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Nucleic Acid Chemistry & Structure. Andy Howard Introductory Biochemistry 2 October 2008. What we’ll discuss. Syn, anti revisited Nucleotides Oligo- and polynucleotides DNA duplexes and helicity RNA: structure & types. Syn versus anti. Mono-phosphorylated nucleosides.

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Nucleic acid chemistry structure

Nucleic AcidChemistry & Structure

Andy HowardIntroductory Biochemistry2 October 2008

Biochemistry: Nucleic Acid Chem&Struct

What we ll discuss
What we’ll discuss

  • Syn, anti revisited

  • Nucleotides

  • Oligo- and polynucleotides

  • DNA duplexes and helicity

  • RNA: structure & types

Biochemistry: Nucleic Acid Chem&Struct

Syn versus anti
Syn versus anti

Biochemistry: Nucleic Acid Chem&Struct

Mono phosphorylated nucleosides
Mono-phosphorylated nucleosides

  • We have specialized names for the 5’-phospho derivatives of the nucleosides, i.e. the nucleoside monophosphates:

  • They are nucleotides

    • Adenosine 5’-monophosphate = AMP = adenylate

    • GMP = guanylate

    • CMP = cytidylate

    • UMP = uridylate

Biochemistry: Nucleic Acid Chem&Struct

P k a s for base n s and po 4 s
pKa’s for base N’s and PO4’s

Biochemistry: Nucleic Acid Chem&Struct

Uv absorbance
UV absorbance

  • These aromatic rings absorb around 260

Biochemistry: Nucleic Acid Chem&Struct


  • Similar nomenclature

    • dAMP = deoxyadenylate

    • dGMP = deoxyguanylate

    • dCMP = deoxycytidylate

    • dTTP (= TTP) = deoxythymidylate = thymidylate

Biochemistry: Nucleic Acid Chem&Struct

Cyclic phospho diesters
Cyclic phospho-diesters

  • 3’ and 5’ hydroxyls are both involvedin -O-P-O bonds, forming a 6-membered ring (-C5’-C4’-C3’-O-P-O-)

  • cAMP and cGMP are the important ones(see previous lecture!)

Biochemistry: Nucleic Acid Chem&Struct

Di and triphosphates
Di- and triphosphates

  • Phosphoanhydride bonds link second and perhaps third phosphates to the 5’-OH on the ribose moiety

Biochemistry: Nucleic Acid Chem&Struct

These are polyprotic acids
These are polyprotic acids

  • They can dissociate 3 protons (XDP) or 4 protons (XTP) from their phosphoric acid groups

  • The ionized forms are frequently associated with divalent cations (Mg2+, Mn2+, others)

  • The -O-P-O bonds beyond the first one are actually phosphoric anhydride linkages

  • Phosphoanhydrides are acid-labile: quantitative liberation of Pi in 1N HCl for 7 minutes @100ºC

Biochemistry: Nucleic Acid Chem&Struct

Ntps carriers of chemical energy
NTPs: carriers of chemical energy

  • ATP is the energy currency

  • GTP is important in protein synthesis

  • CTP used in phospholipid synthesis

  • UTP forms activated intermediates with sugars (e.g. UDP-glucose)

  • … and, of course, they’re substrates to build up RNA and DNA

Biochemistry: Nucleic Acid Chem&Struct

Bases are information symbols
Bases are information symbols

  • Base and sugar aren’t directly involved in metabolic roles of the XTPs

  • But different XTPs do different things, so there are recognition components to the relevant enzymatic systems that notice whether X is A, U, C, or G

  • Even in polynucleotides the bases play an informational role

Biochemistry: Nucleic Acid Chem&Struct

Oligomers and polymers
Oligomers and Polymers

  • Monomers are nucleotides or deoxynucleotides

  • Linkages are phosphodiester linkages between 3’ of one ribose and 5’ of the next ribose

  • It’s logical to start from the 5’ end for synthetic reasons

Biochemistry: Nucleic Acid Chem&Struct

Typical dna dinucleotide
Typical DNA dinucleotide

  • Various notations: this is pdApdCp

  • Leave out the p’s if there’s a lot of them!

Biochemistry: Nucleic Acid Chem&Struct

Dna structure
DNA structure

  • Many years of careful experimental work enabled fabrication of double-helical model of double-stranded DNA

  • Explained [A]=[T], [C]=[G]

  • Specific H-bonds stabilize double-helical structure: see fig. 10.20

Biochemistry: Nucleic Acid Chem&Struct

What does double stranded dna really look like
What does double-stranded DNA really look like?

