The Structure and The Structure and Function of Function of

MacromoleculesMacromoleculesChapter 5Chapter 5

2 – Nucleic Acids2 – Nucleic Acids

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Macromolecules: Macromolecules: The Molecules of LifeThe Molecules of Life

CarbohydratesCarbohydrates Nucleic AcidsNucleic Acids ProteinsProteins LipidsLipids

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The Structure of Nucleic The Structure of Nucleic Acid MonomersAcid Monomers

Nucleotide -- nitrogenous base, a Nucleotide -- nitrogenous base, a pentose sugar, and a phosphate pentose sugar, and a phosphate groupgroup

NucleoNucleoside -- side -- portion of a nucleotide portion of a nucleotide without the phosphate group without the phosphate group

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5

Nucleotide MonomersNucleotide MonomersThere are two families of There are two families of

nitrogenous bases: nitrogenous bases: Pyrimidines have a single six-Pyrimidines have a single six-

membered ringmembered ring Purines have a six-membered ring Purines have a six-membered ring

fused to a five-membered ringfused to a five-membered ring

5 end

3 end

Nucleoside

Nitrogenousbase

Phosphategroup

Nucleotide

Polynucleotide, ornucleic acid

Pentosesugar

Nitrogenous bases

Pyrimidines

Purines

Pentose sugars

CytosineC

Thymine (in DNA)T

Uracil (in RNA)U

AdenineA

GuanineG

Deoxyribose (in DNA)

Nucleoside components

Ribose (in RNA)

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Purines vs PyrimidinesPurines vs Pyrimidines

King CUT lives in a Pyramid!King CUT lives in a Pyramid! CUT = Cytosine, Uracil, Thymine CUT = Cytosine, Uracil, Thymine Cytosine, Uracil, Thymine are Cytosine, Uracil, Thymine are

PyrimidinesPyrimidines

Pyrimidines are CUT from PurinesPyrimidines are CUT from Purines Pyrimidines are single-ring Pyrimidines are single-ring

compounds, Purines are double ring compounds, Purines are double ring compoundscompounds

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Non-polymer NucleotidesNon-polymer Nucleotidesnotnot large molecules or large molecules or

polymerspolymers

Intracellular messengersIntracellular messengers Energy carriersEnergy carriers Enzyme assistantsEnzyme assistants

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Other NucleotidesOther NucleotidesNucleotides as intracellular messengersNucleotides as intracellular messengers

Cyclic nucleotides (e.g. cyclic AMP) carry Cyclic nucleotides (e.g. cyclic AMP) carry chemical signals between moleculechemical signals between molecule

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Other NucleotidesOther Nucleotides Nucleotides as energy carriersNucleotides as energy carriers

Adenosine triphosphate (ATP)Adenosine triphosphate (ATP) carries carries energy stored in bonds between energy stored in bonds between phosphate groupsphosphate groups

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NAD+: Nicotinamide Adenine Dinucleotide

Vitamin B3

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NADP+: Nicotinamide Adenine Dinucleotide Phosphate

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FAD: Flavin Adenine Dinucleotide

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Other NucleotidesOther Nucleotides

Nucleotides as enzyme assistantsNucleotides as enzyme assistants Coenzymes help enzymes promote and Coenzymes help enzymes promote and

guide chemical reactionsguide chemical reactions

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Nucleotide PolymersNucleotide Polymers

Nucleotide monomers – build Nucleotide monomers – build polynucleotidepolynucleotide

Covalent bonds Covalent bonds ––OH group on the 3´ carbon of one nucleotide OH group on the 3´ carbon of one nucleotide phosphate on the 5´ carbon on the nextphosphate on the 5´ carbon on the next

Backbone of sugar-phosphate units Backbone of sugar-phosphate units nitrogenous bases as appendages nitrogenous bases as appendages

LE 5-26aLE 5-26a5 end

3 end

Nucleoside

Nitrogenousbase

Phosphategroup

Nucleotide

Polynucleotide, ornucleic acid

Pentosesugar

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Nucleotide PolymersNucleotide Polymers Two types:Two types:

Deoxyribonucleic acid (DNA)Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA)Ribonucleic acid (RNA)

DNA antiparallelDNA antiparallel Backbones in opposite 5´ to 3´ directionsBackbones in opposite 5´ to 3´ directions

DNA makes more DNADNA makes more DNA DNA directs synthesis of messenger RNA DNA directs synthesis of messenger RNA

(mRNA) (mRNA) mRNA controls protein synthesismRNA controls protein synthesis Occurs in ribosomesOccurs in ribosomes

