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© 2010 Pearson Education, Inc.

DNA: STRUCTURE AND REPLICATION• DNA:

– Was known to be a chemical in cells by the end of the nineteenth century

– Has the capacity to store genetic information

– Can be copied and passed from generation to generation


DNA and RNA Structure

• DNA and RNA are nucleic acids.

– They consist of chemical units called nucleotides.

– The nucleotides are joined by a sugar-phosphate backbone.

Animation: Hershey-Chase Experiment

Animation: DNA and RNA Structure

Sugar-phosphatebackbone

Phosphate group

Nitrogenous base

DNA nucleotide

Nucleotide Thymine (T)

Sugar

Polynucleotide

DNAdouble helix

Sugar(deoxyribose)

Phosphategroup

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

Figure 10.1

Sugar-phosphatebackbone

Phosphate group

Nitrogenous base

DNA nucleotide

Nucleotide Thymine (T)

Sugar

Polynucleotide

Sugar(deoxyribose)

Phosphategroup


Figure 10.1a

DNA nucleotide

Thymine (T)

Sugar(deoxyribose)

Phosphategroup


Figure 10.1b


• The four nucleotides found in DNA differ in their nitrogenous bases. These bases are:

– Thymine (T)

– Cytosine (C)

– Adenine (A)

– Guanine (G)

• RNA has uracil (U) in place of thymine.


Watson and Crick’s Discovery of the Double Helix

• James Watson and Francis Crick determined that DNA is a double helix.

James Watson (left) and Francis CrickFigure 10.3a


• Watson and Crick used X-ray crystallography data to reveal the basic shape of DNA.

– Rosalind Franklin collected the X-ray crystallography data.

X-ray image of DNA

Rosalind Franklin

Figure 10.3b


• The model of DNA is like a rope ladder twisted into a spiral.

– The ropes at the sides represent the sugar-phosphate backbones.

– Each wooden rung represents a pair of bases connected by hydrogen bonds.

TwistFigure 10.4


• DNA bases pair in a complementary fashion:

– Adenine (A) pairs with thymine (T)

– Cytosine (C) pairs with guanine (G)

Animation: DNA Double Helix

Blast Animation: Hydrogen Bonds in DNA

Blast Animation: Structure of DNA Double Helix

(c) Computermodel

(b) Atomic model(a) Ribbon model

Hydrogen bond

Figure 10.5


DNA Replication

• When a cell reproduces, a complete copy of the DNA must pass from one generation to the next.

• Watson and Crick’s model for DNA suggested that DNA replicates by a template mechanism.

Animation: DNA Replication Review

Animation: DNA Replication Overview


• DNA can be damaged by ultraviolet light.

• DNA polymerases:

– Are enzymes

– Make the covalent bonds between the nucleotides of a new DNA strand

– Are involved in repairing damaged DNA


• DNA replication in eukaryotes:

– Begins at specific sites on a double helix

– Proceeds in both directions

Animation: Origins of Replication

Animation: Leading Strand

Animation: Lagging Strand

Origin ofreplication



Parental strands

Parental strand

Daughter strand

Two daughter DNA molecules

Bubble

Figure 10.7

THE FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN

• DNA functions as the inherited directions for a cell or organism.

• How are these directions carried out?


How an Organism’s Genotype Determines Its Phenotype

• An organism’s genotype is its genetic makeup, the sequence of nucleotide bases in DNA.

• The phenotype is the organism’s physical traits, which arise from the actions of a wide variety of proteins.



• DNA specifies the synthesis of proteins in two stages:

– Transcription, the transfer of genetic information from DNA into an RNA molecule

– Translation, the transfer of information from RNA into a protein

DNA

Cytoplasm

Nucleus

Figure 10.8-1

RNA

TRANSCRIPTION

DNA

Cytoplasm

Nucleus

Figure 10.8-2

TRANSLATION

Protein

RNA

TRANSCRIPTION

DNA

Cytoplasm

Nucleus

Figure 10.8-3


From Nucleotides to Amino Acids: An Overview

• Genetic information in DNA is:

– Transcribed into RNA, then

– Translated into polypeptides


• What are the rules for translating the RNA message into a polypeptide?