  • Picture on previous slide emphasizes only the H-bond interactions; it ignores the orientation of the sugars, which are actually tilted relative to the helix axis

  • Planes of the bases are almost perpendicular to the helical axes on both sides of the double helix

Biochemistry: Nucleic Acid Chem&Struct

Sizes cf fig 10 20 11 7
Sizes (cf fig. 10.20, 11.7)

  • Diameter of the double helix: 2.37nm

  • Length along one full turn:10.4 base pairs = pitch = 3.40nm

  • Distance between stacked base pairs = rise = 0.33 nm

  • Major groove is wider and shallower;minor groove is narrower and deeper

Biochemistry: Nucleic Acid Chem&Struct

What stabilizes this
What stabilizes this?

  • Variety of stabilizing interactions

    • Stacking of base pairs

    • Hydrogen bonding between base pairs

    • Hydrophobic effects (burying bases, which are less polar)

    • Charge-charge interactions:phosphates with Mg2+ and cationic proteins


Biochemistry: Nucleic Acid Chem&Struct

How close to instability is it
How close to instability is it?

  • Pretty close.

  • Heating DNA makes it melt: fig. 11.14

  • The more GC pairs, the harder it is to melt

    • Weaker stacking interactions in A-T

    • One more H-bond per GC than per AT

  • We’ll get into DNA structure a lot more later in this lecture

Biochemistry: Nucleic Acid Chem&Struct

Iclicker quiz
iClicker quiz

  • 1. What positions of a pair of aromatic rings leads to stabilizing interactions?

    • (a) Parallel to one another

    • (b) Perpendicular to one another

    • (c) At a 45º angle to one another

    • (d) Both (a) and (b)

    • (e) All three: (a), (b), and ( c)

Biochemistry: Nucleic Acid Chem&Struct

Second iclicker question
Second iClicker question

  • 2. Which has the highest molecular mass among the compounds listed?

    • (a) cytidylate

    • (b) thymidylate

    • (c) adenylate

    • (d) adenosine triphosphate

    • (e) they’re all the same MW

Biochemistry: Nucleic Acid Chem&Struct

Base composition for dna
Base composition for DNA

  • As noted, [A]=[T], [C]=[G] because of base pairing

  • [A]/[C] etc. not governed by base pairing

    • Can vary considerably (table 10.3)

    • E.coli : [A], [C] about equal

    • Mycobacterium tuberculosis: [C] > 2*[A]

    • Mammals: [C] < 0.74*[A]

Biochemistry: Nucleic Acid Chem&Struct

Molar ratios for various organisms dna table 10 3
Molar ratios for various organisms’ DNA (table 10.3)

Biochemistry: Nucleic Acid Chem&Struct

What did this mean in 1950
What did this mean in 1950?

  • [A]=[T] and [C]=[G] suggested that if the molecule involved two strands, there should be complementarity between them, i.e., if there’s an A on one strand, there will be a T on the other one

  • Unfortunately it wasn’t entirely clear that the molecule was two-stranded!

Biochemistry: Nucleic Acid Chem&Struct

The watson crick contribution
The Watson-Crick contribution

  • Interpreting the X-ray fiber diffraction photographs taken by Rosalind Franklin and Maurice Wilkins, W&C built a ball-and-stick model for a two-stranded form of DNA

  • They were able to show that their model was consistent with Franklin’s data

Biochemistry: Nucleic Acid Chem&Struct

So how is dna organized
So how is DNA organized?

  • Linear sequence is simple to describe:

  • Two strands, each very long and containing 105 - 108 bases

  • Each base has a complementary base on the other strand

  • Specific hydrogen bonding patterns define the complementarity

Biochemistry: Nucleic Acid Chem&Struct

Higher levels of organization
Higher levels of organization

  • Just as with protein tertiary structure, DNA structure has higher levels beyond the base-pairing, beginning with coiling into a double helix

  • Eukaryotes:

    • Organization of double helix into loop structures of ~200 base pairs coiled around a protein complex called the histone octamer

    • Further organization of those loops into larger structures culminating in formation of chromosomes

  • Prokaryotes: similar but simpler higher-level structures culminating in (often circular) chromosomes

Biochemistry: Nucleic Acid Chem&Struct


  • Refers to levels of organization of DNA beyond the immediate double-helix

  • We describe circular DNA as relaxed if the closed double helix could lie flat

  • It’s underwound or overwound if the ends are broken, twisted, and rejoined.

  • Supercoils restore 10.4 bp/turn relation upon rejoining

Biochemistry: Nucleic Acid Chem&Struct

Supercoiling and flat dna
Supercoiling and flat DNA

Diagram courtesy SIU Carbondale

Biochemistry: Nucleic Acid Chem&Struct

Ribonucleic acid
Ribonucleic acid

  • We’re done with DNA for the moment.

  • Let’s discuss RNA.

