Chapter 17 From Gene to Protein (Protein Synthesis) From Gene to Protein (Protein Synthesis)

Chapter 17Chapter 17From Gene to Protein

(Protein Synthesis)

From Gene to Protein

(Protein Synthesis)

Protein SynthesisProtein Synthesis

The information content of DNA

Is in the form of specific sequences of nucleotides along the DNA strands

The DNA inherited by an organism

Leads to specific traits by dictating the synthesis of proteins

Gene expression is the process by which DNA directs protein synthesis

Early experiments led researchers to:

One Gene—One Polypeptide Hypothesis

The information content of DNA

Is in the form of specific sequences of nucleotides along the DNA strands

The DNA inherited by an organism

Leads to specific traits by dictating the synthesis of proteins

Gene expression is the process by which DNA directs protein synthesis

Early experiments led researchers to:

One Gene—One Polypeptide Hypothesis

Protein Synthesis OverviewProtein Synthesis Overview

Gene expression occurs in 2 stages:

1. Transcription

Is the synthesis of RNA under the direction of DNA

Produces messenger RNA (mRNA)


1. Transcription

Is the synthesis of RNA under the direction of DNA

Produces messenger RNA (mRNA)

Protein Synthesis OverviewProtein Synthesis Overview


2. Translation

Is the actual synthesis of a polypeptide, which occurs under the direction of mRNA

Occurs on ribosomes


2. Translation

Is the actual synthesis of a polypeptide, which occurs under the direction of mRNA

Occurs on ribosomes

TRANSCRIPTIONTRANSCRIPTIONDNADNA

mRNAmRNA

(a) Bacterial cell(a) Bacterial cell

TRANSLATIONTRANSLATION

RibosomeRibosome

PolypeptidePolypeptide

Protein Synthesis Overview Protein Synthesis Overview

In eukaryotes

RNA transcripts are modified before becoming true mRNA

Initial RNA transcript is called primary transcript or pre-mRNA.

Cellular chain of command

In eukaryotes

RNA transcripts are modified before becoming true mRNA

Initial RNA transcript is called primary transcript or pre-mRNA.

Cellular chain of command

RNARNARNARNADNADNADNADNA ProteinProteinProteinProtein

RNA PROCESSINGRNA PROCESSING

Nuclear

envelope

Nuclear

envelope

DNADNA

Pre-mRNAPre-mRNA

(b) Eukaryotic cell(b) Eukaryotic cell

mRNAmRNA

TRANSCRIPTIONTRANSCRIPTION

TRANSLATIONTRANSLATION RibosomeRibosome


The Genetic CodeThe Genetic Code

Genetic information

Is encoded as a sequence of non-overlapping base triplets, or codons

4 bases allow for 64 unique codons

Codons must be read in the correct reading frame

For the specified polypeptide to be produced

Genetic information

Is encoded as a sequence of non-overlapping base triplets, or codons

4 bases allow for 64 unique codons

Codons must be read in the correct reading frame

For the specified polypeptide to be produced

Different Reading FramesDifferent Reading Frames

Transcription & TranslationTranscription & Translation

During transcription

One of the two DNA strands (template strand) provides order of complementary RNA nucleotides for mRNA transcript

Template strand always the same for a given gene

Base pairing rules apply except with uracil (U) replacing thymine (T) on the mRNA strand

During transcription

One of the two DNA strands (template strand) provides order of complementary RNA nucleotides for mRNA transcript

Template strand always the same for a given gene

Base pairing rules apply except with uracil (U) replacing thymine (T) on the mRNA strand

Transcription & TranslationTranscription & Translation

During translation

mRNA codons are read in 5’ to 3’ direction

Each codon specifies 1 of the 20 amino acids for correct primary order for that polypeptide

Genetic code is redundant but not ambiguous

61 codons code for amino acids; 3 are stop codons

No codon specifies more than 1 amino acid!!!