• A codon is a triplet of bases, which codes for one amino acid.


The Genetic Code

• The genetic code is:

– The set of rules relating nucleotide sequence to amino acid sequence

– Shared by all organisms


• Of the 64 triplets:

– 61 code for amino acids

– 3 are stop codons, indicating the end of a polypeptide

TRANSLATION

Amino acid

RNA

TRANSCRIPTION

DNA strand

Polypeptide

Codon

Gene 1

Gene 3

Gene 2DNA molecule

Figure 10.10

TRANSLATION

Amino acid

RNA

TRANSCRIPTION

DNA strand

Polypeptide

Codon

Figure 10.10


Transcription: From DNA to RNA

• Transcription:

– Makes RNA from a DNA template

– Uses a process that resembles DNA replication

– Substitutes uracil (U) for thymine (T)

• RNA nucleotides are linked by RNA polymerase.


Initiation of Transcription

• The “start transcribing” signal is a nucleotide sequence called a promoter.

• The first phase of transcription is initiation, in which:

– RNA polymerase attaches to the promoter

– RNA synthesis begins


RNA Elongation

• During the second phase of transcription, called elongation:

– The RNA grows longer

– The RNA strand peels away from the DNA template

Blast Animation: Roles of RNA

Blast Animation: Transcription


Termination of Transcription

• During the third phase of transcription, called termination:

– RNA polymerase reaches a sequence of DNA bases called a terminator

– Polymerase detaches from the RNA

– The DNA strands rejoin


The Processing of Eukaryotic RNA

• After transcription:

– Eukaryotic cells process RNA

– Prokaryotic cells do not


• RNA processing includes:

– Adding a cap and tail

– Removing introns

– Splicing exons together to form messenger RNA (mRNA)

Animation: Transcription

(b) Transcription of a gene

RNA polymerase

Completed RNA

Growing RNATermination

Elongation

Initiation Terminator DNA

Area shown in part (a) at leftRNA

Promoter DNA

RNA polymerase

DNA of gene

Figure 10.13b


Translation: The Players

• Translation is the conversion from the nucleic acid language to the protein language.


Messenger RNA (mRNA)

• Translation requires:

– mRNA

– ATP

– Enzymes

– Ribosomes

– Transfer RNA (tRNA)

TranscriptionAddition of cap and tail

Coding sequence

mRNA

DNA

Cytoplasm

Nucleus

Exons spliced together

Introns removed Tail

CapRNAtranscriptwith capand tail

Exon Exon ExonIntronIntron

Figure 10.14


Transfer RNA (tRNA)

• Transfer RNA (tRNA):

– Acts as a molecular interpreter

– Carries amino acids

– Matches amino acids with codons in mRNA using anticodons

tRNA polynucleotide(ribbon model)

RNA polynucleotidechain

Anticodon

Hydrogen bond

Amino acid attachment site

tRNA (simplifiedrepresentation)

Figure 10.15


Ribosomes

• Ribosomes are organelles that:

– Coordinate the functions of mRNA and tRNA

– Are made of two protein subunits

– Contain ribosomal RNA (rRNA)


• A fully assembled ribosome holds tRNA and mRNA for use in translation.

Next amino acidto be added to polypeptide

Growingpolypeptide

tRNA

mRNA

tRNA binding sites

Codons

Ribosome

(b) The “players” of translation(a) A simplified diagramof a ribosome

Largesubunit

Smallsubunit

P site

mRNA binding

site

A site

Figure 10.16

tRNA binding sites

Ribosome

(a) A simplified diagramof a ribosome

Largesubunit

Smallsubunit

P site

mRNA binding

site

A site

Figure 10.16a

Next amino acidto be added to polypeptide

Growingpolypeptide

tRNA

mRNA

Codons

(b) The “players” of translationFigure 10.16b


Translation: The Process

• Translation is divided into three phases:

– Initiation

– Elongation

– Termination


Initiation

• Initiation brings together:

– mRNA

– The first amino acid, Met, with its attached tRNA

– Two subunits of the ribosome

• The mRNA molecule has a cap and tail that help it bind to the ribosome.

