2010-chapter 16 - transcription and translation-students

7/30/2019 2010-Chapter 16 - Transcription and Translation-students

1/78

Copyright 2008 Pearson Education Inc., publishing as Pearson Addison-Wesley

Generating information fromgenes

Transcription and translation

Chapter 16


2/78


Introduction A cell builds the proteins it needs from instructions encoded in its

genome.

The flow of information in the cell is as follows:


3/78


Transcription in Bacteria Transcription

RNA polymerase performs this synthesis by transcribingonly one strand of DNA, called the template strand.

The other DNA strand is called the non-templatestrand. The sequence of the non-template strand

matches the sequence of the RNA, except that RNA hasuracil (U) in place of thymine (T).

Transcription consists of three phases:


4/78


Transcription Is the Synthesis of RNA

from a DNA TemplateNon-template(coding) strand DNA

RNA

RNA

Template strand

5

5

5

5

3

3

3

3DNA template

3

5

3

5Phosphodiester bond isformed by RNA polymeraseafter base pairing occurs

Hydrogen bonds form betweencomplementary base pairs


5/78


6/78


The 3D Structure of RNA Polymerase

Bound to DNA

Holoenzyme

DNA

Core enzyme

Sigma


7/78Copyright 2008 Pearson Education Inc., publishing as Pearson Addison-Wesley

Initiation: How Does Transcription Begin

in Bacteria? Transcription of bacterial genes is initiated at specific sections of DNA

called

Promoters have two key regions: the 10 box and the 35 box. Thenames come from their locations: for example, the 10 box is found tenbases upstream from the transcription start site. (Downstream is in thedirection RNA polymerase moves during transcription; upstream is in theopposite direction.)

The sigma subunit is required for the initiation phase of transcription.



Transcription initiation site?Figure 16-3-1

Promoter (on non-template strand)

35 box 10 box

+1 siteUpstreamDNA Sigma

Activesite

DownstreamDNA

RNA polymerase

1. Initiation beginsSigma binds to promoterregion of DNA.



Initiation: How Does Transcription Begin

in Bacteria?

Next, sigma opens the DNA double helix andthe template strand is threaded through the

RNA polymerase active site.

An incoming ribonucleoside triphosphate

(NTP) pairs with a complementary base on theDNA template strand, and RNA polymerizationbegins.



In Bacteria, Sigma Plays a Key Role in

Initiating Transcription

+1 site

RNA

Figure 16-3-2

HOW TRANSCRIPTION BEGINS

2. Initiation continuesSigma opens the DNA helix;transcription begins.

+1 site

RNA

Template strand

NTPs

Non-templatestrand



In Bacteria, Sigma Plays a Key Role in

Initiating TranscriptionFigure 16-3-3

HOW TRANSCRIPTION BEGINS

RNA

RNAexitsite

3. Initiation is completeSigma releases; mRNAsynthesis continues.

UpstreamDNA

Zipper

Rudder

DownstreamDNA



Elongation and Termination During the elongation phase of

transcription, RNA polymerase moves alongthe DNA template and synthesizes RNA in the5' 3' direction.

Transcription ends with a terminationphase. In this phase, RNA polymeraseencounters a transcription termination signalin the DNA template. This signal codes forRNA forming a hairpin structure.


13/78



Transcription Terminates When a Hairpin

FormsFigure 16-4-2

HOW TRANSCRIPTION ENDS

2. The RNA hairpin causes the RNA strandto separate from the RNA polymerase,terminating transcription.

DNA

RNA



Transcription and RNA Processing in

Eukaryotes

Eukaryotic transcription shares many fundamentalcharacteristics with prokaryotic transcription.

Transcription in eukaryotes is initiated by proteins called basaltranscription factors. These factors begin transcription bymatching RNA polymerase with the appropriate promoterregion in DNA, a function analogous to that of sigma inbacteria.

Eukaryotic cells contain three types of RNA polymerase, namedI, II, and III. Each of these enzymes transcribes differentclasses of RNA.



Transcription and RNA Processing in

Eukaryotes The promoters in eukaryotic RNA are more diverse and

complex than are bacterial promoters.