During translation

mRNA codons are read in 5’ to 3’ direction

Each codon specifies 1 of the 20 amino acids for correct primary order for that polypeptide

Genetic code is redundant but not ambiguous

61 codons code for amino acids; 3 are stop codons

No codon specifies more than 1 amino acid!!!

Genetic CodeGenetic Code

Second mRNA baseSecond mRNA base

Firs

t m

RN

A b

ase

(5′

end o

f co

don

)Fi

rst

mR

NA

base

(5′

end o

f co

don

)

Th

ird m

RN

A b

ase

(3′

end o

f co

don

)Th

ird m

RN

A b

ase

(3′

end o

f co

don

)

UUUUUU

UUCUUC

UUAUUA

CUUCUU

CUCCUC

CUACUA

CUGCUG

PhePhe

LeuLeu

LeuLeu

IleIle

UCUUCU

UCCUCC

UCAUCA

UCGUCG

SerSer

CCUCCU

CCCCCC

CCACCA

CCGCCG

UAUUAU

UACUACTyrTyr

ProPro

ThrThr

UAA StopUAA Stop

UAG StopUAG Stop

UGA StopUGA Stop

UGUUGU

UGCUGCCysCys

UGGUGG TrpTrp

GGCC

UU

UU

CC

AA

UU

UU

CC

CC

CCAA

UU

AA

AA

AA

GG

GG

HisHis

GlnGln

AsnAsn

LysLys

AspAsp

CAUCAU CGUCGU

CACCAC

CAACAA

CAGCAG

CGCCGC

CGACGA

CGGCGG

GG

AUUAUU

AUCAUC

AUAAUA

ACUACU

ACCACC

ACAACA

AAUAAU

AACAAC

AAAAAA

AGUAGU

AGCAGC

AGAAGA

ArgArg

SerSer

ArgArg

GlyGly

ACGACGAUGAUG AAGAAG AGGAGG

GUUGUU

GUCGUC

GUAGUA

GUGGUG

GCUGCU

GCCGCC

GCAGCA

GCGGCG

GAUGAU

GACGAC

GAAGAA

GAGGAG

ValVal AlaAla

GGUGGU

GGCGGC

GGAGGA

GGGGGGGluGlu

GlyGly

GG

UU

CC

AA

Met or

start

Met or

start

UUGUUG

GG

Using the Genetic Code OverviewUsing the Genetic Code Overview

DNAtemplatestrand

DNAtemplatestrand


mRNAmRNA


ProteinProtein

Amino acidAmino acid

CodonCodon

TrpTrp PhePhe GlyGly

5′5′

5′5′

SerSer

UU UU UU UU UU3′3′

3′3′

5′5′3′3′

GG

GG

GG GG CC CC

TT

CC

AA

AA

AAAAAAAAAA

TT TT TT TT

TT

GG

GG GG GG

CC CC CC GG GGDNADNAmoleculemolecule

Gene 1Gene 1

Gene 2Gene 2

Gene 3Gene 3

CC CC

Reading FrameReading FrameReading FrameReading Frame

TranscriptionTranscription

RNA synthesis is catalyzed by RNA polymerase

Separates the DNA strands apart, hooks together the RNA nucleotides

Follows the same base-pairing rules as DNA, except that in RNA, uracil substitutes for thymine

DNA sequence where RNA polymerase attaches:

Promoter

Stretch of DNA transcribed: Transcription unit

RNA synthesis is catalyzed by RNA polymerase

Separates the DNA strands apart, hooks together the RNA nucleotides

Follows the same base-pairing rules as DNA, except that in RNA, uracil substitutes for thymine

DNA sequence where RNA polymerase attaches:

