Dn ato protein

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The Molecular Basis of Inheritance

• Overview: Life’s Operating Instructions

• In 1953, James Watson and Francis Crick shook the world

– With an elegant double-helical model for the structure of deoxyribonucleic acid, or DNA

Figure 16.1


• Hereditary information

– Is encoded in the chemical language of DNA and reproduced in all the cells of your body

• It is the DNA program

– That directs the development of many different types of traits


Evidence That DNA Can Transform Bacteria

• The role of DNA in heredity

– Was first worked out by studying bacteria and the viruses that infect them

• Frederick Griffith was studying Streptococcus pneumoniae

– A bacterium that causes pneumonia in mammals

• He worked with two strains of the bacterium

– A pathogenic strain and a nonpathogenic strain


• Griffith found that when he mixed heat-killed remains of the pathogenic strain

– With living cells of the nonpathogenic strain, some of these living cells became pathogenic

Bacteria of the “S” (smooth) strain of Streptococcus pneumoniae are pathogenic because they have a capsule that protects them from an animal’s defense system. Bacteria of the “R” (rough) strain lack a capsule and are nonpathogenic. Frederick Griffith injected mice with the two strains as shown below:

Griffith concluded that the living R bacteria had been transformed into pathogenic S bacteria by anunknown, heritable substance from the dead S cells.

EXPERIMENT

RESULTS

CONCLUSION

Living S(control) cells

Living R(control) cells

Heat-killed(control) S cells

Mixture of heat-killed S cellsand living R cells

Mouse dies Mouse healthy Mouse healthy Mouse dies

Living S cellsare found inblood sample.

Figure 16.2


• Griffith called the phenomenon transformation

Bacteria of the “S” (smooth) strain of Streptococcus pneumoniae are pathogenic because they have a capsule that protects them from an animal’s defense system. Bacteria of the “R” (rough) strain lack a capsule and are nonpathogenic. Frederick Griffith injected mice with the two strains as shown below:

Griffith concluded that the living R bacteria had been transformed into pathogenic S bacteria by anunknown, heritable substance from the dead S cells.

EXPERIMENT

RESULTS

CONCLUSION

Living S(control) cells

Living R(control) cells

Heat-killed(control) S cells

Mixture of heat-killed S cellsand living R cells

Mouse dies Mouse healthy Mouse healthy Mouse dies

Living S cellsare found inblood sample.

Figure 16.2


Evidence That Viral DNA Can Program Cells

• Additional evidence for DNA as the genetic material

– Came from studies of a virus that infects bacteria


• Viruses that infect bacteria, bacteriophages

– Are widely used as tools by researchers in molecular genetics

Figure 16.3

Phagehead

Tail

Tail fiber

DNA

Bacterialcell

100

nm


Experiments showing that DNA is the genetic material of a phage (T2)

• The Hershey and Chase experiment In their famous 1952 experiment, Alfred Hershey and Martha Chase used radioactive sulfur and phosphorus to trace the fates of the protein and DNA, respectively, of T2 phages that infected bacterial cells.

Radioactivity(phage protein)in liquid

Phage

Bacterial cell

Radioactiveprotein

Emptyprotein shell

PhageDNA

DNA

Centrifuge

Pellet (bacterialcells and contents)

RadioactiveDNA

Centrifuge

Pellet

Batch 1: Phages weregrown with radioactivesulfur (35S), which wasincorporated into phageprotein (pink).

Batch 2: Phages weregrown with radioactivephosphorus (32P), which was incorporated into phage DNA (blue).

1 2 3 4Agitated in a blender toseparate phages outsidethe bacteria from thebacterial cells.

Mixed radioactivelylabeled phages withbacteria. The phagesinfected the bacterial cells.

Centrifuged the mixtureso that bacteria formeda pellet at the bottom ofthe test tube.

Measured theradioactivity inthe pellet and the liquid

Phage proteins remained outside the bacterial cells during infection, while phage DNA entered the cells. When cultured, bacterial cells with radioactive phage DNA released new phages with some radioactive phosphorus.

Hershey and Chase concluded that DNA, not protein, functions as the T2 phage’s genetic material.