The promoters recognized by each type of RNA polymerasediffer.

Many promoters recognized by RNA polymerase II include asequence called a TATA box analogous in function to theprokaryotic 10 and 35 boxes.

In eukaryotes, transcription is followed by several importantRNA processing steps.



The Startling Discovery of Eukaryotic Genes The RNA made in the nucleus was much longer than the mRNA molecules

found in the cytoplasm ,

Seems the protein-coding regions of eukaryotic genes are interrupted bynoncoding regions.

Exons are the coding regions of eukaryotic genes that will be part of thefinal mRNA product.

The intervening noncoding sequences are called introns, and are not inthe final mRNA.

Therefore, Eukaryotic genes



Processing of Eukaryote RNA transcripts

Primary RNA transcript

DNA

Promoter

Intron 1 Intron 2

Exon 1 Exon 2 Exon 3

Spliced transcript

3

5

5

3

5

3


19/78


Exons, Introns, and RNA Splicing The transcription of eukaryotic genes by RNA

polymerase generates a primary RNAtranscript that contains exons and introns.

Introns are removed by splicing.

Small nuclear ribonucleoproteins (snRNPs,pronounced snurps) form a complex called aspliceosome.


20/78


Introns Are Spliced Out of the Original

mRNAFigure 16-7b

snRNPs ARE THE EDITORS.

PrimaryRNA

snRNPs

Exon 1 Exon 2Intron

Spliceosome

35

35

335

5

5

1. Several snRNPs andproteins assemble toform a spliceosome.The 2 hydroxyl groupon an adeninenucleotide (A) reactswith the 5 end of theintron, breaking RNA.

35

Excisedintron

Exon 1 Exon 2Mature mRNA

2. The 5 end of theintron becomes attachedto the A nucleotide,forming a loop of RNA.The free 3 end of one

exon reacts with the 5end of the other.

3. The 3 and 5 endsof adjacent exons bondcovalently, releasing theintron (which is thendegraded).

A

A

A

A


21/78


Additional processing - Adding Caps and

Tails to RNA Transcripts Primary RNA transcripts are also processed by

the addition of a 5' cap and a poly (A) tail.

With the addition of cap and tail, processing iscomplete; the product is a mature mRNA.

The 5' cap serves as a

The poly (A) tail extends the life of an mRNAby protecting it from degradation.


22/78


In Eukaryotes, mRNAs Are Given a Cap

and a Tail

35

Poly(A) tail5 cap

5 untranslatedregion

3 untranslatedregion

Coding region


23/78


Translation In translation, the sequence of bases in

the mRNA is converted to an amino acid

sequence in a protein.


24/78


Ribosomes Are the Site of Protein

Synthesis Ribosomes catalyze translation of the mRNA sequence into

protein.

In bacteria, transcription and translation can occursimultaneously. Bacterial ribosomes begin translating anmRNA before RNA polymerase has finished transcribing it.

In eukaryotes, transcription and translation are separated.mRNAs are synthesized and processed in the nucleus andtransported to the cytoplasm for translation by ribosomes.


25/78


Transcription and Translation Occur

Simultaneously in Bacteria

Ribosome translatesmRNA as it is beingsynthesized by RNApolymerase

5 endof mRNA

1

2

1 1

2

3

Protein

Ribosome

RNA polymerase

(3 end of template strand)

Start of gene End of gene

(5 end of template strand)


26/78


Transcription and Translation Are Separated in Space

and Time in EukaryotesFigure 16-10

mRNA

DNA

Mature

mRNA

Transcription andRNA processingin nucleus

Mature

mRNA

Translationin cytoplasm

Protein

Ribosome


27/78


How Does an mRNA Triplet Specify an

Amino Acid?Figure 16-11

Hypothesis 1: Amino acids interact directly withmRNA codons.

Aminoacids

Hypothesis 2: Adapter molecules hold amino acids andinteract with mRNA codons.

