCA

UCG

UCU

UCC

U

C

A

G

U

The Genetic Code

Valine

GUG

GUA

GUC

AUG

AUCAUA

AUU

GUU

CUC

CUACUG

CUU

UUG

UUAUUC

UUUPhenylalanine

FirstLetter

Isoleucine

Methionine; Start

Leucine

Leucine

TRANSLATION

• Translation occurs in ribosomes, which are the protein-making factories of the cell• Each ribosome is a complex of proteins and

several segments of ribosomal RNA (rRNA).• Ribosomes are comprised of two subunits:

• Small subunit • Large subunit

TRANSLATION

• The small subunit has a short sequence of rRNA exposed that is identical to a leader sequence that begins all genes.• mRNA binds to the small subunit.

TRANSLATION

• The large RNA subunit has three binding sites for transfer RNA (tRNA) located directly adjacent to the exposed rRNA sequence on the small subunit.

• These binding sites are called the A, P, and E sites.• It is the tRNA molecules that bring amino acids to

the ribosome to use in making proteins.

E P A

A site

mRNAbindingsite

Smallsubunit

Largesubunit

Large ribosomalsubunit P siteE site

Small ribosomalsubunit

TRANSLATION

• The structure of a tRNA molecule is important to its function.• It has an amino acid attachment site at one

end and a three-nucleotide sequence at the other end.

5′

3′

3′5′

Amino acidattaches here

Anticodon

OH

Anticodon

TRANSLATION

• This three-nucleotide sequence is called the anticodon and is complementary to 1 of the 64 codons of the genetic code.

• Activating enzymes match amino acids with their proper tRNAs.

TRANSLATION

• Once an mRNA molecule has bound to the small ribosomal subunit, the other larger ribosomal subunit binds as well, forming a complete ribosome.• During translation, the mRNA threads through

the ribosome three nucleotides at a time.• A new tRNA holding an amino acid to be added

enters the ribosome at the A site.

TRANSLATION

• Before a new tRNA can be added, the previous tRNA in the A site shifts to the P site.

• At the P site, peptide bonds form between the incoming amino acid and the growing chain of amino acids.

• The now empty tRNA in the P site eventually shifts to the E site where it is released.

KEY BIOLOGICAL PROCESS: TRANSLATION

G GU U UAA

A A

C

GA

CC

UG G

GU U UAA A

A AC C G A C

CU

G GU U

U

UU

AA A A

A

CC

UG G

GU U U

UA

A

AA

AU A

C

CC

U

1 2 3 4

The initiating tRNA leavesthe ribosome at the E site,and the next tRNA entersat the A site.

The initial tRNA occupiesthe P site on the ribosome.Subsequent tRNAs withbound amino acids firstenter the ribosome at theA site.

The tRNA that binds to theA site has an anticodoncomplementary to thecodon on them RNA.

The ribosome moves threenucleotides to the right asthe initial amino acid istransferred to the secondamino acid at the P site.

Ribosome

Amino acid

E site

Met

tRNALeu

Asn

Met

LeuLeuMet

Asn

Codon

Anticodon

Met LeuP site

A site

mRNA

http://www.dnalc.org/resources/3d/15-translation-basic.html

TRANSLATION

• Translation continues until a “stop” codon is encountered that signals the end of the protein.

• The ribosome then falls apart and the newly made protein is released into the cell.

3′

5′

tRNA

Aminoacid

mRNA

Ribosome

Growingpolypeptidechain

GENE EXPRESSION

• Gene expression works the same way in all organisms.

Key end product

Key end product

Two DNAduplexes

Key end product

mRNA

DNA ReplicationKey starting materials

DNA

DNA polymerase

LigaseHelicase

Process

TranscriptionProcessKey starting materials

DNA

TranslationProcess

Ribosome

Key starting materials

RNA polymerase

tRNA

mRNAPolypeptide

Aminoacids

GENE EXPRESSION

• In prokaryotes, a gene can be translated as it is transcribed.