RESULTS

CONCLUSION

EXPERIMENT

Radioactivity(phage DNA)in pellet

Figure 16.4

Animation of experiment


Additional Evidence That DNA Is the Genetic Materia

• Prior to the 1950s, it was already known that DNA

– Is a polymer of nucleotides, each consisting of three components: a nitrogenous base, a sugar, and a phosphate group

Sugar-phosphatebackbone

Nitrogenousbases

5 endO–

O P O CH2

5

4O–

HH

OH

HH

3

1H O

CH3

N

O

NH

Thymine (T)

O

O P OO–

CH2

HH

OH

HH

HN

N

N

H

NH

H

Adenine (A)O

O P O

O–

CH2

HH

OH

HH

HH H

HN

NN

OCytosine (C)

O

O P O CH2

5

4O–

H

O

HH

3

1

OH2

H

N

NN H

ON

N HH

H H

Sugar (deoxyribose)3 end

Phosphate

Guanine (G)

DNA nucleotide

2

N

Figure 16.5


• Erwin Chargaff analyzed the base composition of DNA

– From a number of different organisms

• In 1947, Chargaff reported

– That DNA composition varies from one species to the next

• This evidence of molecular diversity among species

– Made DNA a more credible candidate for the genetic material


Building a Structural Model of DNA: Scientific Inquiry

• Maurice Wilkins and Rosalind Franklin

– Were using a technique called X-ray crystallography to study molecular structure

• Rosalind Franklin

– Produced a picture of the DNA molecule using this technique

(a) Rosalind Franklin Franklin’s X-ray diffractionPhotograph of DNA

(b)Figure 16.6 a, b


Figure 16.7a, c

C

T

A

A

T

CG

GC

A

C G

AT

AT

A T

TA

C

TA0.34 nm

3.4 nm

(a) Key features of DNA structure

G

1 nm

G

(c) Space-filling model

T

• Watson and Crick deduced that DNA was a double helix

– Through observations of the X-ray crystallographic images of DNA


• Franklin had concluded that DNA

– Was composed of two antiparallel sugar-phosphate backbones, with the nitrogenous bases paired in the molecule’s interior

• The nitrogenous bases

– Are paired in specific combinations: adenine with thymine, and cytosine with guanine


O

–O O

OH

O

–OO

O

H2C

O

–OO

O

H2C

O

–OO

O

OH

O

O

OT A

C

GC

A T

O

O

O

CH2

OO–

OO

CH2

CH2

CH2

5 end

Hydrogen bond3 end

3 end

G

P

P

P

P

O

OH

O–

OO

O

P

P

O–

OO

O

P

O–

OO

O

P

(b) Partial chemical structure

H2C

5 endFigure 16.7b

O


• Watson and Crick reasoned that there must be additional specificity of pairing

– Dictated by the structure of the bases

• Each base pair forms a different number of hydrogen bonds

– Adenine and thymine form two bonds, cytosine and guanine form three bonds


N H O CH3

N

N

O

N

N

N

N H

Sugar

Sugar

Adenine (A) Thymine (T)

N

N

N

N

Sugar

O H N

H

NH

N OH

H

N

Sugar

Guanine (G) Cytosine (C)Figure 16.8

H


• Many proteins work together in DNA replication and repair (DNA-Protein like Chicken-Egg debate, which came first?)

• Since the two strands of DNA are complementary

– Each strand acts as a template for building a new strand in replication


• In DNA replication

– The parent molecule unwinds, and two new daughter strands are built based on base-pairing rules

(a) The parent molecule has two complementary strands of DNA. Each base is paired by hydrogen bonding with its specific partner, A with T and G with C.

(b) The first step in replication is separation of the two DNA strands.

(c) Each parental strand now serves as a template that determines the order of nucleotides along a new, complementary strand.

(d) The nucleotides are connected to form the sugar-phosphate backbones of the new strands. Each “daughter” DNA molecule consists of one parental strand and one new strand.

A

C

T

A

G

A

C

T

A

G

A

C

T

A

G

A

C

T

A

G

T

G

A

T

C

T

G

A

T

C

A

C

T

A

G

A

C

T

A

G

T

G

A

T

C

T

G

A

T

C

T

G

A

T

C

T

G

A

T

C

Figure 16.9 a–d


Figure 16.10 a–c

Conservativemodel. The twoparental strandsreassociate after acting astemplates fornew strands,thus restoringthe parentaldouble helix.

Semiconservativemodel. The two strands of the parental moleculeseparate, and each functionsas a templatefor synthesis ofa new, comple-mentary strand.

Dispersivemodel. Eachstrand of bothdaughter mol-ecules containsa mixture ofold and newlysynthesizedDNA.

Parent cellFirstreplication

Secondreplication

• DNA replication is semiconservative

– Each of the two new daughter molecules will have one old strand, derived from the parent molecule, and one newly made strand

(a)

(b)

(c)


DNA Replication: A Closer Look

• The copying of DNA

– Is remarkable in its speed and accuracy

• More than a dozen enzymes and other proteins

– Participate in DNA replication

• The replication of a DNA molecule

– Begins at special sites called origins of replication, where the two strands are separated


• A eukaryotic chromosome

– May have hundreds or even thousands of replication origins

Replication begins at specific siteswhere the two parental strandsseparate and form replicationbubbles.

The bubbles expand laterally, asDNA replication proceeds in bothdirections.

Eventually, the replicationbubbles fuse, and synthesis ofthe daughter strands iscomplete.