Adaptermolecules

mRNA

Codon Codon Codon Codon

Codon Codon Codon Codon

Aminoacids

mRNA

Peptide bond


28/78


The Role of Transfer RNA The adapter molecule was later found to be a small

RNA called transfer RNA (tRNA).

A tRNA covalently linked to its corresponding aminoacid is called an

Enzymes called aminoacyl tRNA synthetases.


29/78


Aminoacyl tRNAsynthetase specificto leucine

1. Active site on aminoacyltRNA synthetase binds ATPand amino acid. Eachaminoacyl tRNA synthetaseis specific to one amino acid.

Activatedenzymecomplex

ATP

2. Reaction leaves AMP andamino acid bound to enzyme;two phosphate groupsreleased. Activated aminoacid has high potential energy.

HOW AMINO ACIDS ARE LOADED ONTO tRNAs


30/78


Aminoacyl tRNA

HOW AMINO ACIDS ARE LOADED ONTO tRNAs

tRNAspecific toleucine

3. The activated amino acid istransferred from tRNAsynthetase to the tRNA

specific to that amino acid;AMP leaves.

4. The finished aminoacyltRNA is ready to participatein translation.


31/78


The Role of Transfer RNA For each of the 20 amino acids, there is a

different aminoacyl tRNA synthetase and one or

more tRNAs.

Each tRNA.


32/78


Experimental Evidence that Amino Acids

Are Transferred from tRNAs to Proteins


33/78





34/78





35/78


What Do tRNAs Look Like? tRNAs have a cloverleaf structure.

The CCA sequence at the 3' end of each tRNA is the

The triplet loop at the opposite end of the cloverleaf is theanticodon that base pairs with the mRNA codon.

The cloverleaf structure of tRNA folds over to produce amolecule with an L-shaped tertiary structure.

.


36/78


Secondary structure of tRNA

Amino acid

Early model of aminoacyl tRNA function

Binding site for

amino acid

Binding site formRNA codonSerine anticodon

mRNASerine codon

5

5

5

3

3

3

5

3

mRNACodon

Anticodon

3

5

Revised model incorporating tertiary structure of tRNA


37/78


How Many tRNAs Are There? There are 61 different codons but only about 40

tRNAs in most cells.

To resolve this deficit, Francis Crick proposed thewobble hypothesis. This hypothesis proposes thatthe anticodon of tRNAs can still bind successfully to a

codon whose third position requires a nonstandardbase pairing.

Thus, one tRNA is able to base pair with more than

one type of codon.


38/78


Ribosomes and the Mechanism of

Translation Ribosomes contain both protein and ribosomal

RNA (rRNA).

Ribosomes can be separated into two subunits, thelarge subunit and the small subunit.


39/78


The Structure of the Ribosome during

Translation

5 3

Smallsubunit

Codon

tRNA in E site(blue)

Ribbon model of ribosome during translation Diagram of ribosome during translation

Largesubunit

tRNA in P site(green)

tRNA in A site(red)

Largesubunit

Smallsubunit

mRNA Anticodon

AminoacyltRNA

The A siteholds anaminoacyltRNA

The P site holdsthe tRNA withgrowing polypeptideattached

The E siteholds a tRNAthat will exit

Polypeptide grows in aminoto carboxyl direction(amino acids in green)

Peptide bondformation occurshere


40/78



Translation All three tRNAs are bound at their anticodons to the

corresponding mRNA codon.

TheA site of the ribosome is the acceptor site for anaminoacyl tRNA.

The P site is where a peptidebond forms that addsan amino acid to the growing polypeptide chain.

The E site is where tRNAs no longer bound to an

amino acid exit the ribosome.


41/78



Translation Translation occurs by a three-step sequence:

(1) An aminoacyl tRNA carrying the correct anticodon for themRNA codon enters the A site;

(2) A peptide bond forms between the amino acid on theaminoacyl tRNA in the A site and the growing polypeptideon the tRNA in the P site;

(3) The ribosome moves ahead three bases and all three

tRNAs move down one position; the tRNA in the E siteexits.