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DNA vs RNADNA vs RNA DNA is double-stranded; RNA singleDNA is double-stranded; RNA single In DNA, the sugar is deoxyribose; in RNA riboseIn DNA, the sugar is deoxyribose; in RNA ribose

Pyrimidine in DNA is Thymine; RNA uracilPyrimidine in DNA is Thymine; RNA uracil DNA directs hereditary information; RNA DNA directs hereditary information; RNA

directs protein synthesisdirects protein synthesis DNA is DNA; RNA comes in 3 formsDNA is DNA; RNA comes in 3 forms

messenger RNA (mRNA)– protein structure from DNA to messenger RNA (mRNA)– protein structure from DNA to ribosomeribosome

ribosomal RNA (rRNA) – makes up ribosomesribosomal RNA (rRNA) – makes up ribosomes transfer RNA (tRNA) – carries amino acids to the transfer RNA (tRNA) – carries amino acids to the

ribosome/mRNAribosome/mRNA

Types of RNATypes of RNA

DNA is DNA; RNA comes in 3 formsDNA is DNA; RNA comes in 3 forms messenger RNA (mRNA)– protein structure messenger RNA (mRNA)– protein structure

from DNA to ribosomefrom DNA to ribosome ribosomal RNA (rRNA) – makes up ribosomesribosomal RNA (rRNA) – makes up ribosomes transfer RNA (tRNA) – carries amino acids to transfer RNA (tRNA) – carries amino acids to

the ribosome/mRNAthe ribosome/mRNA

… …. . not exactly!not exactly!http://en.wikipedia.org/wiki/List_of_RNAs

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LE 16-5LE 16-5

Most celebrated Most celebrated molecule of our molecule of our timetime

Hereditary Hereditary informationinformation

Directs the Directs the development of development of biochemical, biochemical, anatomical, anatomical, physiological, and physiological, and (to some extent) (to some extent) behavioral traitsbehavioral traits

Sugar–phosphatebackbone

5 end

Nitrogenousbases

Thymine (T)

Adenine (A)

Cytosine (C)

DNA nucleotidePhosphate

3 endGuanine (G)

Sugar (deoxyribose)

DNADNA

© 2009 W.W. Norton & Company, Inc. DISCOVER BIOLOGY 4/e

Slight differences Slight differences between closely related between closely related individualsindividuals

Distantly related Distantly related individuals – greater individuals – greater differencesdifferences

Variation and DiversityVariation and Diversity

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The Search for Genetic The Search for Genetic MaterialMaterial It needed to:It needed to:

Contain informationContain information Be easy to copyBe easy to copy Be variable, to account for diversityBe variable, to account for diversity

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DNA or Protein?DNA or Protein? Nucleic AcidsNucleic Acids

First isolated 1869 -- Friedrich MiescherFirst isolated 1869 -- Friedrich Miescher

ProteinsProteins Recognized in 18Recognized in 18thth C. C. First described -- Gerardus Johannes MulderFirst described -- Gerardus Johannes Mulder Named -- Named -- Jöns Jacob Berzelius in 1838.Jöns Jacob Berzelius in 1838.

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DNA or Protein?DNA or Protein? Thomas Hunt Morgan – 1911Thomas Hunt Morgan – 1911

Chromosomes carried genesChromosomes carried genes Composed of DNA and proteinComposed of DNA and protein

Which is the genetic material?Which is the genetic material? Protein is large, complex, and stores infoProtein is large, complex, and stores info DNA seemed too small and unlikelyDNA seemed too small and unlikely

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Griffith Experiment -- Griffith Experiment -- 19281928

Transformation of one strain by another

Two strains of bacteria R—harmless S—deadly

Heat‑killed S is also harmless

Heat‑killed S makes R deadly

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Avery, MacLeod, & Avery, MacLeod, & McCartyMcCarty

19441944Used the same assay system

Isolated compounds from Strain S Added these to Strain R

Only DNA transformed Strain R

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Additional EvidenceAdditional Evidence

1947 -- Erwin Chargaff: DNA composition varies from one species to the next

Makes DNA more credible

By 1950s -- DNA composition known but not structure

LE 16-3LE 16-3

Bacterial cell

Phagehead

Tail

Tail fiber

DNA

100

nm

Hershey and Chase -- 1952

Hershey and Chase -- Hershey and Chase -- 19521952

DNA, not protein, is genetic materialDNA, not protein, is genetic material

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LE 16-6LE 16-6

Franklin’s X-ray diffractionphotograph of DNA

Rosalind Franklin

Watson & CrickWatson & Crick Determined the 3D structure Determined the 3D structure

of DNA of DNA Structure revealed its functionStructure revealed its function

Franklin’s X-ray Franklin’s X-ray crystallographic studies crystallographic studies Double helixDouble helix Ladder twisted into a spiral coilLadder twisted into a spiral coil Uniform diameterUniform diameter