• In eukaryotes, a nuclear membrane separates the processes of transcription and translation, making protein synthesis much more complicated.

5′

5′

3′

5′

3′

3′

3

5

mRNA is transported out of the nucleus. In thecytoplasm, ribosomalsubunits bind to the mRNA

Cap

Cytoplasm

Completedpolypeptide

5′

6 The amino acid chaingrows until the polypeptide is completed.

Aminoacid

DNA

Introns are excised from the RNAtranscript, and the remaining exonsare spliced together, producing mRNA.

Nuclearpore Small

ribosomalsubunit

mRNA

Largeribosomalsubunit

Nuclearmembrane

tRNAs bring their amino acidsin at the A site on the ribosome.Peptide bonds form betweenamino acids at the P site,andtRNAs exit the ribosome fromthe E site.

tRNA moleculesbecome attached tospecific amino acidswith the help ofactivating enzymes. Amino acids are brought to the ribosome in theorder directed by the mRNA.

Ribosome

4

Ribosome movestoward 3′ end

Exons

Poly-Atail

Cap

5′mRNA

PrimaryRNA transcript5′

3′

3′

3′

1

2

RNApolymerase

In the cell nucleus, RNApolymerase transcribes RNAfrom DNA.

Poly-Atail

Introns

Gene 1Gene 2Gene 3

Gene 1 Gene 2Gene 3

Plac

O

O

Protein 3Protein 2Protein 1

(b) lac operon is "induced"

mRNA

OperatorPromoter

(a) lac operon is "repressed"

OperatorPromoter

RNApolymerase Repressor

Allolactose(inducer)

Plac

RNApolymerase

TRANSCRIPTIONAL CONTROL IN PROKARYOTES

• An operon is a segment of DNA containing a cluster of genes that are all transcribed as a unit.• The lac operon in E. coli

contains genes that code for enzymes that break down the sugar lactose.• The operon contains

regulatory elements: the operator and promoter

• Lactose affects a repressor protein and causes it to fall off the operator, allowing transcription.

TRANSCRIPTIONAL CONTROL IN EUKARYOTES

• Gene regulation in eukaryotes is geared toward the whole organism, not the individual cell.

• Eukaryotic DNA is packaged around histone proteins to form nucleosomes, which are further packaged into higher-order chromosome structures.• This structure of the chromosomal material (chromatin) affects the availability of DNA for transcription.

20 nm

Core complexof histones

Exteriorhistone

DNA

COMPLEX REGULATION OF GENE EXPRESSION

• Gene expression in eukaryotes is controlled in many ways• Chromatin structure• Initiation of transcription• Alternative splicing• RNA interference• Availability of translational proteins• Post-translation modification of protein products

3„

5„

5′

3′

5. Protein synthesisMany proteinstake part in thetranslation process,and regulation ofthe availability ofany of them altersthe rate of geneexpression byspeeding or slowingprotein synthesis.

4. Gene silencingCell scan silencegenes with siRNAs,which are cut frominverted sequencesthat fold intodouble-strandedloops. siRNAs bind tomRNAs and blocktheir translation.

3. RNA splicingGene expressioncan be controlledby altering therate of splicing ineukaryotes.Alternative splicingcan producemultiple mRNAsfrom one gene.

2. Initiation oftranscriptionMost control ofgene expression isachievedby regulatingthe frequencyof transcriptioninitiation.

1. ChromatinstructureAccess to manygenesis affectedby the packagingof DNA and bychemicallyaltering thehistone proteins.

6. Post-translationalmodificationPhosphorylation orother chemicalmodifications canalter the activity ofa protein after it isproduced.

Completedpolypeptidechain

siRNA

Dicer enzyme

RNA hairpins

ExonIntron

Cutintron

Mature RNA transcript

5′ cap

3′ poly-A tail

RNApolymerase

Primary RNA transcript

DNA

DNA availablefor transcription

Histones

DNA tightlypacked