Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings Molecular Biology Of The Gene Chapter 10

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

Molecular Biology Of The Gene

Chapter 10


Sabotage Inside Our Cells

• A saboteur

– Lies low waiting for the right moment to strike


• Viruses are biological saboteurs

– Hijacking the genetic material of host cells in order to reproduce themselves

• Viruses provided some of the earliest evidence

– That genes are made of DNA


THE STRUCTURE OF THE GENETIC MATERIAL

10.1 Experiments showed that DNA is the genetic material

• The Hershey-Chase experiment showed that certain viruses reprogram host cells

– To produce more viruses by injecting their DNA

Figure 10.1A

Head

Tail

Tail fiber

DNA

300

,00

0


• The Hershey-Chase experiment

Phage

Bacterium

Radioactiveprotein

DNA

Phage DNA

Empty protein shell Radioactivity

in liquid

PelletCentrifuge

Batch 1Radioactiveprotein

Batch 2RadioactiveDNA

RadioactiveDNA

Centrifuge

Pellet

Radioactivityin pellet

Figure 10.1B

Mix radioactively labeled phages with bacteria. The phages infect the bacterial cells.

1 Agitate in a blender to separate phages outside the bacteria from the cells and their contents.

2 Centrifuge the mixture so bacteria form a pelletat the bottom of the testtube.

3 Measure the radioactivity in the pellet and the liquid.

4


• Phage reproductive cycle

Figure 10.1C

Phage attachesto bacterial cell.

Phage injects DNA. Phage DNA directs hostcell to make more phageDNA and protein parts.New phages assemble.

Cell lyses and releases new phages.


DNA polynucleotide

A

C

T

G

T

Sugar-phosphate backbone

Phosphate group

Nitrogenous base

SugarA

C

T

G

T

Phosphategroup

O

O–

OO P CH2

H3C C

C

C

CN

C

N

H

H

O

O

C

O

O

H

C H H

H

C

H

Nitrogenous base(A, G, C, or T)

Thymine (T)

Sugar(deoxyribose)

DNA nucleotide

DNA nucleotide

10.2 DNA and RNA are polymers of nucleotides

• DNA is a nucleic acid

– Made of long chains of nucleotide monomers

Figure 10.2A


• DNA has four kinds of nitrogenous bases

– A, T, C, and G

CC

C

CC

C

O

N

C

H

H

ONH

H3C

H H

H

H

N

N

N

H

OC

H HN

H C

N

N N

N

C

CC

C

H

H

N

N

H

C

CN

C HN

CN

H C

O

H

H

Thymine (T) Cytosine (C) Adenine (A) Guanine (G)

PurinesPyrimidines

Figure 10.2B


• RNA is also a nucleic acid

– But has a slightly different sugar

– And has U instead of TNitrogenous base

(A, G, C, or U)

Phosphategroup

O

O–

OO P CH2

HC

C

C

CN

C

N

H

H

O

O

C

O

O

H

C H H

OH

C

H

Uracil (U)

Sugar(ribose)

KeyHydrogen atomCarbon atom

Nitrogen atom

Oxygen atom

Phosphorus atom

Figure 10.2C, D


10.3 DNA is a double-stranded helix

• James Watson and Francis Crick

– Worked out the three-dimensional structure of DNA, based on work by Rosalind Franklin

Figure 10.3A, B


• The structure of DNA

– Consists of two polynucleotide strands wrapped around each other in a double helix

