Dr Tayyaba Nucleotides and Nucleic Acids + Some Basics * Nucleic Acid Structure * Nucleic Acid Chemistry * Other Functions of Nucleotides Fig. X-ray diffraction pattern of DNA bersIntro. to Nucleotides and Nucleic Acids Nucleotides have a variety of roles in cellular metabolism. They are the energy currency in metabolic reactions, the essential chemical links in the response of cells to hormones and other stimuli, and the structural components of a variety of enzyme cofactors and metabolic intermediates. The storage and transmission of biological information are the only known functions of DNA. RNAs have a broader range of functions. Ribosomal RNAs (rRNAs) are structural and catalytic components of ribosomes. Messenger RNA (mRNAs) carry genetic information specifying the sequences of proteins. Transfer RNAs (tRNAs) are adaptor molecules that participate in translating the information in mRNA into a specific sequence of amino acids in a polypeptide. There is also a wide variety of special-function RNAs, including some called ribozymes that have enzymatic activity.Structure of Nucleotides Nucleotides contain three components: 1) a nitrogen containing base, 2) a pentose, and 3) one or more phosphates (Fig. a). In the absence of the phosphate group(s), the molecule is called a nucleoside. The nitrogenous bases are derivatives of pyrimidine and purine. The pamberwa of the ring atoms of pyrimidines and purines \s illustrated in Fig. b. Carbon numbers in the pentoses of nucleotides and nucleosides are given a Prime () designation to distinguish them from the numbered atoms of the bases. The base of a nucleotide is joined covalently {ot N-1 of pyrimidines and N-9 of purines) in an N-8-glycosyl bond ‘o the 1° carbon of the pentose, and the phosphate is esterifie commonly to the 5' carbon. Water is removed in the formation of the N-B-glycosyl bond as occurs in O-glycosidic bond formation. Purine or . pyrimidine H H Fig.a base cen naXc-K 7 N CH 1 s Phosphate -op-to—ch2 0 |] 1? 3] I) ol scr i Hc2 , SCH HCS 3 OCW 9/ y S77 Pentose N H Pyrimidine Purine Fig. bMajor Bases of Nucleic Acids Both DNA and RNA contain two major purine bases, adenine (A) and guanine (6) (Fig.). Both nucleic acids also contain the pyrimidine, cytosine (C), and a second pyrimidine that is thymine (T) in DNA and uracil (U) in RNA. Only occasionally does thymine occur in RNA or uracil in DNA. In some cases the names of the bases reflect the sources from which they originally were isolated. Guanine, for example, was first isolated from guano (bird manure) and thymine was first isolated from thymus tissue. " i SN ANN ye ey HN’ oN Lip TOT a atta ‘ 5 1 I AN AH AN, HN’ HN’ cH ! YO a AH AN A x ; aa” PyrimidinesNomenclature of Nucleosides & Nucleotides The names of the nucleosides and nucleotides containing the five common bases are listed in Table. ar\:i83:55 8 Nucleotide and Nucl ic Acid Nomenclature Base Nucleoside Nucleotide Nucleic acid Purines Adenine ‘Adenosine Adenylate RNA Deoxyadenosine Deoxyadenylate DNA Guanine Guanosine Guanylate RNA Deoxyguanosine Deoxyguanylate DNA Pyrimidines Cytosine cytidine Cytidylate RNA Deoxycytidine Deoxycytidylate DNA Thymine Thymidine or deoxythymidine ‘Thymidylate or deoxythymidylate DNA Uracil Uridine Uridylate RNA leotide” are generic terms that include both ribo- and deoxyribo- forms. Also ribonucleosides and ribonucleotides simply as nucleosides and nucleotides (e.g. riboadenosine as adenosinel, and deoxyribonucleosides and deoxyribonucleotides as deoxynucleosides and deoxynucleotides (e.g. deoxyriboadenosine as deoxyadenosine). Both forms of naming are acceptable, but the shortened names are more commonly used. Thymin san exception vibothymidine”s used to describe its unusualThe Pentoses of Nucleotides Nucleotides have two kinds of pentoses. The recurrit deoxyribonucleotide units of DNA contain 2'-deoxy-D-ribose, an the ribonucleotide units of RNA contain D-ribose. In both types of nucleotides the pentoses exist in their B-furanose (closed five- membered ring) forms. The formation of the 8-D-ribofuranose ring from the straight-chain aldehyde form of D-ribose in solution is illustrated in Fig.a. Deoxyribose undergoes a_ similar interconverion in solution, but in DNA exists solely as B-2'-deoxy- D-ribofuranose. Deoxyribofuranose and ribofuranose rings_ in nucleotides exist in four different puckered conformations (Fig. b). In all cases, four of the five ring atoms are nearly in the same plane. The fifth atom (C-2' or C-3') is on either the same (endo) or the opposite (exo) side of the plane relative to the C-5' atom. i c=0 of oe Hy oH I — Ka a H—G—0H d ‘4 fron OH OH CH,OH Aldehyde B-Furanose Fig.aDeoxyribonucleotides of DNA The structures and names of the four major deoxyribonucleotides (deo: eonacleoside . 