Pyrimidines and Purines • In order to understand the structure and properties of DNA and RNA, we need to look at their structural components. • We begin with certain heterocyclic aromatic compounds called pyrimidines and purines.
6 6 7 5 1 5 N N 1 N 8 4 2 2 9 N H 4 N N 3 3 Pyrimidines and Purines • Pyrimidine and purine are the names of the parent compounds of two types of nitrogen-containing heterocyclic aromatic compounds. Pyrimidine Purine
H NH2 H N N N H H2N H N H N N H Pyrimidines and Purines • Amino-substituted derivatives of pyrimidine and purine have the structures expected from their names. 4-Aminopyrimidine 6-Aminopurine
H H H H N N HO H O H N N H Pyrimidines and Purines • But hydroxy-substituted pyrimidines and purines exist in keto, rather than enol, forms. enol keto
O OH H N N N H N H N H N N H N H H keto Pyrimidines and Purines • But hydroxy-substituted pyrimidines and purines exist in keto, rather than enol, forms. enol
O O CH3 HN HN O O NH NH Important Pyrimidines • Pyrimidines that occur in DNA are cytosine and thymine. Cytosine and uracil are the pyrimidines in RNA. NH2 HN O NH Uracil Thymine Cytosine
NH2 O N N HN N NH NH H2N N N Important Purines • Adenine and guanine are the principal purines of both DNA and RNA. Adenine Guanine
O O CH3 CH3 H3C N N N HN N O O N N N CH3 CH3 Caffeine Theobromine Caffeine and Theobromine • Caffeine (coffee) and theobromine (coffee and tea) are naturally occurring purines.
Nucleosides • The classical structural definition is that a nucleoside is a pyrimidine or purine N-glycoside of D-ribofuranose or 2-deoxy-D-ribofuranose. • Informal use has extended this definition to apply to purine or pyrimidine N-glycosides of almost any carbohydrate. • The purine or pyrimidine part of a nucleoside is referred to as a purine or pyrimidine base.
NH2 N N O HOCH2 O HO OH Table 26.2 • Pyrimidine nucleosides Cytidine Cytidine occurs in RNA; its 2-deoxy analog occurs in DNA.
O H3C NH O N HOCH2 O HO Table 26.2 • Pyrimidine nucleosides Thymidine Thymidine occurs in DNA.
O NH O N HOCH2 O HO OH Table 26.2 • Pyrimidine nucleosides Uridine Uridine occurs in RNA.
NH2 N N N N HOCH2 O HO OH Table 26.2 • Purine nucleosides Adenosine Adenosine occurs in RNA; its 2-deoxy analog occurs in DNA.
O N NH N NH2 N HOCH2 O HO OH Table 26.2 • Purine nucleosides Guanosine Guanosine occurs in RNA; its 2-deoxy analog occurs in DNA.
26.3Nucleotides • Nucleotides are phosphoric acid esters of nucleosides.
NH2 O N OCH2 HO N P 5' HO N N O 1' 4' 3' 2' HO OH Adenosine 5'-Monophosphate (AMP) • Adenosine 5'-monophosphate (AMP) is also called 5'-adenylic acid.
NH2 N N O O N N OCH2 HO O P P O HO HO HO OH Adenosine Diphosphate (ADP)
NH2 N N O O O N N HO OCH2 P O O P P O HO HO HO HO OH Adenosine Triphosphate (ATP) • ATP is an important molecule in several biochemical processes including: energy storage (Sections 26.4-26.5) phosphorylation
HOCH2 O O HO HO ATP + HO HO HO HO OH OH O (HO)2POCH2 ADP + ATP and Phosphorylation hexokinase This is the first step in the metabolism of glucose.