1

2

3

Origin of replication

Bubble

Parental (template) strand

Daughter (new) strand

Replication fork

Two daughter DNA molecules

In eukaryotes, DNA replication begins at many sites along the giantDNA molecule of each chromosome.

In this micrograph, three replicationbubbles are visible along the DNA ofa cultured Chinese hamster cell (TEM).

(b)(a)

0.25 µm

Figure 16.12 a, b


Figure 16.13

New strand Template strand5 end 3 end

Sugar A TBase

C

G

G

C

A

C

T

PP

P

OH

P P

5 end 3 end

5 end 5 end

A T

C

G

G

C

A

C

T

3 endPyrophosphate

2 P

OH

Phosphate

Elongating a New DNA Strand

• Elongation of new DNA at a replication fork

– Is catalyzed by enzymes called DNA polymerases, which add nucleotides to the 3 end of a growing strand

Nucleosidetriphosphate


• DNA polymerases add nucleotides

– Only to the free 3end of a growing strand

• Along one template strand of DNA, the leading strand

– DNA polymerase III can synthesize a complementary strand continuously, moving toward the replication fork


• To elongate the other new strand of DNA, the lagging strand

– DNA polymerase III must work in the direction away from the replication fork

• The lagging strand

– Is synthesized as a series of segments called Okazaki fragments, which are then joined together by DNA ligase


Parental DNA

DNA pol Ill elongatesDNA strands only in the5 3 direction.

1

Okazakifragments

DNA pol III

Templatestrand

Lagging strand3

2

Templatestrand DNA ligase

Overall direction of replication

One new strand, the leading strand,can elongate continuously 5 3 as the replication fork progresses.

2

The other new strand, thelagging strand must grow in an overall3 5 direction by addition of shortsegments, Okazaki fragments, that grow5 3 (numbered here in the orderthey were made).

3

DNA ligase joins Okazakifragments by forming a bond betweentheir free ends. This results in a continuous strand.

4

Figure 16.14

35

5

3

35

21

Leading strand

1

• Synthesis of leading and lagging strands during DNA replication


Priming DNA Synthesis

• DNA polymerases cannot initiate the synthesis of a polynucleotide

– They can only add nucleotides to the 3 end

• The initial nucleotide strand

– Is an RNA or DNA primer


• Only one primer is needed for synthesis of the leading strand

– But for synthesis of the lagging strand, each Okazaki fragment must be primed separately


Replication Animation****

Overall direction of replication

3

3

3

35

35

35

35

3

5

3

5

3

5

3 5

5

1

1

21

12

5

5

12

35

Templatestrand

RNA primer

Okazakifragment

Figure 16.15

Primase joins RNA nucleotides into a primer.

1

DNA pol III adds DNA nucleotides to the primer, forming an Okazaki fragment.

2

After reaching the next RNA primer (not shown), DNA pol III falls off.

3

After the second fragment is primed. DNA pol III adds DNAnucleotides until it reaches the first primer and falls off.

4

DNA pol 1 replaces the RNA with DNA, adding to the 3 end of fragment 2.

5

DNA ligase forms a bond between the newest DNAand the adjacent DNA of fragment 1.

6 The lagging strand in this region is nowcomplete.

7


Other Proteins That Assist DNA Replication

• Helicase, topoisomerase, single-strand binding protein

– Are all proteins that assist DNA replication

Table 16.1


Figure 16.16

Overall direction of replication Leadingstrand

Laggingstrand

Laggingstrand

LeadingstrandOVERVIEW

Leadingstrand

Replication fork

DNA pol III

Primase

PrimerDNA pol III Lagging

strand

DNA pol I

Parental DNA

5

3

43

2

Origin of replication

DNA ligase

1

5

3

Helicase unwinds theparental double helix.1

Molecules of single-strand binding proteinstabilize the unwoundtemplate strands.

2 The leading strand issynthesized continuously in the5 3 direction by DNA pol III.

3

Primase begins synthesisof RNA primer for fifthOkazaki fragment.

4

DNA pol III is completing synthesis ofthe fourth fragment, when it reaches theRNA primer on the third fragment, it willdissociate, move to the replication fork,and add DNA nucleotides to the 3 endof the fifth fragment primer.

5 DNA pol I removes the primer from the 5 endof the second fragment, replacing it with DNAnucleotides that it adds one by one to the 3 endof the third fragment. The replacement of thelast RNA nucleotide with DNA leaves the sugar-phosphate backbone with a free 3 end.

6 DNA ligase bondsthe 3 end of thesecond fragment tothe 5 end of the firstfragment.

7

Replication Animation #2 Recap

• A summary of DNA replication


The DNA Replication Machine as a Stationary Complex

• The various proteins that participate in DNA replication

– Form a single large complex, a DNA replication “machine”

• The DNA replication machine

– Is probably stationary during the replication process


Proofreading and Repairing DNA

• DNA polymerases proofread newly made DNA

– Replacing any incorrect nucleotides

• In mismatch repair of DNA

– Repair enzymes correct errors in base pairing


Figure 16.17

Nuclease

DNApolymerase

DNAligase

A thymine dimerdistorts the DNA molecule.1

A nuclease enzyme cutsthe damaged DNA strandat two points and thedamaged section isremoved.