Figure 10.3C Twist


• Hydrogen bonds between bases

– Hold the strands together

• Each base pairs with a complementary partner

– A with T, and G with C

Figure 10.3D

G C

T A

A T

G

G

C

C

A T

GC

T A

T A

A T

A T

G C

A T

O

O

OH–O

P

OO

–OPO

OO

P– O

– O OP

OO

O

OH

H2C

H2C

H2C

H2C

O

O

O

O

O

O

O

O

PO–

O–

O–

O–

OH

HO

O

O

O

P

P

P

O

O

O

O

O

O

O

O

T A

G C

C G

A T

CH2

CH2

CH2

CH2

Hydrogen bond

Basepair

Ribbon model Partial chemical structure Computer model


DNA REPLICATION

10.4 DNA replication depends on specific base pairing

• DNA replication

– Starts with the separation of DNA strands

• Then enzymes use each strand as a template

– To assemble new nucleotides into complementary strands

Figure 10.4A

A T

C G

G C

A T

T A

A T

C G

G C

A T

T A

A T

C G

G C

A T

T A

A T

C G

G C

A

T

A T

C G

AC

T

A

Parental moleculeof DNA

Both parental strands serve as templates

Two identical daughtermolecules of DNA

Nucleotides


• DNA replication is a complex process

– Due in part to the fact that some of the helical DNA molecule must untwist

Figure 10.4B

G C

A T

G C

A T

C G

AGA

CG

C

GC

G

TA

G

C

TAT

AA

TT

A

CG

CG

CG

T

AG

C

T

A

T

A

AT

T

A

TC

T


10.5 DNA replication: A closer look

• DNA replication

– Begins at specific sites on the double helix

Figure 10.5A

Origin of replication

Two daughter DNA molecules

Parental strand

Daughter strand

Bubble


• Each strand of the double helix

– Is oriented in the opposite direction

Figure 10.5B

P

P

P

P

P

P

P

P

HO

OH

A

C

G

T

T

C

G

A

2 134

5

15 4

32

5 end 3 end

3 end 5 end


• Using the enzyme DNA polymerase

– The cell synthesizes one daughter strand as a continuous piece

• The other strand is synthesized as a series of short pieces

– Which are then connected by the enzyme DNA ligase

Figure 10.5C

3

53

53

5

53

Daughter strandsynthesizedcontinuously

Daughter strandsynthesizedin pieces

Parental DNA

DNA ligase

DNA polymerasemolecule

Overall direction of replication


THE FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN

• 10.6 The DNA genotype is expressed as proteins, which provide the molecular basis for phenotypic traits

• The information constituting an organism’s genotype

– Is carried in its sequence of its DNA bases

• A particular gene, a linear sequence of many nucleotides

– Specifies a polypeptide


• The DNA of the gene is transcribed into RNA

– Which is translated into the polypeptide

Figure 10.6A

DNA

Transcription

RNA

Protein

Translation


• Studies of inherited metabolic disorders in mold

– First suggested that phenotype is expressed through proteins

Figure 10.6B


10.7 Genetic information written in codons is translated into amino acid sequences

• The “words” of the DNA “language”

– Are triplets of bases called codons

• The codons in a gene

– Specify the amino acid sequence of a polypeptide


DNA strand

Transcription

Translation

Polypeptide

RNA

Amino acid

Codon

A A A C C G G C A A A A

U U U G G C C G U U U U

Gene 1

Gene 2

Gene 3

DNA molecule

Figure 10.7


10.8 The genetic code is the Rosetta stone of life

• Nearly all organisms

– Use exactly the same genetic code

Figure 10.8A

UUC

UGUUGC

UGA Stop

Met or start

Phe

Leu

Leu

Ile

Val Ala

Thr

Pro

Ser

Asn

Lys

His

Gln

Asp

Glu

Ser

Arg

Arg

Gly

CysTyr

G

A

C

U

U C A G

Th

ird

bas

e

Second base

Fir

st b

ase

UUA

UUU

CUC

CUU

CUG

CUA

AUC

AUU

AUG

AUA

GUC

GUU

GUG

GUA

UCC

UCU

UCG

UCA

CCC

CCU

CCG

CCA

ACC

ACU

ACC

ACA

GCC

GCU

GCG

GCA

UAC

UAU

UAG Stop

UAA Stop

CAC

CAU

CAGCAA

AAC

AAU

AAG

AAA

GAC

GAU

GAG

GAA

UGG Trp

CGC

CGU

CGGCGA

AGCAGU

AGG

AGA

GGC

GGU

GGG

GGA

U

C

A

G

U

C

A

G

U

C

A

G

U

C

A

G

UUG


• An exercise in translating the genetic code

Figure 10.8B

T A C T T C A A A A T C

A T G A A G T T T T A G

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

Transcription

Translation

RNA

DNA

Met Lys PhePolypeptide

Startcondon

Stopcondon

Strand to be transcribed


10.9 Transcription produces genetic messages in the form of RNA

• A close-up view of transcription

RNApolymerase

RNA nucleotides

Direction of transcription

Template Strand of DNA

Newly made RNA

TC

AT C C A A T

T

GG

CC

AATTGGAT

G

U

C A U C C AA

U

Figure 10.9A


• In the nucleus, the DNA helix unzips

– And RNA nucleotides line up along one strand of the DNA, following the base pairing rules