42/78


43/78


3

INITIATING TRANSLATION IN BACTERIA

Startcodon

Ribosomebinding

site

Initiationfactor

Initiationfactor

Small subunitof ribosome

5

1. Ribosome binding site sequence bindsto a complementary sequence in an RNAmolecule in the small subunit of the ribosome,with the help of protein initiation factors.


44/78


Small subunitof ribosome

AminoacyltRNA

Startcodon

5 3

2. Initiator aminoacyl tRNA bindsto start codon.



45/78


5

Largesubunit ofribosome

3

3. Large subunit of ribosome binds.Translation begins.



46/78


Initiation

Once the small ribosomal subunit is bound to themRNA, the initiator aminoacyl tRNA binds to the

AUG sequence.

The large subunit binds and completes theinitiation complex.


47/78


Elongation

At the start of the elongation phase, theinitiator tRNA is in the P site, and the E and

A sites are empty.

An aminoacyl tRNA binds to the codon inthe A site via complementary base pairing

between anticodon and codon.

.


48/78


ELONGATION OF POLYPEPTIDES DURING TRANSLATION

Peptidyl site

1. Incoming aminoacyl tRNANew tRNA moves into A site, whereits anticodon base pairs with themRNA codon.

Start

codon

5 3mRNA

Exit site Aminoacyl site

tRNA

Ribosome


49/78


5 3

2. Peptide bond formationThe amino acid attached to the tRNAin the P site is transferred to thetRNA in the A site.



50/78


Moving Down the mRNA

After peptide bond formation, the polypeptide onthe tRNA in the P site is transferred to the tRNA inthe A site.

The ribosome translocates down the mRNA bythree nucleotides, and the tRNA attached to the

growing protein moves into the P site.


51/78


5 3

3. TranslocationRibosome moves down mRNA. ThetRNA attached to polypeptide chainmoves into P site. The A site is empty.



52/78



The A site is now available to accept a new

aminoacyl tRNA for binding to the next codon.


53/78


3

4. Incoming aminoacyl tRNANew tRNA moves into A site, whereits anticodon base pairs with themRNA codon.


5


54/78


5 3

5. Peptide bond formationThe polypeptide chain attached tothe tRNA in the P site is transferredto the aminoacyl tRNA in the A site.



55/78



The tRNA that was in the P site moves to the E

site, and if the E site is occupied, that tRNA isejected.


56/78


5

Elongation cycle

continues

3

Exit tunnel

6. TranslocationRibosome moves down mRNA. ThetRNA attached to polypeptide chainmoves into P site. Empty tRNA fromP site moves to E site, where tRNA isejected. The A site is empty again.



57/78


Is the Ribosome an Enzyme or a

Ribozyme? The active site of the ribosome is entirely

ribosomal RNA.

Thus, ribosomal RNA catalyzes peptide bondformation and the ribosome is a ribozyme.


58/78


Elongation

Polyribosomes, strings of translatingribosomes, assemble along an mRNA

to increase the rate of proteinproduction.


59/78


53

mRNA

Ribosomes

Growing polypeptides

Polyribosomes


60/78


Termination

The termination phase starts when the Asite encounters a.

This causes a protein called a release factorto enter the site.

These factors catalyze hydrolysis of thebond linking the tRNA in the P site with thepolypeptide chain.


61/78


5 3

mRNA

tRNA Releasefactor

STOPcodon

TERMINATION OF TRANSLATION

Hydrolysis ofbond linkingtRNA andpolypeptide

1. When translocation opens the A siteand exposes one of the stop codons, aprotein called a release factor fills the Asite. The release factor catalyzes thehydrolysis of the bond linking the tRNA

in the P site with the polypeptide chain.


62/78


mRNA

5 3


2. The hydrolysis reaction frees thepolypeptide, which is released from theribosome. The empty tRNAs are released

either along with the polypeptide or


63/78


mRNA

Smallsubunit

Largesubunit

3

5


3. when the ribosome separates from themRNA, and the two ribosomal subunitsdissociate. The subunits are ready toattach to the start codon of anothermessage and start translation anew.