2

Repair synthesis bya DNA polymerasefills in the missingnucleotides.

3

DNA ligase seals theFree end of the new DNATo the old DNA, making thestrand complete.

4

• In nucleotide excision repair

– Enzymes cut out and replace damaged stretches of DNA


Replicating the Ends of DNA Molecules

• The ends of eukaryotic chromosomal DNA

– Get shorter with each round of replication

Figure 16.18

End of parentalDNA strands

Leading strandLagging strand

Last fragment Previous fragment

RNA primer

Lagging strand

Removal of primers andreplacement with DNAwhere a 3 end is available

Primer removed butcannot be replacedwith DNA because

no 3 end availablefor DNA polymerase

Second roundof replication

New leading strand

New lagging strand 5

Further roundsof replication

Shorter and shorterdaughter molecules

5

3

5

3

5

3

5

3

3


• Eukaryotic chromosomal DNA molecules

– Have at their ends nucleotide sequences, called telomeres, that postpone the erosion of genes near the ends of DNA molecules

Figure 16.19 1 µm


• If the chromosomes of germ cells became shorter in every cell cycle

– Essential genes would eventually be missing from the gametes they produce

• An enzyme called telomerase

– Catalyzes the lengthening of telomeres in germ cells


From Gene to Protein

• The DNA inherited by an organism

– Leads to specific traits by dictating the synthesis of proteins

• The process by which DNA directs protein synthesis, gene expression

– Includes two stages, called transcription and translation


• The ribosome

– Is part of the cellular machinery for translation, polypeptide synthesis

Figure 17.1


Genes specify proteins via transcription and translation

• In 1909, British physician Archibald Garrod

– Was the first to suggest that genes dictate phenotypes through enzymes that catalyze specific chemical reactions in the cell

• Beadle and Tatum causes bread mold to mutate with X-rays

– Creating mutants that could not survive on minimal medium


• Using genetic crosses

– They determined that their mutants fell into three classes, each mutated in a different gene

Figure 17.2

Working with the mold Neurospora crassa, George Beadle and Edward Tatum had isolated mutants requiring arginine in their growth medium and had shown genetically that these mutants fell into three classes, each defective in a different gene. From other considerations, they suspected that the metabolic pathway of arginine biosynthesis included the precursors ornithine and citrulline. Their most famous experiment, shown here, tested both their one gene–one enzyme hypothesis and their postulated arginine pathway. In this experiment, they grew their three classes of mutants under the four different conditions shown in the Results section below.

The wild-type strain required only the minimal medium for growth. The three classes of mutants had different growth requirements

EXPERIMENT

RESULTS

Class IMutants

Class IIMutants

Class IIIMutantsWild type

Minimal medium(MM)(control)

MM +Ornithine

MM +Citrulline

MM +Arginine(control)


CONCLUSION From the growth patterns of the mutants, Beadle and Tatum deduced that each mutant was unable to carry out one step in the pathway for synthesizing arginine, presumably because it lacked the necessary enzyme. Because each of their mutants was mutated in a single gene, they concluded that each mutated gene must normally dictate the production of one enzyme. Their results supported the one gene–one enzyme hypothesis and also confirmed the arginine pathway. (Notice that a mutant can grow only if supplied with a compound made after the defective step.)

Class IMutants(mutationin gene A)

Class IIMutants(mutationin gene B)

Class IIIMutants(mutationin gene C)Wild type

Gene A

Gene B

Gene C

Precursor Precursor Precursor Precursor

Ornithine Ornithine Ornithine Ornithine

Citrulline Citrulline Citrulline Citrulline

Arginine Arginine Arginine Arginine

EnzymeA

EnzymeB

EnzymeC

A A A

B B B

C C C


• Beadle and Tatum developed the “one gene–one enzyme hypothesis”

– Which states that the function of a gene is to dictate the production of a specific enzyme

• As researchers learned more about proteins

– They made minor revision to the one gene–one enzyme hypothesis

• Genes code for polypeptide chains or for RNA molecules


Basic Principles of Transcription and Translation

• Transcription

– Is the synthesis of RNA under the direction of DNA

– Produces messenger RNA (mRNA)

• Translation

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

– Occurs on ribosomeshttp://vcell.ndsu.nodak.edu/animations/transcription/index.htm - animations


• In prokaryotes

– Transcription and translation occur together

Figure 17.3a

Prokaryotic cell. In a cell lacking a nucleus, mRNAproduced by transcription is immediately translatedwithout additional processing.

