Chapter 19 Nucleic Acids Nucleic acids represent the fourth major class of biomolecules (proteins, carbohydrates, fats)Nucleic acids represent the fourth.

Chapter 19 Nucleic AcidsChapter 19 Nucleic Acids

•Nucleic acidsNucleic acids represent the fourth major represent the fourth major class of biomolecules (proteins, class of biomolecules (proteins, carbohydrates, fats)carbohydrates, fats)

Like other Macromolecules- contain multiple similar monomeric units covalently joined to produce large polymers

Ch 19 Nucleic AcidsCh 20 DNA ReplicationCh 21 Transcription and RNA ProcessingCh 22 Protein Synthesis

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Chapter 19 Nucleic AcidsChapter 19 Nucleic Acids

•Nucleic acidsNucleic acids represent the fourth major represent the fourth major class of biomolecules (proteins, class of biomolecules (proteins, carbohydrates, fats)carbohydrates, fats)

•GenomeGenome - the - the genetic informationgenetic information of an of an organismorganism

1889: Isolated acidic molecule from nuclei (nucleic acid)1889: Isolated acidic molecule from nuclei (nucleic acid)1944: DNA is the mol that carries genetic information1944: DNA is the mol that carries genetic information

Oswald AveryOswald Avery1953: Watson/Crick determine structure of DNA 1953: Watson/Crick determine structure of DNA

Like other Macromolecules- contain multiple similar monomeric units covalently joined to produce large polymers

1953: James Watson and Francis Crick determine structure of 1953: James Watson and Francis Crick determine structure of DNA DNA

Feb. 28Feb. 28thth 1953: Eagle pub in Cambridge 1953: Eagle pub in Cambridge

““we have found the secret of life” we have found the secret of life”

Information specifying protein Information specifying protein structurestructure

• InformationInformation flowflow::

• DNADNA RNA RNAPROTEINPROTEIN

•TranscriptionTranscription - copying of the DNA - copying of the DNA sequence information into RNA sequence information into RNA

•TranslationTranslation - Information in RNA - Information in RNA molecules is translated during molecules is translated during polypeptide chain synthesispolypeptide chain synthesis

Reverse transcriptaseReverse transcriptase(retro-viruses)(retro-viruses)

F. Crick 1958: F. Crick 1958: Central dogmaCentral dogma

•Nucleic acids are Nucleic acids are polynucleotidespolynucleotides

•Nucleotides have Nucleotides have threethree components: components:

(1)(1) A five-carbon sugarA five-carbon sugar(2)(2) A weakly basic nitrogen A weakly basic nitrogen

basebase(3)(3) PhosphatePhosphate

Nucleotides Are the Building Blocks of Nucleic AcidsNucleotides Are the Building Blocks of Nucleic Acids

Unsaturated (double bonds)Planar and absorb UV

Nucleotides have Nucleotides have threethree components: components:

five-carbon sugarfive-carbon sugar

weakly basic nitrogen baseweakly basic nitrogen base

PhosphatePhosphate

Nucleotides Are the Building Blocks of Nucleic AcidsNucleotides Are the Building Blocks of Nucleic Acids

What type of bond?

Nucleic acids are Nucleic acids are polynucleotidespolynucleotides

Nucleotides have Nucleotides have threethree components: components: A five-carbon sugarA five-carbon sugarA weakly basic nitrogen A weakly basic nitrogen basebasePhosphatePhosphate

Nucleotides Are the Building Blocks of Nucleic AcidsNucleotides Are the Building Blocks of Nucleic Acids

Tautomeric forms in equilibrium

Amino and Lactam (keto) forms more stableand predominate

keto enol

Fig Fig 19.619.6

•HydrogeHydrogen bond n bond sites in sites in nucleic nucleic acidsacids

X

•HydrogeHydrogen bond n bond sites in sites in nucleic nucleic acidsacids

NucleosidesNucleosides

RNARNA

NucleosidesNucleosides

RNARNA

DNADNA

• RibonucleosidesRibonucleosides contain three contain three

hydroxyl groups hydroxyl groups

(2’, 3’ and 5’)(2’, 3’ and 5’)

• DeoxyribonucleosidesDeoxyribonucleosides can be can be phosphorylated at the phosphorylated at the

3’ and 5’ positions3’ and 5’ positions

NucleotidesNucleotides

A A nucleotidenucleotide is assumed to be is assumed to be 5’-phosphate5’-phosphate unless specified otherwise unless specified otherwise

AMP=pA ATP=pppA

phosphate esters of nucleophosphate esters of nucleosidessides

Potential sites of phosphate: Potential sites of phosphate:

Purine vrs Pyrimidine Thymine Cytosine Guanine

Uracil Adenine

Purine vrs Pyrimidine Thymine Cytosine Guanine

Uracil Adenine

Nucleoside vrs Nucleotide

Macromolecules

Nucleoside vrs Nucleotide

Tues Quiz:

Know the difference between nucleoside/nucleotide, purine/pyrimidine

Be able to identify and name the base structures (adenine etc)

Name the nucleoside (adenosine etc)

Anti form predominatesAnti form predominates

Nucleotides Nucleotides joined by 3’-5’ joined by 3’-5’ phosphodiestphosphodiester linkageser linkages