5- _nonophosphates), Es fae All. nucleotides are s' own in their free form at pH 7.0. The deoxyribonucleotide units of DNA me usually symbe ized 7 z G, T, and C, and sometimes as dA, In their free forms, the deneyribonclecties are Rome’ abbreviated dAMP, dG cTMP, and dCMP. For each nucleotide in the figure, the more common name is followed by the complete name in parentheses. All abbreviations assume that the phosphate group is at the 5' position. The nucleoside portion of each molecule is shaded in light red. NH2 ° 9 wt CH, CL ele) Os ie t r r t Lom obo eye | -0-f oe oto am lal lan ua Nucleotide: Deoyadente _—_Deoygnnynte-—Deymyte——_Dennotee iigndcntne Getting "ietline —_Uaeroine stcoereans —gatetereaes leans gat ent ‘Symbols: A, dA, dAMP G, dG,dGmP 1, dT, dTMP C, dc, deMP Mueoset Oneyedenerne Oeerygunesin Destine = eee DeoxyribonucleotidesRibonucleotides of RNA The structures and names of the four major ribonucleotides (ribonucleoside 5'-monophosphates) of RNA. All nucleotides are shown in their free form at pH 7.0. The ribonucleotide units of RNA are usually symbolized as A, G, U, and C. In their free forms, the ribonucleotides are commonly abbreviated AMP, GMP, UMP, and CMP. For each nucleotide in the figure, the more common name is followed by the complete name in parentheses. All abbreviations assume that the phosphate group is at the 5’ position. The nucleoside portion of each molecule is shaded in light red. r v “0-f-0 “oto “04 fo é é Nucleotide: Adenylate adenosingGuanylate guanosine Uridylate (uridine Spare erecing '5'-monophosphate) 5-monophosphate) Symbols: AMP GMP vu, UMP CMP Nucleoside: ‘Adenosine Guanosine Uridine cytidine RibonucleotidesMinor Bases Both DNA and RNA also contain some minor bases (Fig.). In DNA, the most common of these are methylated forms of the major bases (Panel a). Minor bases of many types occur in tRNAs (Panel b). If the modification occurs directly on one of the ring atoms of the pyrimidine or purine base, the convention is to simply indicate the ring position of the substituent by its number, e.g., 5-methylcytidine. The convention changes when the substituent atom is exocyclic (not within the ring structure). In this case the type of atom is identified and the ring position to which it is attached is denoted with a superscript, e.g., Ne- methyladenosine. Hyc— 4 a [bse] S-Methyleytidine 9 HN ‘\ Ryn Ribose N?-Methylguanosine 9 J 5 bose ror HIN” 3' direction. A short nucleic acid such as shown in the figure is referred to as an oligonucleotide. This term is generally applied to nucleotides of 50 or fewer residues. Longer nucleic acids are referred to as polynucleotides.The Properties of Nucleotide Bases Affect the Three-Dimensional Structure of Nucleic Acids Free pyrimidines and purines are weakly basic compounds and are thus called bases. They have a variety of chemical properties that affect the structure, and ultimately the function, of nucleic acids. The purines and pyrimidines common in DNA and RNA are highly conjugated molecules, a property with important consequences for the structure, electron distribution, and light absorption of nucleic acids. Resonance among atoms in the ring gives most of the bonds partial double-bond character. One result is that pyrimidines are planar molecules; purines are very nearly planar, with a slight pucker.Tautomeric Forms of Uracil Free pyrimidine and purine bases may exist in two or more tautomeric forms depending on the pH. Uracil, for example, occurs in lactam, lactim, and double lactim forms depending on the pH (Fig.). Certain tautomeric forms predominate at neutral pH. These are the tautomers that are present in the bases in DNA and RNA. ° OH OH HN’ |— y pena *) os N oN N oes N Lactam hae Double lactim UracilNucleotide Absorption Spectra All nucleotide bases absorb UV light, and nucleic acids are characterized by a strong absorption at wavelengths near 260 nm (Fig.). Plotted in this figure is the variation in molar extinction coefficient, «, as a function of wavelength. The molar extinction coefficients at 260 nm are listed in the attached table. The spectra of corresponding ribonucleotides and deoxyribonucleotides are essentially identical. For mixtures of nucleotides, a wavelength of 260 nm is used for absorption measurements. Molar extinction coefficient at 260 nm, Molar extinction coefficient. ¢ L 230240250260 270 280 ‘Wavelength nm)a flatson and Crick Base-pairing in DNA functional groups of yrimidines and puri are ri hi ang onyl groups, and exo vel ic me groups. en involvi le amino d carb on are the’ mos my ortan Pos mo le $e! interactions etwe ene 3 com plementai Franke of nucleic + common hydr er i , ing parte enng an those son anc CMe 1 1! wich A pon Is sj all Stree) and 8 E'bonde ch EE ese tM Types ser Bast ries predominate ind foul je; strai NA. ‘automers shown in Fi a = onsible for, Nee ase pairs. Lt is this Gaccific pairing pon bases th that permits ef duplication of genetic information in DNA, as decks low.Watson-Crick Model for the Structure of Double-helical DNA (I) A model for the structure of DNA was proposed by Watson and Crick in 1953. Their model was based on a number of pieces of information that were available at the time about the composition of DNA and the x-ray diffraction i properties of DNA fibers. Most importantly, x-ray diffraction studies of DNA fibers performed by Rosalind Franklin and Maurice Wilkins (Fig. 8-12) showed that BNA molecules are helical and exhibit two periodicities ngpeating along the length of the fiber a primary repeat of 3.4 A anda secondary repeat of 34 A. In addition, Erwin Chargaff and colleagues had shown through DNA compositional analysis that the number of T residues always equals the number of A residues (A = T), and the number of G residues always equals the number of C residues (6 = C). As a result, the sum of purine residues equals the sum of pyrimidine residues (A + 6 = re T + C). Watson and Crick then set about to develop a structure that was consistent with these two sets of data (next slide).Watson-Crick Model for the Structure of Double-helical DNA (IT) In DNA, Watson and Crick proposed that two helical DNA chains are wound around the same axis to form a right- handed double helix (Fig. 8-13). They speculated that the two chains have an antiparallel orientation, and this was later proven to be true. The one hydrophilic backbones of alternating deoxyribose and phosphate groups are — Minor on the outside of the helix facing the *°"" surrounding water. The furanose ring of each deoxyribose is in the C-2' endo conformation. The purine and pyrimidine bases of both strands are 2am d inside the double helix with their hydrophobic and nearly planar ring structures very close together and erpendicular to the axis of the helix. FGohtinued on the next slide). Cc)Watson-Crick Model for the Structure of Double-helical DNA (III) tackir \t 4k Bese arom cera Fhe St toed ee eee es tain ie Sate a a ase pairs linens solution. Wes aor ne fe pee was pro} josed lal on the ia le Sega el hy hee ae g Sreated a neligr nd. JCOe grae e su ace oF the duplex TP Shou veoh sci Soy Ww. the double helix not onl as stabilize Watson,¢ Crick base ce parring 20h betwee: redid ame helix, bi also stal lized ase- sig gcking ases from interaction: rel cl sentact wit! ipaten. qtures of the heli leat Wmodel oft ucture re su yy much chemical ‘and Bren he PROT eS SidenneDouble-helical Strand comelementary The two antiparallel chains of double-helical DNA are not identical in either base sequence or composition. Instead, they are complementary to one another. Wherever adenine occurs in one chain, thymine occurs in the other. Similarly, guanine occurs opposite cytosine in the two chains (Fig.8-14).