(a)

TRANSLATION

TRANSCRIPTION DNA

mRNA

Ribosome

Polypeptide


Prokaryote/Eukaryote differences animation

• In eukaryotes

– RNA transcripts are modified before becoming true mRNA

Figure 17.3b

Eukaryotic cell. The nucleus provides a separatecompartment for transcription. The original RNAtranscript, called pre-mRNA, is processed in various ways before leaving the nucleus as mRNA.

(b)

TRANSCRIPTION

RNA PROCESSING

TRANSLATION

mRNA

DNA

Pre-mRNA

Polypeptide

Ribosome

Nuclearenvelope


• Cells are governed by a cellular chain of command

– DNA RNA protein

• Genetic information

– Is encoded as a sequence of nonoverlapping base triplets, or codons


• During transcription

– The gene determines the sequence of bases along the length of an mRNA molecule

Figure 17.4

DNAmolecule

Gene 1

Gene 2

Gene 3

DNA strand(template)

TRANSCRIPTION

mRNA

Protein

TRANSLATION

Amino acid

A C C A A A C C G A G T

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

Trp Phe Gly Ser

Codon

3 5

35


Cracking the Code

• A codon in messenger RNA

– Is either translated into an amino acid or serves as a translational stop signal

Second mRNA baseU C A G

U

C

A

G

UUUUUCUUAUUG

CUUCUCCUACUG

AUUAUCAUAAUG

GUUGUCGUAGUG

Met orstart

Phe

Leu

Leu

lle

Val

UCUUCCUCAUCG

CCUCCCCCACCG

ACUACCACAACG

GCUGCCGCAGCG

Ser

Pro

Thr

Ala

UAUUAC

UGUUGC

Tyr Cys

CAUCACCAACAG

CGUCGCCGACGG

AAUAACAAAAAG

AGUAGCAGAAGG

GAUGACGAAGAG

GGUGGCGGAGGG

UGGUAAUAG Stop

Stop UGA StopTrp

His

Gln

Asn

Lys

Asp

Arg

Ser

Arg

Gly

U

CA

GUCAG

UCAG

UCAG

Fir

st m

RN

A b

ase

(5

en

d)

Th

ird

mR

NA

bas

e (3

e

nd

)

Glu

Codons must be read in the correct reading frame

For the specified polypeptide to be produced


Molecular Components of Transcription

• RNA synthesis

– Is catalyzed by RNA polymerase, which pries the DNA strands apart and hooks together the RNA nucleotides

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


Synthesis of an RNA Transcript

• The stages of transcription are

– Initiation

– Elongation

– Termination

Figure 17.7

PromoterTranscription unit

RNA polymerase

Start point

53

35

35

53

53

35

53

35

5

5

Rewound

RNA

RNA

transcript

3

3

Completed RNA transcript

Unwound

DNA

RNA

transcript

Template strand of DNA

DNA

1 Initiation. After RNA polymerase binds to

the promoter, the DNA strands unwind, and

the polymerase initiates RNA synthesis at the

start point on the template strand.

2 Elongation. The polymerase moves downstream, unwinding the

DNA and elongating the RNA transcript 5 3 . In the wake of

transcription, the DNA strands re-form a double helix.

3 Termination. Eventually, the RNA

transcript is released, and the

polymerase detaches from the DNA.


Elongation

RNApolymerase

Non-templatestrand of DNA

RNA nucleotides

3 end

C A E G C AA

U

T A G G T TA

AC

G

U

AT

CA

T C C A AT

T

GG

3

5

5

Newly madeRNA

Direction of transcription(“downstream”) Template

strand of DNA


RNA Polymerase Binding and Initiation of Transcription

• Promoters signal the initiation of RNA synthesis

• Transcription factors

– Help eukaryotic RNA polymerase recognize promoter sequences

Figure 17.8Figure 17.8

TRANSCRIPTION

RNA PROCESSING

TRANSLATION

DNA

Pre-mRNA

mRNA

Ribosome

Polypeptide

T A T AAA AAT AT T T T

TATA box Start point TemplateDNA strand

53

35

Transcriptionfactors

53

35

Promoter

53

355

RNA polymerase IITranscription factors

RNA transcript

Transcription initiation complex

Eukaryotic promoters1

Several transcriptionfactors

2

Additional transcriptionfactors

3


Elongation of the RNA Strand

• As RNA polymerase moves along the DNA

– It continues to untwist the double helix, exposing about 10 to 20 DNA bases at a time for pairing with RNA nucleotides

• The mechanisms of termination

– Are different in prokaryotes and eukaryotes


• Eukaryotic cells modify RNA after transcription

• Enzymes in the eukaryotic nucleus

– Modify pre-mRNA in specific ways before the genetic messages are dispatched to the cytoplasm