Promoter

Stretch of DNA transcribed: Transcription unit

TranscriptionTranscription

3 stages of transcription are

Initiation

Elongation

Termination

3 stages of transcription are

Initiation

Elongation

Termination

PromoterPromoter Transcription unitTranscription unit

DNADNAStart pointStart point

RNA polymeraseRNA polymeraseInitiationInitiation11

RNA

transcript

RNA

transcript

Unwound

DNA

Unwound

DNA

Template strand

of DNA

Template strand

of DNA

22 ElongationElongation

Rewound

DNA

Rewound

DNA

RNA

transcript

RNA

transcript33TerminationTermination

Completed RNA transcriptCompleted RNA transcript

Detailed View of Synthesis of a mRNA transcriptDetailed View of Synthesis of a mRNA transcript

ElongationElongation

RNA

polymerase

RNA

polymerase

Non-template strand of DNA

Non-template strand of DNA RNA nucleotidesRNA nucleotides

3end3end

CC AAUU CC CC AA AA

UU

TT AA GG GG TT TTAA

AACC

GG

UU

AATT

CCAA

TT CC CC AA AA TTTT

GGGG

3′3′

5′5′

5′5′

Newly

made RNA

Newly

made RNA

Direction of transcription

(“downstream”)

Direction of transcription

(“downstream”)

Template

strand of DNA

Template

strand of DNA

Initiation Initiation

Promoters

Signal the transcriptional start point

TATA box: Important promoter in eukaryotes

Transcription factors

Mediate the binding of RNA polymerase

Transcription factors + RNA polymerase = Transcription Initiation Complex

Promoters

Signal the transcriptional start point

TATA box: Important promoter in eukaryotes

Transcription factors

Mediate the binding of RNA polymerase

Transcription factors + RNA polymerase = Transcription Initiation Complex

Initiation Initiation

Transcription initiation

complex forms

Transcription initiation

complex forms

33

DNADNAPromoterPromoter

Nontemplate strandNontemplate strand

5′5′3′3′

5′5′3′3′

5′5′3′3′

Transcription

factors

Transcription

factors

RNA polymerase IIRNA polymerase IITranscription factorsTranscription factors

5′5′3′3′

5′5′3′3′

5′5′3′3′

RNA transcriptRNA transcript

Transcription initiation complexTranscription initiation complex

5′5′ 3′3′

TATA boxTATA box

TT

TT TT TT TT TT

AA AA AA AA AA

AA AA

TT

Several transcription

factors bind to DNA

Several transcription

factors bind to DNA

22

A eukaryotic promoterA eukaryotic promoter11

Start pointStart point Template strandTemplate strand

Elongation Elongation

RNA polymerase moves along the DNA

Untwists the double helix, 10 to 20 bases at a time

A gene can be transcribed simultaneously by several RNA polymerases

Nucleotides are added to the 3’ end of the growing RNA molecule

RNA polymerase moves along the DNA

Untwists the double helix, 10 to 20 bases at a time

A gene can be transcribed simultaneously by several RNA polymerases

Nucleotides are added to the 3’ end of the growing RNA molecule

Processing of pre-mRNA in EukaryotesProcessing of pre-mRNA in Eukaryotes

Each end of a pre-mRNA molecule is modified in a particular way

5′ end receives a modified nucleotide 5’ cap

3′ end gets a poly-A tail

Each end of a pre-mRNA molecule is modified in a particular way

5′ end receives a modified nucleotide 5’ cap

3′ end gets a poly-A tail

Processing of pre-mRNA in EukaryotesProcessing of pre-mRNA in Eukaryotes

These modifications share several functions

Facilitate the export of mRNA to the cytoplasm

Protect mRNA from hydrolytic enzymes

Help ribosomes attach to the 5’ end

These modifications share several functions

Facilitate the export of mRNA to the cytoplasm

Protect mRNA from hydrolytic enzymes

Help ribosomes attach to the 5’ end

RNA ProcessingRNA Processing

Protein-coding

segment

Protein-coding

segment

Polyadenylation

signal

Polyadenylation

signal5′5′ 3′3′

3′3′5′5′ 5′5′CapCap UTRUTRStart

codon

Start

codon

GG PP PP PP

Stop

codon

Stop

codonUTRUTR

AAUAAAAAUAAA

Poly-A tailPoly-A tail

AAAAAA AAAAAA……

More pre-mRNA ProcessingMore pre-mRNA Processing RNA splicing

Removes introns (intervening) and joins exon (expressed)

