Flow of Genetic Information The central dogma is the concept that cells are governed by a cellular...

Flow of Genetic Information

• The central dogma is the concept that cells are governed by a cellular chain of command:

DNA RNA protein

© 2011 Pearson Education, Inc.

Figure 17.3

DNA

mRNARibosome

Polypeptide

TRANSCRIPTION

TRANSLATION

TRANSCRIPTION

TRANSLATION

Polypeptide

Ribosome

DNA

mRNA

Pre-mRNARNA PROCESSING

(a) Bacterial cell (b) Eukaryotic cell

Nuclearenvelope

Figure 17.4

DNAtemplatestrand

TRANSCRIPTION

mRNA

TRANSLATION

Protein

Amino acid

Codon

Trp Phe Gly

5

5

Ser

U U U U U3

3

53

G

G

G G C C

T

C

A

A

AAAAA

T T T T

T

G

G G G

C C C G G

DNAmolecule

Gene 1

Gene 2

Gene 3

C C

Cracking the Genetic Code• 20 amino acids but there are only four nucleotide

bases in DNA• All 64 codons ( 43) were deciphered by the mid-

1960s• Of the 64 triplets, 61 code for amino acids; 3

triplets are “stop” signals to end translation• The genetic code is redundant (more than one

codon may specify a particular amino acid) but not ambiguous; no codon specifies more than one amino acid


Figure 17.5Second mRNA base

Fir

st m

RN

A b

ase

(5 e

nd

of

cod

on

)

Th

ird

mR

NA

bas

e (3

en

d o

f co

do

n)

UUU

UUC

UUA

CUU

CUC

CUA

CUG

Phe

Leu

Leu

Ile

UCU

UCC

UCA

UCG

Ser

CCU

CCC

CCA

CCG

UAU

UACTyr

Pro

Thr

UAA Stop

UAG Stop

UGA Stop

UGU

UGCCys

UGG Trp

GC

U

U

C

A

U

U

C

C

CA

U

A

A

A

G

G

His

Gln

Asn

Lys

Asp

CAU CGU

CAC

CAA

CAG

CGC

CGA

CGG

G

AUU

AUC

AUA

ACU

ACC

ACA

AAU

AAC

AAA

AGU

AGC

AGA

Arg

Ser

Arg

Gly

ACGAUG AAG AGG

GUU

GUC

GUA

GUG

GCU

GCC

GCA

GCG

GAU

GAC

GAA

GAG

Val Ala

GGU

GGC

GGA

GGGGlu

Gly

G

U

C

A

Met orstart

UUG

G

Transcription (DNA to mRNA)• RNA synthesis is catalyzed by RNA polymerase,

which prys the DNA strands apart and hooks together the RNA nucleotides

• DNA sequence where RNA polymerase attaches is called the promoter; in bacteria, the sequence signaling the end of transcription is called the terminator


Stage 1: Initiation• Promoters signal the transcriptional start point

and usually extend several dozen nucleotide pairs upstream of the start point

• Transcription factors mediate the binding of RNA polymerase and the initiation of transcription

• The completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a transcription initiation complex

• A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes


Figure 17.8

Transcription initiationcomplex forms

3

DNAPromoter

Nontemplate strand

53

53

53

Transcriptionfactors

RNA polymerase II

Transcription factors

53

53

53

RNA transcript

Transcription initiation complex

5 3

TATA box

T

T T T T T

A A A AA

A A

T

Several transcriptionfactors bind to DNA

2

A eukaryotic promoter1

Start point Template strand

Stage 2: Elongation

• As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time

• Transcription progresses at a rate of 40 nucleotides per second in eukaryotes in the 5’ to 3’ direction on growing RNA molecule

• A gene can be transcribed simultaneously by several RNA polymerases


Nontemplatestrand of DNA

RNA nucleotides

RNApolymerase

Templatestrand of DNA

3

35

5

5

3

Newly madeRNA

Direction of transcription

A

A A A

AA

A

T

TT

T

TTT G

GG

C

C C

CC

G

C CC A AA

U

U

U

end

Figure 17.9

Stage 3: Termination

• The mechanisms of termination are different in bacteria and eukaryotes

• In bacteria, the polymerase stops transcription at the end of the terminator and the mRNA can be translated without further modification

• In eukaryotes, RNA polymerase II transcribes the polyadenylation signal sequence