Alteration of mRNA Ends

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

– The 5 end receives a modified nucleotide cap

– The 3 end gets a poly-A tail

Figure 17.9

A modified guanine nucleotideadded to the 5 end

50 to 250 adenine nucleotidesadded to the 3 end

Protein-coding segment Polyadenylation signal

Poly-A tail3 UTRStop codonStart codon

5 Cap 5 UTR

AAUAAA AAA…AAA

TRANSCRIPTION

RNA PROCESSING

DNA

Pre-mRNA

mRNA

TRANSLATIONRibosome

Polypeptide

G P P P

5 3

Video clip


Split Genes and RNA Splicing

• RNA splicing

– Removes introns (supposed “Junk-DNA”) and joins exons

Figure 17.10

TRANSCRIPTION

RNA PROCESSING

DNA

Pre-mRNA

mRNA

TRANSLATION

Ribosome

Polypeptide

5 CapExon Intron

1

5

30 31

Exon Intron

104 105 146

Exon 3Poly-A tail

Poly-A tail

Introns cut out andexons spliced together

Codingsegment

5 Cap1 146

3 UTR3 UTR

Pre-mRNA

mRNA


• Is carried out by spliceosomes in some cases

Figure 17.11

RNA transcript (pre-mRNA)

Exon 1 Intron Exon 2

Other proteinsProtein

snRNA

snRNPs

Spliceosome

Spliceosomecomponents

Cut-outintron

mRNA

Exon 1 Exon 2

5

5

5

1

2

3

Animation

RibozymesAre catalytic RNA molecules that function as enzymes and can splice RNA


• Proteins often have a modular architecture

– Consisting of discrete structural and functional regions called domains

• In many cases

– Different exons code for the different domains in a protein

Figure 17.12

GeneDNA

Exon 1 Intron Exon 2 Intron Exon 3

Transcription

RNA processing

Translation

Domain 3

Domain 1

Domain 2

Polypeptide


• A cell translates an mRNA message into protein

– With the help of transfer RNA (tRNA)

Figure 17.13

TRANSCRIPTION

TRANSLATION

DNA

mRNARibosome

Polypeptide

Polypeptide

Aminoacids

tRNA withamino acidattachedRibosome

tRNA

Anticodon

mRNA

Trp

Phe Gly

A G C

A A A

CC

G

U G G U U U G G C

Codons5 3


• Molecules of tRNA are not all identical

– Each carries a specific amino acid on one end

– Each has an anticodon on the other end

(b) Three-dimensional structureSymbol used in this book

Amino acidattachment site

Hydrogen bonds

AnticodonAnticodon

A AG

53

3 5

(c)


The Structure and Function of Transfer RNA

ACC

• A tRNA molecule

– Consists of a single RNA strand that is only about 80 nucleotides long

Figure 17.14a

Two-dimensional structure. The four base-paired regions and three loops are characteristic of all tRNAs, as is the base sequence of the amino acid attachment site at the 3 end. The anticodon triplet is unique to each tRNA type. (The asterisks mark bases that have been chemically modified, a characteristic of tRNA.)

(a)

3

CCACGCUUAA

GACACCU*

GC

* *G U G U *CU

* G AGGU**A

*A

A GUC

AGACC*

C G A GA G G

G*

*GA

CUC*AUUUAGGCG5

Amino acidattachment site

Hydrogenbonds

Anticodon

A


• A specific enzyme called an aminoacyl-tRNA synthetase

– Joins each amino acid to the correct tRNA

Figure 17.15

Amino acid

ATP

Adenosine

Pyrophosphate

Adenosine

Adenosine

Phosphates

tRNA

P P P

P

P Pi

Pi

Pi

P

AMP

Aminoacyl tRNA(an “activatedamino acid”)

Aminoacyl-tRNAsynthetase (enzyme)

Active site binds theamino acid and ATP. 1

ATP loses two P groupsand joins amino acid as AMP.2

3 AppropriatetRNA covalentlyBonds to aminoAcid, displacingAMP.

Activated amino acidis released by the enzyme.4


Ribosomes

• Ribosomes

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


• The ribosomal subunits

– Are constructed of proteins and RNA molecules named ribosomal RNA or rRNA

Figure 17.16a

TRANSCRIPTION

TRANSLATION

DNA

mRNA

Ribosome

Polypeptide Exit tunnelGrowingpolypeptide

tRNAmolecules

EP A

Largesubunit

Smallsubunit

mRNA

Computer model of functioning ribosome. This is a model of a bacterial ribosome, showing its overall shape. The eukaryotic ribosome is roughly similar. A ribosomal subunit is an aggregate of ribosomal RNA molecules and proteins.

(a)

53


• The ribosome has three binding sites for tRNA

– The P site

– The A site

– The E site

Figure 17.16b

E P A

P site (Peptidyl-tRNAbinding site)

E site (Exit site)

mRNAbinding site

A site (Aminoacyl-tRNA binding site)

Largesubunit

Smallsubunit

Schematic model showing binding sites. A ribosome has an mRNA binding site and three tRNA binding sites, known as the A, P, and E sites. This schematic ribosome will appear in later diagrams.