64/78


5 3

mRNA

tRNA Releasefactor

STOPcodon


Hydrolysis ofbond linkingtRNA andpolypeptide

1. When translocation opens the A siteand exposes one of the stop codons, aprotein called a release factor fills the Asite. The release factor catalyzes thehydrolysis of the bond linking the tRNA

in the P site with the polypeptide chain.


65/78


mRNA

5 3


2. The hydrolysis reaction frees thepolypeptide, which is released from theribosome. The empty tRNAs are released

either along with the polypeptide or


66/78


mRNA

Smallsubunit

Largesubunit

3

5


3. when the ribosome separates from themRNA, and the two ribosomal subunitsdissociate. The subunits are ready toattach to the start codon of anothermessage and start translation anew.


67/78


Post-Translational Modifications

Most proteins go through an extensive series ofprocessing steps, collectively called post-translational modification, before they are ready to

go to work in a cell.

Molecular chaperones speed folding of the protein.Folding determines a protein's shape and therefore itsfunction.


68/78


What Is the Molecular Basis of Mutation?

Amutation is any permanent change in anorganisms DNA.

DNA mutations change the genotype of a cell. Thisleads to the production of novel types of proteinsand so can affect phenotype.


69/78


Point Mutations

A single base change is called a pointmutation.

Point mutations can result from errorsin DNA replication.


70/78


Unrepaired Mistakes in DNA

Synthesis Lead to Point Mutations

5

3

DNAreplication

Original DNAMUTANT

5

3

Base-pair mismatch

DNAreplication

Changedbase pair

Likeoriginal

DNA


71/78


72/78


Sickle-Cell Disease Results from a PointMutation in the Gene for Hemoglobin

5

3

Mutant

5

3

Normal

DNA sequenceof non-template(coding) strand

DNA sequenceof non-template(coding) strand

Amino acidsequence

Amino acidsequence

DNA point mutation can lead to a different amino acid sequence. Phenotype

Sickled red blood cells

Normal red blood cells


73/78


Chromosome-Level Mutations

Mutations can also involve larger-scalechanges in the composition of chromosomes.

For example, changes in chromosome numbercan occur -.

These result from chance mistakes in thepartitioning of chromosomes during meiosis ormitosis.


74/78


Chromosome-Level Mutations The composition of individual chromosomes

can also change.

Inversion occurs when a chromosomalsegment detaches, flips, and reattaches to thechromosome.

Chromosomal translocation occurs when achromosomal segment detaches and becomesattached to a different chromosome.

Figure 12-6bc


75/78


Translocations are abnomalities - translocation

Sex chromosomes in Klinefelter syndrome polyploidy

Pieces of chromosomes

have been swapped

Two X chromosomesand one Y chromosome

Leads to uncontrolledcell growth chronic

myelogenous leukemia

Causes males that aresterile


76/78


Key Concepts

Inside ribosomes, mRNAs are translated to proteinsvia intermediary molecules called transfer RNAs.Transfer RNAs carry an amino acid and have a three-

base-pair anticodon, which binds to a three-base-long mRNA codon. The amino acid carried by thetransfer RNA is then added to the growing proteinvia formation of a peptide bond.

Mutations are random changes in the DNA that mayor may not produce changes in the phenotype.


77/78


Key Concepts

After the enzyme RNA polymerase binds to aspecific site in DNA with the help of otherproteins, it catalyzes the production of an RNA

molecule. The base sequence of the RNAproduced is complementary to the base sequenceof the DNA template strand.

Some sections of an RNA are encoded by generegions called exons, while others are encoded bygene regions called introns. During RNAprocessing, introns are removed and the ends ofthe RNA receive a cap and tail.


78/78

Key Concepts

Inside ribosomes, mRNAs are translated toproteins via intermediary molecules called transferRNAs. Transfer RNAs carry an amino acid and

have a three-base-pair anticodon, which binds toa three-base-long mRNA codon. The amino acidcarried by the transfer RNA is then added to thegrowing protein via formation of a peptide bond.

Mutations are random changes in the DNA thatmay or may not produce changes in thephenotype.

2010-chapter 16 - transcription and translation-students

Documents