RNA splicing

Removes introns (intervening) and joins exon (expressed)


RNA PROCESSINGRNA PROCESSING

DNADNA

Pre-mRNAPre-mRNA

mRNAmRNA


RibosomeRibosome


5′ Cap5′ CapExonExonIntronIntron

11 3030 3131

ExonExon IntronIntron

104104 105105 146146

ExonExonPoly-A tailPoly-A tail

Poly-A tailPoly-A tail

Introns cut out and

exons spliced together

Introns cut out and

exons spliced together

Coding

segment

Coding

segment

5′ Cap5′ Cap11 146146

3UTR3UTR UTR UTR

Pre-mRNAPre-mRNA

mRNAmRNA

TranslationTranslation

A cell translates a mRNA message into protein

With the help of transfer RNA (tRNA)

A cell translates a mRNA message into protein

With the help of transfer RNA (tRNA)

TranslationTranslation

Molecules of tRNA are not all identical

Each carries a specific amino acid on one end

Each has an anticodon on the other end

Anticodons base pair with complementary codons on mRNA

Molecules of tRNA are not all identical

Each carries a specific amino acid on one end

Each has an anticodon on the other end

Anticodons base pair with complementary codons on mRNA

Structure of a tRNA moleculeStructure of a tRNA moleculeAmino acid

attachment

site

Amino acid

attachment

site

3′3′

5′5′

Hydrogen

bonds

Hydrogen

bonds

AnticodonAnticodon

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

in bookin book

AnticodonAnticodon AnticodonAnticodon3′3′ 5′5′

Hydrogen

bonds

Hydrogen

bonds

Amino acid

attachment

site

Amino acid

attachment

site5′5′

3′3′

AA AA GG

RibosomesRibosomes Ribosomes

Facilitate the specific coupling of tRNA anticodons with mRNA codons during protein synthesis

Ribosomes are made of 2 subunits, one large and one small

Constructed of proteins and RNA molecules named ribosomal RNA (rRNA)

Ribosomes

Facilitate the specific coupling of tRNA anticodons with mRNA codons during protein synthesis

Ribosomes are made of 2 subunits, one large and one small

Constructed of proteins and RNA molecules named ribosomal RNA (rRNA)

RibosomesRibosomes Ribosomes have three binding sites

for tRNA

P site holds the tRNA that carries the growing polypeptide chain

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

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

Ribosomes have three binding sites for tRNA

P site holds the tRNA that carries the growing polypeptide chain

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

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

Ribosome StructureRibosome Structure

A siteA site

Small

subunit

Small

subunit

Large

subunit

Large

subunit

PP AA

P siteP site

mRNA

binding site

mRNA

binding site

E site E site

EE

Overview of TranslationOverview of TranslationTRANSCRIPTIONTRANSCRIPTION


DNADNA

mRNAmRNARibosomeRibosome



Amino

acids

Amino

acids

tRNA with amino

acid

attached

tRNA with amino

acid

attached

RibosomeRibosome

tRNAtRNA

AnticodonAnticodon

mRNAmRNA

TrpTrp

PhePhe GlyGly

AAGG CC

AA AA AA

CCCC

GG

UU GG GG UU UU UU GG GG CC

CodonsCodons

Initiation of TranslationInitiation of Translation

The initiation stage of translation

Brings together mRNA, tRNA bearing the first amino acid of the polypeptide, and two subunits of a ribosome

The initiation stage of translation

Brings together mRNA, tRNA bearing the first amino acid of the polypeptide, and two subunits of a ribosome