  • RNA is generally, but not always, single-stranded

  • The regions where localized base-pairing occurs (local double-stranded regions) often are of functional significance

Biochemistry: Nucleic Acid Chem&Struct

Rna physics chemistry
RNA physics & chemistry

  • RNA molecules vary widely in size, from a few bases in length up to 10000s of bases

  • There are several types of RNA found in cells

    Type % %turn- Size, Hbond Role

    RNA over bases stabil.? in translation

    mRNA 3 25 50-104 no protein template

    tRNA 15 21 55-94 yes aa activation

    rRNA 80 50 102-104 yes transl. catalysis

    & scaffolding

    sRNA 2 4 12-200 yes various

Biochemistry: Nucleic Acid Chem&Struct

Unusual bases in rna
Unusual bases in RNA

  • mRNA, sRNA mostly A,C,G,U

  • rRNA, tRNA have some odd ones

Biochemistry: Nucleic Acid Chem&Struct

Messenger rna
Messenger RNA

  • Contains the codons that define protein sequence

  • Each codon (3 bases) codes for 1 amino acid

  • Synthesized during transcription, like all other types of RNA

  • Relatively small % of RNA mass in the cell; but short-lived, so:

  • Higher % of RNA synthesis devoted to mRNA

Biochemistry: Nucleic Acid Chem&Struct

Prokaryotic mrna
Prokaryotic mRNA

  • One mRNA with a single promoter will contain coding information for several proteins, i.e., 1 promoter, several genes

  • Defined stop codons show the ribosome where to put in the breaks

  • Translation closely coupled to transcription, unlike eukaryotic systems, where they’re separated in space & time

Biochemistry: Nucleic Acid Chem&Struct

Eukaryotic mrna
Eukaryotic mRNA

  • One mRNA per protein

  • But the mRNA will be initially synthesized with noncoding segments (introns) interspersed between the coding segments (exons):heterogeneous nuclear RNA, hnRNA

  • snRNPs (q.v.) in nucleus splice out the introns, tying together the exons to make the mature transcript

  • Each mRNA will end with a poly(A) tail, added after transcription

Biochemistry: Nucleic Acid Chem&Struct

Ribosomes and rrna
Ribosomes and rRNA

  • Ribosome is 65% RNA, rest protein

  • Lots of intrastrand H-bonds

  • Ribosomes characterized by sedimentation coefficients

    • E.coli: 50S piece+30S piece  70S total

    • Eukaryotes 60S + 40S  80S total

  • rRNA has pseudouridine, ribothymidine, methylated bases

Biochemistry: Nucleic Acid Chem&Struct

Prokaryotic ribosomes fig 10 25a
Prokaryotic ribosomes (fig.10.25a)

Biochemistry: Nucleic Acid Chem&Struct

Eukaryotic ribosomes fig 10 25b
Eukaryotic ribosomes (fig. 10.25b)

Biochemistry: Nucleic Acid Chem&Struct

Transfer rna
Transfer RNA

  • Each tRNA carries a specific amino acid to the ribosomal protein synthesis machine

  • One full set of tRNA at each cellular site of protein synthesis (cytoplasm, mitochondrion, chloroplast)

  • These are small molecules: 55-94 bases

A/T site

tRNA model based on cryoEM complex


Biochemistry: Nucleic Acid Chem&Struct

Trna contents
tRNA contents

  • Many modified bases

  • CCA on the 3’-end is attached to the amino acid

  • Catalytic attachment of amino acid to protein is catalyzed by an adenine in one of the 50S rRNAs

Dieter Söll

Biochemistry: Nucleic Acid Chem&Struct

Small nuclear rnas
Small nuclear RNAs

  • snRNA found mostly in nucleus

  • 100-200 nucleotides

  • closely associated with proteins& with other RNA molecules

  • Mostly in ribonucleoprotein particles (snRNPs), which are involved in mRNA processing, converting full-length transcript into smaller transcript in which introns have been removed, leaving only the exons

Image courtesy Richard Lührmann, Göttingen

Biochemistry: Nucleic Acid Chem&Struct

Other small rnas
Other small RNAs

  • 21-28 nucleotides

  • Target RNA or DNA through complementary base-pairing

  • Several types, based on function:

    • Small interfering RNAs (q.v.)

    • microRNA: control developmental timing

    • Small nucleolar RNA: catalysts that (among other things) create the oddball bases

snoRNA77courtesy Wikipedia

Biochemistry: Nucleic Acid Chem&Struct

Iclicker question 3
iClicker question 3

  • Suppose you isolate an RNA molecule that consists of 1500 bases. It is probably:

  • (a) tRNA

  • (b) mRNA

  • (c) rRNA

  • (d) either mRNA or rRNA

  • (e) none of the above.

Biochemistry: Nucleic Acid Chem&Struct