(b)


Figure 17.16c

Amino end Growing polypeptide

Next amino acidto be added topolypeptide chain

tRNA

mRNA

Codons

3

5

Schematic model with mRNA and tRNA. A tRNA fits into a binding site when its anticodon base-pairs with an mRNA codon. The P site holds the tRNA attached to the growing polypeptide. The A site holds the tRNA carrying the next amino acid to be added to the polypeptide chain. Discharged tRNA leaves via the E site.

(c)


Building a Polypeptide

• We can divide translation into three stages

– Initiation

– Elongation

– Termination


Ribosome Association and Initiation 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

Largeribosomalsubunit

The arrival of a large ribosomal subunit completes the initiation complex. Proteins called initiationfactors (not shown) are required to bring all the translation components together. GTP provides the energy for the assembly. The initiator tRNA is in the P site; the A site is available to the tRNA bearing the next amino acid.

2

Initiator tRNA

mRNA

mRNA binding site Smallribosomalsubunit

Translation initiation complex

P site

GDPGTP

Start codon

A small ribosomal subunit binds to a molecule of mRNA. In a prokaryotic cell, the mRNA binding site on this subunit recognizes a specific nucleotide sequence on the mRNA just upstream of the start codon. An initiator tRNA, with the anticodon UAC, base-pairs with the start codon, AUG. This tRNA carries the amino acid methionine (Met).

1

MetMet

U A CA U G

E A

3

5

53

35 35

Figure 17.17


Elongation of the Polypeptide Chain

• In the elongation stage of translation

– Amino acids are added one by one to the preceding amino acid

Figure 17.18

Amino endof polypeptide

mRNA

Ribosome ready fornext aminoacyl tRNA

E

P A

E

P A

E

P A

E

P A

GDPGTP

GTP

GDP

2

2

site site5

3

TRANSCRIPTION

TRANSLATION

DNA

mRNARibosome

Polypeptide

Codon recognition. The anticodon of an incoming aminoacyl tRNA base-pairs with the complementary mRNA codon in the A site. Hydrolysisof GTP increases the accuracy andefficiency of this step.

1

Peptide bond formation. An rRNA molecule of the large subunit catalyzes the formation of a peptide bond between the new amino acid in the A site and the carboxyl end of the growing polypeptide in the P site. This step attaches the polypeptide to the tRNA in the A site.

2

Translocation. The ribosome translocates the tRNA in the A site to the P site. The empty tRNA in the P site is moved to the E site, where it is released. The mRNA moves along with its bound tRNAs,bringing the next codon to be translated into the A site.

3


Termination of Translation

• The final stage of translation is termination

– When the ribosome reaches a stop codon in the mRNA

Figure 17.19

Release factor

Freepolypeptide

Stop codon(UAG, UAA, or UGA)

5

3 3

5

35

When a ribosome reaches a stop codon on mRNA, the A site of the ribosome accepts a protein called a release factor instead of tRNA.

1 The release factor hydrolyzes the bond between the tRNA in the P site and the last amino acid of the polypeptide chain. The polypeptide is thus freed from the ribosome.

2 3 The two ribosomal subunits and the other components of the assembly dissociate.

Protein Synthesis Animation


Polyribosomes

• A number of ribosomes can translate a single mRNA molecule simultaneously

– Forming a polyribosome

Figure 17.20a, b

Growingpolypeptides

Completedpolypeptide

Incomingribosomalsubunits

Start of mRNA(5 end)

End of mRNA(3 end)

Polyribosome

An mRNA molecule is generally translated simultaneously by several ribosomes in clusters called polyribosomes.

(a)

Ribosomes

mRNA

This micrograph shows a large polyribosome in a prokaryotic cell (TEM).

0.1 µm(b)


Protein Folding and Post-Translational Modifications

• After translation

– Proteins may be modified in ways that affect their three-dimensional shape


Targeting Polypeptides to Specific Locations

• Two populations of ribosomes are evident in cells

– Free and bound

• Free ribosomes in the cytosol

– Initiate the synthesis of all proteins


• Proteins destined for the endomembrane system or for secretion

– Must be transported into the ER

– Have signal peptides to which a signal-recognition particle (SRP) binds, enabling the translation ribosome to bind to the ER


Figure 17.21

Ribosome

mRNASignalpeptide

Signal-recognitionparticle(SRP) SRP

receptorprotein

Translocationcomplex

CYTOSOL

Signalpeptideremoved

ERmembrane

Protein

ERLUMEN

• The signal mechanism for targeting proteins to the ER

Polypeptidesynthesis beginson a freeribosome inthe cytosol.