Large ribosomal subunitLarge ribosomal subunit

22

mRNAmRNA

mRNA binding sitemRNA binding siteSmall ribosomal

subunit

Small ribosomal

subunit

GDPGDPGTPGTP

Start codonStart codon

11

MetMet

MetMet

UU AA CCAA UU GG

EE AA

Amino end ofpolypeptideAmino end ofpolypeptide

mRNAmRNA

5′5′

EE

AsiteA

site

3′3′

EE

GTPGTP

GDPGDP PP ii

PP AA

EE

PP AA

GTPGTP

GDPGDP PP ii

PP AA

EE

Ribosome ready fornext tRNARibosome ready fornext tRNA

PsiteP

site

Termination of TranslationTermination of Translation

Termination occurs when a stop codon reaches the A site

A site accepts a protein called a release factor

Reaction releases the polypeptide

Termination occurs when a stop codon reaches the A site

A site accepts a protein called a release factor

Reaction releases the polypeptide

ReleasefactorReleasefactor

Stop codonStop codon(UAG, UAA, or UGA)(UAG, UAA, or UGA)

3′3′

5′5′

3′3′

5′5′

FreepolypeptideFreepolypeptide

22 GTPGTP

5′5′

3′3′

22 GDPGDP 22 iiPP

Termination of Translation

MutationsMutations

Mutations

Are changes in the genetic material (DNA)

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

Mutagens are physical or chemical agents that can cause mutations

Mutations

Are changes in the genetic material (DNA)

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

Mutagens are physical or chemical agents that can cause mutations

MutationsMutations Point mutations

Are changes in just one base pair of a gene

Can be divided into two general categories

Base-pair substitutions

Base-pair insertions or deletions

Point mutations

Are changes in just one base pair of a gene

Can be divided into two general categories

Base-pair substitutions

Base-pair insertions or deletions

Mutations SummaryMutations Summary

• Nucleotide-pair substitution: Replaces one nucleotide with a different one

• Silent mutations: Has no effect on the amino acid produced because of redundancy

• Missense mutations: Still codes for an amino acid, but not the correct one

• Nonsense mutations: Changes into a stop codon, nearly always leading to a nonfunctional protein

• Nucleotide-pair substitution: Replaces one nucleotide with a different one

• Silent mutations: Has no effect on the amino acid produced because of redundancy

• Missense mutations: Still codes for an amino acid, but not the correct one

• Nonsense mutations: Changes into a stop codon, nearly always leading to a nonfunctional protein

Wild typeWild type

DNA template strandDNA template strand

mRNA5′mRNA5′

5′5′

ProteinProtein

Amino endAmino endStopStopCarboxyl endCarboxyl end

3′3′3′3′

3′3′

5′5′

MetMet LysLys PhePhe GlyGly

A instead of GA instead of G

(a) Nucleotide-pair substitution: silent(a) Nucleotide-pair substitution: silent

StopStopMetMet LysLys PhePhe GlyGly

U instead of CU instead of C

AA

AA

AA AA

AA AA AA AA

AA AATT

TT TT TT TT TT

TT TT TTTT

CC CC CC CC

CC

CC

GG GG GG GG

GG

GG

AA

AA AA AA AAGG GGGGUU UU UU UU UU

5′5′3′3′

3′3′5′5′AA

AA AA

AA AA AA AA

AA AATT

TT TT TT TT TT

TT TT TTTT

CC CC CC CC

GG GG GG GG

AA

AA

AA GG AA AA AA AAGG GGGGUU UU UU UU UU

TT

UU 3′3′5′5′

Wild typeWild type


mRNA5′mRNA5′

5′5′

ProteinProtein


3′3′3′3′

3′3′

5′5′


T instead of CT instead of C

(a) Nucleotide-pair substitution: missense(a) Nucleotide-pair substitution: missense