Blast Animation: Translation

Start of geneticmessage

Tail

End

Cap

Figure 10.17


• Initiation occurs in two steps:

– First, an mRNA molecule binds to a small ribosomal subunit, then an initiator tRNA binds to the start codon.

– Second, a large ribosomal subunit binds, creating a functional ribosome.

InitiatortRNA

mRNA

Startcodon

Met

P site

Small ribosomalsubunit

A site

Large ribosomalsubunit

Figure 10.18


Elongation

• Elongation occurs in three steps.

– Step 1, codon recognition:

– the anticodon of an incoming tRNA pairs with the mRNA codon at the A site of the ribosome.


– Step 2, peptide bond formation:

– The polypeptide leaves the tRNA in the P site and attaches to the amino acid on the tRNA in the A site

– The ribosome catalyzes the bond formation between the two amino acids


– Step 3, translocation:

– The P site tRNA leaves the ribosome

– The tRNA carrying the polypeptide moves from the A to the P site

Animation: Translation

Figure 10.19-1

mRNA

P site

Polypeptide

ELONGATION

Codon recognition

Asite

Codons

Anticodon

Amino acid

mRNA

P site

Peptide bond formation

Polypeptide

ELONGATION

Codon recognition

Asite

Codons

Anticodon

Amino acid

Figure 10.19-2

Newpeptidebond

mRNAmovement

mRNA

P site

Translocation


Polypeptide

ELONGATION

Codon recognition

Asite

Codons

Anticodon

Amino acid

Figure 10.19-3

Newpeptidebond

Stopcodon

mRNAmovement

mRNA

P site

Translocation


Polypeptide

ELONGATION

Codon recognition

Asite

Codons

Anticodon

Amino acid

Figure 10.19-4


Termination

• Elongation continues until:

– The ribosome reaches a stop codon

– The completed polypeptide is freed

– The ribosome splits into its subunits


Review: DNA RNA Protein• In a cell, genetic information flows from DNA to RNA in the

nucleus and RNA to protein in the cytoplasm.

Transcription RNA polymerase

mRNA DNA

Intron

Nucleus

Figure 10.20-1


mRNA DNA

Intron

Nucleus

mRNAIntron

TailCap

RNA processing

Figure 10.20-2


mRNA DNA

Intron

Nucleus

mRNAIntron

TailCap

RNA processing

tRNA

Amino acid

Amino acidattachment

EnzymeATP

Figure 10.20-3


mRNA DNA

Intron

Nucleus

mRNAIntron

TailCap

RNA processing

tRNA

Amino acid


EnzymeATP Initiation

of translation

Ribosomalsubunits

Figure 10.20-4


mRNA DNA

Intron

Nucleus

mRNAIntron

TailCap

RNA processing

tRNA

Amino acid



of translation

Ribosomalsubunits

Elongation

AnticodonCodon

Figure 10.20-5


mRNA DNA

Intron

Nucleus

mRNAIntron

TailCap

RNA processing

tRNA

Amino acid



of translation

Ribosomalsubunits

Elongation

AnticodonCodon

Termination

Polypeptide

Stopcodon

Figure 10.20-6


• As it is made, a polypeptide:

– Coils and folds

– Assumes a three-dimensional shape, its tertiary structure

• Several polypeptides may come together, forming a protein with quaternary structure.


• Transcription and translation are how genes control:

– The structures

– The activities of cells


Mutations

• A mutation is any change in the nucleotide sequence of DNA.

• Mutations can change the amino acids in a protein.