1 An SRP binds to the signal peptide, halting synthesismomentarily.

2 The SRP binds to areceptor protein in the ERmembrane. This receptoris part of a protein complex(a translocation complex)that has a membrane poreand a signal-cleaving enzyme.

3 The SRP leaves, andthe polypeptide resumesgrowing, meanwhiletranslocating across themembrane. (The signalpeptide stays attachedto the membrane.)

4 The signal-cleaving enzymecuts off thesignal peptide.

5 The rest ofthe completedpolypeptide leaves the ribosome andfolds into its finalconformation.

6


• RNA plays multiple roles in the cell: a review

• RNA

– Can hydrogen-bond to other nucleic acid molecules

– Can assume a specific three-dimensional shape

– Has functional groups that allow it to act as a catalyst


• Types of RNA in a Eukaryotic Cell

Table 17.1


• Comparing gene expression in prokaryotes and eukaryotes reveals key differences

• Prokaryotic cells lack a nuclear envelope

– Allowing translation to begin while transcription is still in progress

Figure 17.22

DNA

Polyribosome

mRNA

Direction oftranscription

0.25 mRNApolymerase

Polyribosome

Ribosome

DNA

mRNA (5 end)

RNA polymerase

Polypeptide(amino end)


• In a eukaryotic cell

– The nuclear envelope separates transcription from translation

– Extensive RNA processing occurs in the nucleus


What is a gene? revisiting the question

• A gene

– Is a region of DNA whose final product is either a polypeptide or an RNA molecule


• A summary of transcription and translation in a eukaryotic cell

Figure 17.26

TRANSCRIPTION RNA is transcribedfrom a DNA template.

DNA

RNApolymerase

RNAtranscript

RNA PROCESSING

In eukaryotes, theRNA transcript (pre-mRNA) is spliced andmodified to producemRNA, which movesfrom the nucleus to thecytoplasm.

Exon

Poly-A

RNA transcript(pre-mRNA)

Intron

NUCLEUSCap

FORMATION OFINITIATION COMPLEX

After leaving thenucleus, mRNA attachesto the ribosome.

CYTOPLASM

mRNA

Poly-A

Growingpolypeptide

Ribosomalsubunits

Cap

Aminoacyl-tRNAsynthetase

AminoacidtRNA

AMINO ACID ACTIVATION

Each amino acidattaches to its proper tRNAwith the help of a specificenzyme and ATP.

Activatedamino acid

TRANSLATION

A succession of tRNAsadd their amino acids tothe polypeptide chainas the mRNA is movedthrough the ribosomeone codon at a time.(When completed, thepolypeptide is releasedfrom the ribosome.)

Anticodon

A CC

A A AUG GUU UA U G

UACE A

Ribosome

1

Poly-A

5

5

3

Codon

2

3 4

5


• Point mutations can affect protein structure and function

• Mutations

– Are changes in the genetic material of a cell

• Point mutations

– Are changes in just one base pair of a gene


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

– Leads to the production of an abnormal protein

Figure 17.23

In the DNA, themutant templatestrand has an A where the wild-type template has a T.

The mutant mRNA has a U instead of an A in one codon.

The mutant (sickle-cell) hemoglobin has a valine (Val) instead of a glutamic acid (Glu).

Mutant hemoglobin DNAWild-type hemoglobin DNA

mRNA mRNA

Normal hemoglobin Sickle-cell hemoglobin

Glu Val

C T T C A T

G A A G U A

3 5 3 5

5 35 3


Types of Point Mutations

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

– Base-pair substitutions

– Base-pair insertions or deletions (indels)


Substitutions

• A base-pair substitution

– Is the replacement of one nucleotide and its partner with another pair of nucleotides

– Can cause missense or nonsense

Figure 17.24

Wild type

A U G A A G U U U G G C U A AmRNA 5Protein Met Lys Phe Gly Stop

Carboxyl endAmino end

3

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

Met Lys Phe Gly

Base-pair substitutionNo effect on amino acid sequence

U instead of C

Stop

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

Met Lys Phe Ser Stop

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

Met Stop

Missense A instead of G

NonsenseU instead of A


Insertions and Deletions

• Insertions and deletions

– Are additions or losses of nucleotide pairs in a gene

– May produce frameshift mutations

Figure 17.25

mRNAProtein

Wild type

A U G A A G U U U G G C U A A5

Met Lys Phe Gly

Amino end Carboxyl end

Stop

Base-pair insertion or deletionFrameshift causing immediate nonsense

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

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

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

Met Stop

U

Met Lys Leu Ala

Met Phe GlyStop

MissingA A G

Missing

Extra U

Frameshift causing extensive missense

Insertion or deletion of 3 nucleotides:no frameshift but extra or missing amino acid

3


Mutagens

• Spontaneous mutations

– Can occur during DNA replication, recombination, or repair

• Mutagens

– Are physical or chemical agents that can cause mutations

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