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LE 16-UN298LE 16-UN298

Purine + purine: too wide

Pyrimidine + pyrimidine: too narrow

Purine + pyrimidine: widthconsistent with X-ray data

Base-Pairing Rules Base-Pairing Rules Strands held together by hydrogen Strands held together by hydrogen

bondsbonds Strict base-pairing rules followedStrict base-pairing rules followed

Purine to PyrimidinePurine to Pyrimidine A binds to TA binds to T G binds to CG binds to C

Makes copying sequence possibleMakes copying sequence possible

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LE 5-27LE 5-27

Sugar-phosphatebackbone

3 end5 end

Base pair (joined byhydrogen bonding)

Old strands

Nucleotideabout to beadded to anew strand

5 end

New strands

3 end

5 end3 end

5 end

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DNA Structure Explains DNA Structure Explains FunctionFunction

Easily copiedEasily copied Each strand is a template for the otherEach strand is a template for the other

DNA sequence is informationDNA sequence is information Information contained in the order of the Information contained in the order of the

four basesfour bases Millions of bases in lengthMillions of bases in length

Accounts for diversityAccounts for diversity Alleles have different DNA sequencesAlleles have different DNA sequences

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ReplicatReplication ion

ModelsModels Meselson & Meselson & Stahl (1958)Stahl (1958) Labeled Labeled

strand -- strand -- heavy isotope heavy isotope of nitrogenof nitrogen

Labeled free Labeled free nucleotides -- nucleotides -- lighter isotope lighter isotope of nitrogenof nitrogen

Conservative model. The two parental strands reassociate after acting as templates for new strands, thus restoring the parental double helix.

Semiconservative model. The two strands of the parental moleculeseparate, and each functions as a template for synthesis of a new, comple-mentary strand.

Dispersive model. Each strand of both daughter molecules contains a mixture of old and newly synthesized DNA.

Parent cellFirstreplication

Secondreplication

LE 16-11LE 16-11Bacteriacultured in mediumcontaining15N

DNA samplecentrifugedafter 20 min(after firstreplication)

DNA samplecentrifugedafter 40 min(after secondreplication)

Bacteriatransferred tomediumcontaining14N

Lessdense

Moredense

Conservativemodel

First replication

Semiconservativemodel

Second replication

Dispersivemodel

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DNA Replication: DNA Replication: A Closer A Closer LookLook

Quick and accurateQuick and accurate More than a dozen enzymes and More than a dozen enzymes and

other proteins participateother proteins participate

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ReplicationReplication

Origins of ReplicationOrigins of Replication Eukaryotic chromosome -- hundreds Eukaryotic chromosome -- hundreds

to thousandsto thousands Replication proceeds in Replication proceeds in bothboth

directionsdirections Replication fork – ends of each Replication fork – ends of each

replication bubblereplication bubble

LE 16-12LE 16-12

In eukaryotes, DNA replication begins at may sitesalong the giant DNA molecule of each chromosome.

Two daughter DNA molecules

Parental (template) strand

Daughter (new) strand0.25 µm

Replication fork

Origin of replication

Bubble

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

DNA PolymeraseDNA Polymerase Catalyze elongation at a replication forkCatalyze elongation at a replication fork

Many enzymes and proteins are involvedMany enzymes and proteins are involved Initiate replicationInitiate replication Unwind the DNAUnwind the DNA Stabilize the open strandsStabilize the open strands Connect bases -- nucleoside triphosphateConnect bases -- nucleoside triphosphate

Process takes about 8 hours in humansProcess takes about 8 hours in humans

DNA ReplicationDNA Replication

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LE 16-13LE 16-13

New strand

5 end

Phosphate Base

Sugar

Template strand

3 end 5 end 3 end

5 end

3 end

5 end

3 end

Nucleosidetriphosphate

DNA polymerase

Pyrophosphate

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Antiparallel ElongationAntiparallel Elongation The antiparallel structure of the The antiparallel structure of the

double helix (two strands oriented in double helix (two strands oriented in opposite directions) affects replicationopposite directions) affects replication

DNA polymerases add nucleotides DNA polymerases add nucleotides onlyonly to the free 3 to the free 3end of a growing end of a growing strandstrand DNA elongates DNA elongates

onlyonly in the 5 in the 5toto33directiondirection

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The DNA Replication The DNA Replication Machine Machine

Complex -- Complex -- probablyprobably stationarystationary

DNA DNA polymerasepolymerase ““reels in” reels in”

parental parental DNA DNA

““extrude” extrude” daughter daughter DNADNA