The Free Energy of ATPThe Free Energy of ATP

Phosphoanhydride vrs Phosphoester linkage

Structure of the Structure of the tetranucleotide tetranucleotide pdApdGpdTpdCpdApdGpdTpdC

Nucleotides Nucleotides joined by 3’-5’ joined by 3’-5’ phosphodiester phosphodiester linkageslinkages

Primary structurePrimary structureExtended conformationExtended conformationLong and thinLong and thinDirectionality 5’-3’Directionality 5’-3’

Backbone: phosphate andBackbone: phosphate and3’,4’ and 5’ carbon and 3’ oxygen3’,4’ and 5’ carbon and 3’ oxygen

Erwin Chargaff: Erwin Chargaff: Chargaff rules:Chargaff rules: A and T are present in equal amounts in DNA A and T are present in equal amounts in DNA

Ratio of purine/pyrimidine always 1:1Ratio of purine/pyrimidine always 1:1

DNA is double stranded and A pairs with T (and C with G)DNA is double stranded and A pairs with T (and C with G)

Same with G and CSame with G and CA=TA=T

DNA Is Double-StrandedDNA Is Double-Stranded

G=CG=C

Watson and Crick used all the data---- double helix DNA structureWatson and Crick used all the data---- double helix DNA structure

Two strands run in opposite Two strands run in opposite directionsdirections

Bases in opposite strands Bases in opposite strands pair by pair by complementarycomplementary hydrogenhydrogen bondingbonding

Adenine (A) - Thymine (T)Adenine (A) - Thymine (T)

Guanine (G) - Cytosine (C) Guanine (G) - Cytosine (C)

Two Antiparallel Strands Two Antiparallel Strands Form a Double HelixForm a Double Helix

Complementary:Complementary: can serve as templateFor other strand

Equal distance between backbone

(Purine/pyrimidine 1:1)

• ComplementComplementary base ary base pairing and pairing and stacking in stacking in DNADNA

Stacking of basesStacking of basesStabilizes dsDNAStabilizes dsDNA

Cooperative Cooperative non-covalent non-covalent Within hydrophobicWithin hydrophobicinteriorinterior

Helix allowseffective stacking

Three dimensional structure of Three dimensional structure of DNADNA

• A double helix has two grooves A double helix has two grooves of unequal width: of unequal width: major groovemajor groove and and minor grooveminor groove

• Within each groove base pairs Within each groove base pairs are exposed and are accessible are exposed and are accessible to interactions with other to interactions with other moleculesmolecules

• DNA-binding proteins can use DNA-binding proteins can use these interactions to “read” a these interactions to “read” a specific sequencespecific sequence

B-DNAB-DNA is a is a rightright--handedhanded helixhelix, diam. = 2.37nm, diam. = 2.37nm

• Rise (distance between stacked bases) Rise (distance between stacked bases) =0.33nm=0.33nm

• Pitch (distance to complete one turn) = 3.40 Pitch (distance to complete one turn) = 3.40 nmnm

• 10.4 base pairs per turn10.4 base pairs per turn

Structure of helix allows access to info

Two alternative structures to B-DNA:Two alternative structures to B-DNA:A-DNA A-DNA (forms when DNA is dehydrated)(forms when DNA is dehydrated)Z-DNAZ-DNA (when certain sequences are present) (when certain sequences are present)

A-DNA is more tightly wound than B-DNA, and has grooves of A-DNA is more tightly wound than B-DNA, and has grooves of similar widthsimilar width

Z-DNA has no grooves and a left-handed helixZ-DNA has no grooves and a left-handed helix

Both A-DNA and Z-DNA exist Both A-DNA and Z-DNA exist in vivoin vivo in short regions of DNA in short regions of DNA

AA BB ZZ

Conformations of Double-Stranded DNAConformations of Double-Stranded DNA

G/C rich regions dG residue: base is in Syn conformationG/C rich regions dG residue: base is in Syn conformation

Race to determine the structure of Race to determine the structure of DNA DNA

Watson and Crick model

1953

DATA:

Chargaff rules ; A=T and G=C

Card board cut out puzzle

Proper tautomeric forms of bases

What data did they collect on their own ?????

1944 realized DNA carried genetic info

1947 Crick knew no biology, little organic chemistry or crystallography1951 met Watson1953 determined structure of DNA1954 finished PhD on X-ray diffraction of proteins1962 Nobel prize

Evidence for helical nature

Race to determine the structure of Race to determine the structure of DNA DNA

“Photo 51” Rosalind Franklin

Watson and Crick model

1953

1953

Linus Pauling----wrong !!

1953 paper incorrect triple helical model

1951 same triple helical model thrown out by W/C

Rosalind tore it apart…it ignored her data

1951 solved alpha helix

Diff sizes of bases—had to be on outside Did not have good x ray data—Wilkins turned him down

How to pack neg charge in center? 10x more water in molecule than the model would allow

Did not visit Franklin

Two-fold symmetry (not triple)Cross-like reflections of helix

Rosalind Franklin Dies 1958 (ovarian cancer)Nobel prize 1962

Linus Pauling----wrong !!