StopStopMetMet LysLys PhePhe SerSer

A instead of GA instead of G

AA

AA

AA AA

AA AA AA AA

AA AATT

TT TT TT TT TT

TT TT TTTT

CC CC CC CC

CC

CC

GG GG GG GG

GG

GG

AA


5′5′3′3′

3′3′5′5′AA

AA AA

AA AA AA AA

AA AATT

TT TT TT TT TT

TT TT TTTT

CC CC TT CC

GG

GG

GGAA

AA GG AA AA AA AAAA GGGGUU UU UU UU UU 3′3′5′5′

AA CC

CC

GG

Wild typeWild type


mRNA5′mRNA5′

5′5′

ProteinProtein


3′3′3′3′

3′3′

5′5′


A instead of TA instead of T

(a) Nucleotide-pair substitution: nonsense(a) Nucleotide-pair substitution: nonsense

MetMet

AA

AA

AA AA

AA AA AA AA

AA AATT

TT TT TT TT TT

TT TT TTTT

CC CC CC CC

CC

CC

GG GG GG GG

GG

GG

AA


5′5′3′3′

3′3′5′5′AA

AA

AA AA AA AA

AA AATT

TT AA TT TT TT

TT TT TTTT

CC CC CC

GG

GG

GGAA

AA GG UU AA AA AAGGGGUU UU UU UU UU 3′3′5′5′

CC

CC

GG

T instead of CT instead of C

CC

GGTT

U instead of AU instead of AGG

StopStop

Wild typeWild type


mRNA5′mRNA5′

5′5′

ProteinProtein


3′3′3′3′

3′3′

5′5′


AA

AA

AA AA

AA AA AA AA

AA AATT

TT TT TT TT TT

TT TT TTTT

CC CC CC CC

CC

CC

GG GG GG GG

GG

GG

AA


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

Extra AExtra A

Extra UExtra U

5′5′3′3′

5′5′

3′3′

3′3′

5′5′

MetMet

1 nucleotide-pair insertion1 nucleotide-pair insertion

StopStop

AA CC AA AA GGTT TT AA TTCC TT AA CC GG

TT AA TT AATT GG TT CCTT GGGG AA TT GGAA

AA GG UU AA UU AAUU GGAAUU GG UU UU CC

AA TT

AA

AAGG


mRNA5′mRNA5′

5′5′

ProteinProtein


3′3′3′3′

3′3′

5′5′


AA

AA

AA AA

AA AA AA AA

AA AATT

TT TT TT TT TT

TT TT TTTT

CC CC CC CC

CC

CC

GG GG GG GG

GG

GG

AA


(b) Codon insertion or deletion: no frameshift, but

one

(b) Codon insertion or deletion: no frameshift, but

oneamino acid missingamino acid missing

Wild typeWild type

AATT CC AA AA AA AA TT TTCC CC GG

TT TT CC missingmissing

missingmissing

StopStop

5′5′3′3′

3′3′5′5′

3′3′5′5′

MetMet PhePhe GlyGly

3 nucleotide-pair deletion3 nucleotide-pair deletion

AA GGUU CC AA AAGG GGUU UU UU UU

TT GGAA AA AATT TT TTTT CCGG GG

AA AA GG

Consequences of a Point MutationConsequences of a Point Mutation

The change of a single nucleotide in the DNA’s template strand

Leads to the production of an abnormal protein

The change of a single nucleotide in the DNA’s template strand

Leads to the production of an abnormal proteinMutant hemoglobin DNAMutant hemoglobin DNAWild-type hemoglobin DNAWild-type hemoglobin DNA

mRNAmRNA mRNAmRNA

Normal hemoglobinNormal hemoglobin Sickle-cell hemoglobinSickle-cell hemoglobin

GluGlu ValVal

CC TT TT CC AA TT

GG AA AA GG UU AA

3′3′ 5′5′ 33 55

5′5′ 3′3′5′5′ 3′3′

Chapter 17 From Gene to Protein (Protein Synthesis) From Gene to Protein (Protein Synthesis)

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Transcript of Chapter 17 From Gene to Protein (Protein Synthesis) From Gene to Protein (Protein Synthesis)