• Mutations can involve:

– Large regions of a chromosome

– Just a single nucleotide pair, as occurs in sickle cell anemia


Types of Mutations

• Mutations within a gene can occur as a result of:

– Base substitution, the replacement of one base by another

– Nucleotide deletion, the loss of a nucleotide

– Nucleotide insertion, the addition of a nucleotide

Normal hemoglobin DNA

mRNA

Normal hemoglobin

Mutant hemoglobin DNA

mRNA

Sickle-cell hemoglobin

Figure 10.21


• Insertions and deletions can:

– Change the reading frame of the genetic message

– Lead to disastrous effects


Mutagens

• Mutations may result from:

– Errors in DNA replication

– Physical or chemical agents called mutagens


• Although mutations are often harmful, they are the source of genetic diversity, which is necessary for evolution by natural selection.

mRNA and protein from a normal gene

(a) Base substitution

Figure 10.22a

Deleted

(b) Nucleotide deletion


Figure 10.22b


Inserted

(c) Nucleotide insertionFigure 10.22c


VIRUSES AND OTHER NONCELLULAR INFECTIOUS AGENTS

• Viruses exhibit some, but not all, characteristics of living organisms. Viruses:

– Possess genetic material in the form of nucleic acids

– Are not cellular and cannot reproduce on their own.


Bacteriophages

• Bacteriophages, or phages, are viruses that attack bacteria.

Animation: Phage T2 Reproductive Cycle

Protein coat DNA

Figure 10.24

Figure 10.24


• Phages have two reproductive cycles.

(1) In the lytic cycle:

– Many copies of the phage are made within the bacterial cell, and then

– The bacterium lyses (breaks open)


(2) In the lysogenic cycle:

– The phage DNA inserts into the bacterial chromosome and

– The bacterium reproduces normally, copying the phage at each cell division

Bacterial cell

Head

Tail

Tailfiber

DNAofvirus

Bacteriophage(200 nm tall)

Colorized TEM

Figure 10.25


Plant Viruses

• Viruses that infect plants can:

– Stunt growth

– Diminish plant yields

– Spread throughout the entire plant

Animation: Phage T4 Lytic Cycle

Animation: Phage Lambda Lysogenic and Lytic Cycles

Phage

Phage DNA

Phage injects DNA

Phageattachesto cell.

Bacterialchromosome (DNA)

Phage DNAcircularizes.

Phages assemble

OR

New phage DNA andproteins are synthesized.

LYTIC CYCLE

Cell lyses,releasingphages.

Figure 10.26-1

Phage

Phage DNA

Phage injects DNA

Phageattachesto cell.



Phages assemble

OR


LYTIC CYCLE


LYSOGENIC CYCLE

Phage DNA is inserted intothe bacterial chromosome.

Many cell divisions

Prophage

Occasionally aprophagemay leave the bacterialchromosome.

Lysogenic bacteriumreproduces normally,replicating the prophageat each cell division.

Figure 10.26-2

Phage

Phage DNA

Phage injects DNA

Phage attachesto cell.


Phage DNA circularizes.Phages assemble


LYTIC CYCLE


Figure 10.26a

Phage DNA

Phage injects DNA

Phage attachesto cell.



LYSOGENIC CYCLE

Many cell divisions

Prophage

Occasionally a prophagemay leave the bacterialchromosome.

Lysogenic bacteriumreproduces normally,replicating the prophageat each cell division.

Phage DNA is inserted into thebacterial chromosome.

Phage

Figure 10.26b

Phage lambda

E. coli

Figure 10.26c


• Viral plant diseases:

– Have no cure

– Are best prevented by producing plants that resist viral infection

Tobacco mosaic virus

RNA

Protein

Figure 10.27

Figure 10.27b

Tobacco mosaic virus

RNA

Protein

Figure 10.27a


Animal Viruses

• Viruses that infect animals are:

– Common causes of disease

– May have RNA or DNA genomes

• Some animal viruses steal a bit of host cell membrane as a protective envelope.

Protein coat

RNA

Protein spike

Membranousenvelope

Figure 10.28


• The reproductive cycle of an enveloped RNA virus can be broken into seven steps.