Eukaryotic cells modify RNA after transcription with enzymes


• Modify ends• Each end of a pre-mRNA molecule is

modified with the 5 end receiving a modified nucleotide 5 cap and the 3 end gets a poly-A tail

• Modifications facilitate the export of mRNA to the cytoplasm, protect mRNA from hydrolytic enzymes and help ribosomes attach to the 5 end

• Splice out noncoding regions

Figure 17.10

Protein-codingsegment

Polyadenylationsignal

5 3

35 5Cap UTRStartcodon

G P P P

Stopcodon

UTR

AAUAAA

Poly-A tail

AAA AAA…

Split Genes and RNA Splicing

• Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions called introns

• The other regions are called exons because they are eventually expressed, usually translated into amino acid sequences

• RNA splicing uses splicesomes to recognize small nuclear ribonucleoproteins (snRNPs) and removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence


Figure 17.11

5 Exon Intron Exon

5CapPre-mRNACodonnumbers

130 31104

mRNA 5Cap

5

Intron Exon

3 UTR

Introns cut out andexons spliced together

3

105 146

Poly-A tail

Codingsegment

Poly-A tail

UTR1146

Figure 17.12-3RNA transcript (pre-mRNA)

5Exon 1

Protein

snRNA

snRNPs

Intron Exon 2

Other proteins

Spliceosome

5

Spliceosomecomponents

Cut-outintronmRNA

5Exon 1 Exon 2

Evolutionary/Functional Importance of Introns

• Some introns contain sequences that may regulate gene expression

• Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing

• This is called alternative RNA splicing• Consequently, the number of different proteins an

organism can produce is much greater than its number of genes

• Exon shuffling may result in the evolution of new proteins


GeneDNA

Exon 1 Exon 2 Exon 3Intron Intron

Transcription

RNA processing

Translation

Domain 3

Domain 2

Domain 1

Polypeptide

Figure 17.13

Translation ( mRNA to proteins

• tRNAs transfer amino acids to the growing polypeptide in a ribosome

• Molecules of tRNA are not identical– Each carries a specific amino acid on one end

– Each has an anticodon on the other end; the anticodon base-pairs with a complementary codon on mRNA

• Flattened into one plane to reveal its base pairing, a tRNA molecule looks like a cloverleaf


Figure 17.14

Polypeptide

Ribosome

Trp

Phe Gly

tRNA withamino acidattached

Aminoacids

tRNA

Anticodon

Codons

U U U UG G G G C

AC C

C

CG

A A A

CGC

G

5 3mRNA

Figure 17.15

Amino acidattachmentsite

3

5

Hydrogenbonds

Anticodon

(a) Two-dimensional structure (b) Three-dimensional structure(c) Symbol used

in this book

Anticodon Anticodon3 5

Hydrogenbonds

Amino acidattachmentsite5

3

A A G

• Accurate translation requires two steps– First: a correct match between a tRNA and an

amino acid, done by the enzyme aminoacyl-tRNA synthetase

– Second: a correct match between the tRNA anticodon and an mRNA codon

• Flexible pairing at the third base of a codon is called wobble and allows some tRNAs to bind to more than one codon


Aminoacyl-tRNAsynthetase (enzyme)

Amino acid

P P P Adenosine

ATP

P

P

P

PPi

i

i

Adenosine

tRNA

AdenosineP

tRNA

AMP

Computer model

Aminoacid

Aminoacyl-tRNAsynthetase

Aminoacyl tRNA(“charged tRNA”)

Figure 17.16-4

Ribosomes

• Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis

• The two ribosomal subunits (large and small) are made of proteins and ribosomal RNA (rRNA)

• A ribosome has three binding sites for tRNA– The P site holds the tRNA that carries the growing

polypeptide chain

– The A site holds the tRNA that carries the next amino acid to be added to the chain

– The E site is the exit site, where discharged tRNAs leave the ribosome


tRNAmolecules

Growingpolypeptide Exit tunnel

E PA

Largesubunit

Smallsubunit

mRNA5

3

(a) Computer model of functioning ribosome

Exit tunnel Amino end

A site (Aminoacyl-tRNA binding site)

Smallsubunit

Largesubunit

E P AmRNA

E

P site (Peptidyl-tRNAbinding site)

mRNAbinding site

(b) Schematic model showing binding sites

E site (Exit site)

(c) Schematic model with mRNA and tRNA

5 Codons

3

tRNA

Growing polypeptide

Next aminoacid to beadded topolypeptidechain

Figure 17.17

Building a Polypeptide-Stage 1:Initiation

• The initiation stage of translation brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits

• First, a small ribosomal subunit binds with mRNA and a special initiator tRNA

• Then the small subunit moves along the mRNA until it reaches the start codon (AUG)

• Proteins called initiation factors bring in the large subunit that completes the translation initiation complex


Figure 17.18

InitiatortRNA

mRNA

5

53Start codon

Smallribosomalsubunit

mRNA binding site

3

Translation initiation complex

5 33U

UA

A GC

P

P site

i

GTP GDP

Met Met

Largeribosomalsubunit

E A

5

Stage 2: Elongation of the Polypeptide

• During the elongation stage, amino acids are added one by one to the preceding amino acid

• Each addition involves proteins called elongation factors and occurs in three steps: codon recognition, peptide bond formation, and translocation

• Translation proceeds along the mRNA in a 5′ to 3′ direction


Amino end ofpolypeptide

mRNA

5

E

Asite

3

E

GTP

GDP P i

P A

E

P A

GTP

GDP P i

P A

E

Ribosome ready fornext aminoacyl tRNA

Psite

Figure 17.19-4

Stage 3:Termination of Translation

• Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome

• The A site accepts a protein called a release factor

• The release factor causes the addition of a water molecule instead of an amino acid

• This reaction releases the polypeptide, and the translation assembly then comes apart


Figure 17.20-3

Releasefactor

Stop codon(UAG, UAA, or UGA)

3

5

3

5

Freepolypeptide

2 GTP

5

3

2 GDP 2 iP

Figure 17.21Completedpolypeptide

Incomingribosomalsubunits

Start ofmRNA(5 end)

End ofmRNA(3 end)(a)

Polyribosome

Ribosomes

mRNA

(b)0.1 m

Growingpolypeptides

Completing and Targeting the Functional Protein

• Polypeptide chains are modified after translation or targeted to specific sites in the cell

• During and after synthesis, a polypeptide chain spontaneously coils and folds into its three-dimensional shape

• Proteins may also require post-translational modifications before doing their job

• Some polypeptides are activated by enzymes that cleave them

• Other polypeptides come together to form the subunits of a protein


Targeting Polypeptides to Specific Locations

• Two populations of ribosomes are evident in cells: free ribsomes (in the cytosol) and bound ribosomes (attached to the ER)

• Free ribosomes mostly synthesize proteins that function in the cytosol

• Bound ribosomes make proteins of the endomembrane system and proteins that are secreted from the cell

• Ribosomes are identical and can switch from free to bound


Figure 17.22

Ribosome

mRNA

Signalpeptide

SRP

1

SRPreceptorprotein

Translocationcomplex

ERLUMEN

2

3

45

6

Signalpeptideremoved

CYTOSOL

Protein

ERmembrane

Mutations

• Mutations are changes in the genetic material of a cell or virus

• Point mutations are chemical changes in just one base pair of a gene

• The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein


Figure 17.23

Wild-type hemoglobin

Wild-type hemoglobin DNA3

3

35

5 3

35

5553

mRNA

A AGC T T

A AGmRNA

Normal hemoglobin

Glu

Sickle-cell hemoglobin

Val

AA

AUG

GT

T

Sickle-cell hemoglobin

Mutant hemoglobin DNAC

Types of Small-Scale Mutations

• Point mutations within a gene can be divided into two general categories

– Nucleotide-pair substitutions

– One or more nucleotide-pair insertions or deletions


Substitutions

• A nucleotide-pair substitution replaces one nucleotide and its partner with another pair of nucleotides

• Silent mutations have no effect on the amino acid produced by a codon because of redundancy in the genetic code

• Missense mutations still code for an amino acid, but not the correct amino acid

• Nonsense mutations change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein


Wild type

DNA template strand

mRNA5

5

3

Protein

Amino end

A instead of G

(a) Nucleotide-pair substitution

3

3

5

Met Lys Phe Gly StopCarboxyl end

T T T T T

TTTTTA A A A A

AAAACC

C

C

A

A A A A A

G G G G

GC C

G GGU U U U UG

(b) Nucleotide-pair insertion or deletion

Extra A

35

53

Extra U

5 3

T T T T

T T T T

A

A A A

A

AT G G G G

GAAA

AC

CCCC A

T35

5 3

5T T T T TAAAACCA AC C

TTTTTA A A A ATG G G G

U instead of C

Stop

UA A A A AG GGU U U U UG

MetLys Phe Gly

Silent (no effect on amino acid sequence)