• As the single-stranded messenger RNA (mRNA) peels away from the gene

– The DNA strands rejoin


• Transcription of a gene RNA polymerase

DNA of gene

PromoterDNA Terminator

DNA

Area shownIn Figure 10.9A

GrowingRNA

Completed RNARNApolymerase

Figure 10.9B

1 Initiation

2 Elongation

3 Termination


10.10 Eukaryotic RNA is processed before leaving the nucleus

• Noncoding segments called introns are spliced out

– And a cap and a tail are added to the endsExon Intron Exon Intron Exon

DNA

Cap TranscriptionAddition of cap and tail

RNAtranscript with capand tail

Introns removedTail

Exons spliced together

mRNA

Coding sequence Nucleus

Cytoplasm

Figure 10.10


10.11 Transfer RNA molecules serve as interpreters during translation

• Translation

– Takes place in the cytoplasm


• A ribosome attaches to the mRNA

– And translates its message into a specific polypeptide aided by transfer RNAs (tRNAs)

Amino acid attachment site

Hydrogen bond

RNA polynucleotide chain

AnticodonFigure 10.11A


• Each tRNA molecule

– Is a folded molecule bearing a base triplet called an anticodon on one end

• A specific amino acid

– Is attached to the other endAmino acidattachment site

AnticodonFigure 10.11B, C


10.12 Ribosomes build polypeptides

• A ribosome consists of two subunits

– Each made up of proteins and a kind of RNA called ribosomal RNA

tRNAmolecules

mRNA Small subunit

Growingpolypeptide

Largesubunit

Figure 10.12A


• The subunits of a ribosome

– Hold the tRNA and mRNA close together during translation

Largesubunit

mRNA-binding site

Smallsubunit

tRNA-binding sites

Growing polypeptide

Next amino acid to be added to polypeptide

mRNA

tRNA

Codons

Figure 10.12B, C


10.13 An initiation codon marks the start of an mRNA message

Start of genetic message

End

Figure 10.13A


• mRNA, a specific tRNA, and the ribosome subunits

– Assemble during initiation

Met Met

Initiator tRNA

1 2mRNA Small ribosomal

subunit

Startcodon

Large ribosomalsubunit

A siteU A CAU C

A U G A U G

P site

Figure 10.13B


10.14 Elongation adds amino acids to the polypeptide chain until a stop codon terminates translation

• Once initiation is complete

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


• Each addition of an amino acid

– Occurs in a three-step elongation process

Polypeptide

P site

mRNA Codons

mRNAmovement

Stopcodon

NewPeptidebond

Anticodon

Aminoacid

A site

Figure 10.14

1 Codon recognition

2 Peptide bondformation

3 Translocation


• The mRNA moves a codon at a time

– And a tRNA with a complementary anticodon pairs with each codon, adding its amino acid to the peptide chain


• Elongation continues

– Until a stop codon reaches the ribosome’s A site, terminating translation


10.15 Review: The flow of genetic information in the cell is DNARNAprotein

• The sequence of codons in DNA, via the sequence of codons

– Spells out the primary structure of a polypeptide


Polypeptide

TranscriptionDNA

mRNA

RNApolymerase

Amino acid Translation

tRNA

Enzyme

Anticodon

ATP

InitiatortRNA

Largeribosomalsubunit

Start Codon

Codons

mRNA

Stop codon

Smallribosomalsubunit

Growingpolypeptide

New peptidebond forming

mRNA

Figure 10.15

• Summary of transcription and translation

mRNA is transcribed from a DNA template.1

Each amino acidattaches to its propertRNA with the help of aspecific enzyme and ATP.

2

Initiation ofpolypeptide synthesis

The mRNA, the first tRNA,and the ribosomal subunits come together.

3

Elongation4A succession of tRNAsadd their amino acids to the polypeptide chain as the mRNA is moved through the ribosome, one codon at a time.

5

The ribosome recognizes a stop codon. The poly-peptide is terminated and released.