Animation: Simplified Viral Reproductive Cycle

Protein coat

mRNA

Protein spike

Plasma membraneof host cell

Envelope

Template

New viralgenomeNew viral proteins

Exit

VirusViral RNA (genome)

Viral RNA(genome)

Entry

Uncoating

Assembly

RNA synthesisby viral enzyme

RNA synthesis(other strand)

Protein synthesis

Figure 10.29

Protein coat

Protein spike

Plasma membraneof host cell

Envelope

Virus

Viral RNA (genome)

Viral RNA(genome)

Entry

Uncoating

RNA synthesisby viral enzyme

Figure 10.29a

mRNA Template

New viralgenome

Newviral proteins

Exit

Assembly

RNA synthesis(other strand)

Protein synthesis

Figure 10.29b


HIV, the AIDS Virus

• HIV is a retrovirus, an RNA virus that reproduces by means of a DNA molecule.

• Retroviruses use the enzyme reverse transcriptase to synthesize DNA on an RNA template.

• HIV steals a bit of host cell membrane as a protective envelope.

Envelope

Reverse

transcriptase

Surface protein

Protein

coat

RNA

(two identical

strands)

Figure 10.31


• The behavior of HIV nucleic acid in an infected cell can be broken into six steps.

Animation: HIV Reproductive Cycle

Blast Animation: AIDS Treatment Strategies

Reversetranscriptase

HIV (red dots) infecting a white blood cell

DNAstrand Chromosomal

DNA

Cytoplasm

Nucleus

Provirus

RNA

Viral RNA

DoublestrandedDNA

ViralRNAand proteins

SE

M

Figure 10.32

Reversetranscriptase

DNAstrand Chromosomal

DNA

Cytoplasm

Nucleus

Provirus

RNA

Viral RNA

DoublestrandedDNA

ViralRNAand proteins

Figure 10.32a


• AIDS (acquired immune deficiency syndrome) is:

– Caused by HIV infection and

– Treated with drugs that interfere with the reproduction of the virus

HIV (red dots) infecting a white blood cell

SE

M

Figure 10.32b

Part of a T nucleotide

Thymine(T)

AZT

Figure 10.33


Viroids and Prions

• Two classes of pathogens are smaller than viruses:

– Viroids are small circular RNA molecules that do not encode proteins

– Prions are misfolded proteins that somehow convert normal proteins to the misfolded prion version


• Prions are responsible for neurodegenerative diseases including:

– Mad cow disease

– Scrapie in sheep and goats

– Chronic wasting disease in deer and elk

– Creutzfeldt-Jakob disease in humans

Figure 10.34

Evolution Connection:Emerging Viruses

• Emerging viruses are viruses that have:

– Appeared suddenly or

– Have only recently come to the attention of science



• Avian flu:

– Infects birds

– Infected 18 people in 1997

– Since has spread to Europe and Africa infecting 300 people and killing 200 of them


• If avian flu mutates to a form that can easily spread between people, the potential for a major human outbreak is significant.

Figure 10.35


• New viruses can arise by:

– Mutation of existing viruses

– Spread to new host species

Figure 10.UN1

Figure 10.UN2

Polynucleotide

Phosphategroup

Nucleotide

Sugar

DNA

Nitrogenousbase

Nitrogenousbase

Number ofstrands

Sugar

DNA RNA

RiboseDeoxy-ribose

CGAT

CGAU

12

Figure 10.UN3

Polynucleotide

Phosphategroup

Nucleotide

Sugar

DNA

Nitrogenousbase

Figure 10.UN3a

Nitrogenous base

Number of strands

Sugar

DNA RNA

RiboseDeoxyribose

CGAT

CGAU

12

Figure 10.UN3b

New daughterstrand

ParentalDNA molecule

IdenticaldaughterDNA molecules

Figure 10.UN4

Polypeptide

TRANSLATIONTRANSCRIPTION

mRNA

DNA

Gene

Figure 10.UN5

Growingpolypeptide

mRNA

Codons

Large ribosomalsubunit

tRNA

Small ribosomalsubunit

Anticodon

Amino acid

Figure 10.UN6

Figure 10.UN7

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