T instead of C

T T T T TAAAACCA GT C

T A T T TAAAACCA GC C

A instead of G

CA A A A AG AGU U U U UG UA A A AG GGU U U G AC

AA U U A AU UGU G G C UA

GA U A U AA UGU G U U CG

Met Lys Phe Ser

Stop

Stop Met Lys

missing

missing

Frameshift causing immediate nonsense(1 nucleotide-pair insertion)

Frameshift causing extensive missense (1 nucleotide-pair deletion)

missing

T T T T TTCAACCA AC G

AGTTTA A A A ATG G G C

Leu Ala

Missense

A instead of T

TTTTTA A A A ACG G A G

A

CA U A A AG GGU U U U UG

TTTTTA T A A ACG G G G

Met

Nonsense

Stop

U instead of A

35

35

53

35

53

35 3Met Phe Gly

No frameshift, but one amino acid missing(3 nucleotide-pair deletion)

missing

35

53

5 3U

T CA AA CA TTAC G

TA G T T T G G A ATC

T T C

A A G

Met

3

T

A

Stop

35

53

5 3

Figure 17.24

Insertions and Deletions

• Insertions and deletions are additions or losses of nucleotide pairs in a gene

• These mutations have a disastrous effect on the resulting protein more often than substitutions do

• Insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation


Figure 17.24d

Wild type

DNA template strand

mRNA5

5

Protein

Amino endStopCarboxyl end

33

3

5

Met Lys Phe Gly

A

A

A A

A A A A

A AT

T T T T T

T T TT

C C C C

C

C

G G G G

G

G

A

A A A AG GGU U U U U

(b) Nucleotide-pair insertion or deletion: frameshift causingimmediate nonsense

Extra A

Extra U

53

5

3

3

5

Met

1 nucleotide-pair insertion

Stop

A C A A GT T A TC T A C G

T A T AT G T CT GG A T GA

A G U A U AU GAU G U U C

A T

A

AG

Figure 17.24e

DNA template strand

mRNA5

5

Protein


33

3

5

Met Lys Phe Gly

A

A

A A

A A A A

A AT

T T T T T

T T TT

C C C C

C

C

G G G G

G

G

A


(b) Nucleotide-pair insertion or deletion: frameshift causingextensive missense

Wild type

missing

missing

A

U

A A AT T TC C A T TC C G

A AT T TG GA A ATCG G

A G A A GU U U C A AG G U 3

53

35

Met Lys Leu Ala

1 nucleotide-pair deletion

5

Figure 17.24f

DNA template strand

mRNA5

5

Protein


33

3

5

Met Lys Phe Gly

A

A

A A

A A A A

A AT

T T T T T

T T TT

C C C C

C

C

G G G G

G

G

A


(b) Nucleotide-pair insertion or deletion: no frameshift, but oneamino acid missing

Wild type

AT C A A A A T TC C G

T T C missing

missing

Stop

53

35

35

Met Phe Gly

3 nucleotide-pair deletion

A GU C A AG GU U U U

T GA A AT T TT CG G

A A G

Mutagens

• Spontaneous mutations can occur during DNA replication, recombination, or repair

• Mutagens are physical or chemical agents that can cause mutations


Comparing Gene Expression in Bacteria, Archaea, and Eukarya

• Bacteria and eukarya differ in their RNA polymerases, termination of transcription, and ribosomes; archaea tend to resemble eukarya in these respects

• Bacteria can simultaneously transcribe and translate the same gene

• In eukarya, transcription and translation are separated by the nuclear envelope

• In archaea, transcription and translation are likely coupled


Figure 17.26TRANSCRIPTION

DNA

RNApolymerase

ExonRNAtranscript

RNAPROCESSING

NUCLEUS

Intron

RNA transcript(pre-mRNA)

Poly-A

Poly-A

Aminoacyl-tRNA synthetase

AMINO ACIDACTIVATION

Aminoacid

tRNA

5 C

ap

Poly-A

3

GrowingpolypeptidemRNA

Aminoacyl(charged)tRNA

Anticodon

Ribosomalsubunits

A

AE

TRANSLATION

5 Cap

CYTOPLASM

P

E

Codon

Ribosome

5

3

Flow of Genetic Information The central dogma is the concept that cells are governed by a cellular...

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