Termination


10.16 Mutations can change the meaning of genes

• Mutations are changes in the DNA base sequence

– Caused by errors in DNA replication or recombination, or by mutagens

C T T C A T

Normal hemoglobin

Mutant hemoglobin DNA

G A A G U A

Sickle-cell hemoglobin

Normal hemoglobin DNA

Glu Val

mRNA mRNA

Figure 10.16A


• Substituting, inserting, or deleting nucleotides alters a gene

– With varying effects on the organismNormal gene

mRNA

Base substitution

Base deletion Missing

Met Lys Phe Gly Ala

Met Lys Phe Ser Ala

Met Lys Leu Ala His

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

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

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

U

Protein

Figure 10.16B


MICROBIAL GENETICS

10.17 Viral DNA may become part of the host chromosome

• Viruses

– Can be regarded as genes packaged in protein


• When phage DNA enters a lytic cycle inside a bacterium

– It is replicated, transcribed, and translated

• The new viral DNA and protein molecules

– Then assemble into new phages, which burst from the host cell


• In the lysogenic cycle

– Phage DNA inserts into the host chromosome and is passed on to generations of daughter cells

• Much later

– It may initiate phage production


• Phage reproductive cycles

Lysogenic bacterium reproducesnormally, replicating the prophageat each cell division

Phage DNA inserts into the bacterialchromosome by recombination

New phage DNA andproteins are synthesized

Phages assemble

Cell lyses,releasing phages

Phage

Attachesto cell

Phage DNA

Phage injects DNA

Many celldivisions

Prophage

Lytic cycle Lysogenic cycle

OR

Bacterialchromosome

Phage DNAcircularizes

Figure 10.17

1

2

3

4

5 6

7


Membranousenvelope

RNA

Proteincoat

Glycoprotein spikeFigure 10.18A

CONNECTION

10.18 Many viruses cause disease in animals

• Many viruses cause disease

– When they invade animal or plant cells

• Many, such as flu viruses

– Have RNA, rather than DNA, as their genetic material


• Some animal viruses

– Steal a bit of host cell membrane as a protective envelope

– Can remain latent in the host’s body for long periods Glycoprotein spike

EnvelopeProtein coat

Viral RNA(genome)

VIRUS

Plasma membraneof host cell

Viral RNA(genome)

Template

New viralgenome

Exit

mRNA

7

Newviral proteins

Figure 10.18B

Entry1

Uncoating2

RNA synthesisby viral enzyme3

Proteinsynthesis

4 RNA synthesis(other strand)

5

Assembly6


CONNECTION

10.19 Plant viruses are serious agricultural pests

• Most plant viruses

– Have RNA genomes

– Enter their hosts via wounds in the plant’s outer layers

Protein RNA

Figure 10.19


CONNECTION

10.20 Emerging viruses threaten human health

Co

loriz

ed

TE

M 5

0,0

00

Co

loriz

ed

TE

M 3

70

,00

0

Figure 10.20A, B


10.21 The AIDS virus makes DNA on an RNA template

• HIV, the AIDS virus

– Is a retrovirus Envelope

Glycoprotein

Protein coat

RNA (two identical strands)

Reverse transcriptase

Figure 10.21A


• Inside a cell, HIV uses its RNA as a template for making DNA

– To insert into a host chromosome

Viral RNA

RNAstrand

Double-strandedDNA

Viral RNAand proteins

CYTOPLASM

NUCLEUSChromosomal DNA

Provirus DNA

RNA

Figure 10.21B

1

2

3

45

6


10.22 Bacteria can transfer DNA in three ways

• Bacteria can transfer genes from cell to cell by one of three processes

– Transformation, transduction, or conjugation

DNA enterscell

Fragment of DNAfrom anotherbacterial cell

Bacterial chromosome

(DNA)

Phage

Fragment of DNA fromanotherbacterial cell(former phagehost)

Phage

Sex pili

Mating bridge

Donor cell(“male”)

Recipient cell(“female”)

Figure 10.22A–C


• Once new DNA gets into a bacterial cell

– Part of it may then integrate into the recipient’s chromosome

Recipient cell’schromosome

Recombinantchromosome

Donated DNACrossovers Degraded DNA

Figure 10.22D


10.23 Bacterial plasmids can serve as carriers for gene transfer

• Plasmids

– Are small circular DNA molecules separate from the bacterial chromosome


• Plasmids can serve as carriers

– For the transfer of genes

Plasmids

Co

loriz

ed

TE

M 2

,00

0

Cell now male

Plasmid completes transferand circularizes

F factor starts replication and transfer

Male (donor) cell

Bacterial chromosome

F factor (plasmid)

Recombination can occur

Only part of the chromosome transfers

F factor starts replication and transfer of chromosome

Origin of F replicationBacterial chromosome

Male (donor) cellF factor (integrated)

Recipient cell

Figure 10.23A–C

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Copyright © 2005 Pearson Education, Inc. Publishing as Benjamin Cummings Molecular Biology Of The Gene Chapter 10