NH2 N N N N CH2 O O O OH P O HO cAMP and cGMP • Cyclic AMP and cyclic GMP are "second messengers" in many biological processes. Hormones (the "first messengers") stimulate the formation of cAMP and cGMP. Cyclic adenosine monophosphate (cAMP)
O N NH N NH2 N CH2 O O OH O P O HO cAMP and cGMP • Cyclic AMP and cyclic GMP are "second messengers" in many biological processes. Hormones (the "first messengers") stimulate the formation of cAMP and cGMP. Cyclic guanosine monophosphate (cGMP)
Bioenergetics • Bioenergetics is the thermodynamics of biological processes. • Emphasis is on free energy changes (DG). • When DG is negative, reaction is spontaneous in the direction written. • When DG is 0, reaction is at equilibrium. • When DG is positive, reaction is not spontaneous in direction written.
mA(aq) nB(aq) Standard Free Energy (DG°) • Sign and magnitude of DG depends on what the reactants and products are and their concentrations. • In order to focus on reactants and products, define a standard state. • The standard concentration is 1 M (for a reaction in homogeneous solution). • DG in the standard state is called the standard free-energy change and given the symbol DG°.
mA(aq) nB(aq) Standard Free Energy (DG°) • Exergonic: An exergonic reaction is one for which the sign of DG° is negative. • Endergonic: An exergonic reaction is one for which the sign of DG° is positive.
mA(aq) nB(aq) Standard Free Energy (DG°) • It is useful to define a special standard state for biological reactions. • This special standard state is one for which the pH = 7. • The free-energy change for a process under these conditions is symbolized as DG°'.
Hydrolysis of ATP ATP + H2O ADP + HPO42– • G°' for hydrolysis of ATP to ADP is –31 kJ/mol. • Relative to ADP + HPO42–, ATP is a "high-energy" compound. • When coupled to some other process, the conversion of ATP to ADP can provide the free energy to transform an endergonic process to an exergonic one.
–OCCH2CH2CHCO– + NH4+ +NH3 O O O O H2NCCH2CH2CHCO– + H2O +NH3 Glutamic Acid to Glutamine DG°' = +14 kJ Reaction is endergonic.
DG°' = –17 kJ O O O O H2NCCH2CH2CHCO– + HPO42– + ADP +NH3 Glutamic Acid to Glutamine –OCCH2CH2CHCO– + NH4+ + ATP +NH3 Reaction becomes exergonicwhen coupled to the hydrolysisof ATP.
O O O O O P OCCH2CH2CHCO– + ADP –O –O +NH3 Glutamic Acid to Glutamine –OCCH2CH2CHCO– + ATP +NH3 Mechanism involvesphosphorylation of glutamic acid.
H2NCCH2CH2CHCO– + HPO42– +NH3 O O O O O P OCCH2CH2CHCO– + NH3 –O –O +NH3 Glutamic Acid to Glutamine Followed by reaction of phosphorylated glutamic acid with ammonia.
Phosphodiesters • A phosphodiester linkage between two nucleotides is analogous to a peptide bond between two amino acids. • Two nucleotides joined by a phosphodiester linkage gives a dinucleotide. Three nucleotides joined by two phosphodiester linkages gives a trinucleotide, etc. (See next slide) • A polynucleotide of about 50 or fewer nucleotides is called an oligonucleotide.
free 5' end A T G free 3' end Fig. 26.1The trinucleotide ATG • phosphodiester linkages between 3' of one nucleotide and 5' of the next
26.7Nucleic Acids • Nucleic acids are polynucleotides.
Nucleic Acids • Nucleic acids first isolated in 1869 (Johann Miescher). • Oswald Avery discovered (1945) that a substance which caused a change in the genetically transmitted characteristics of a bacterium was DNA. • Scientists revised their opinion of the function of DNA and began to suspect it was the major functional component of genes.
Composition of DNA • Erwin Chargaff (Columbia Univ.) studied DNAs from various sources and analyzed the distribution of purines and pyrimidines in them. • The distribution of the bases adenine (A), guanine (G), thymine (T), and cytosine (C) varied among species. • But the total purines (A and G) and the total pyrimidines (T and C) were always equal. • Moreover: %A = %T, and %G = %C
Composition of Human DNA For example: • Adenine (A) 30.3% Thymine (T) 30.3% • Guanine (G) 19.5% Cytosine (C) 19.9% • Total purines: 49.8% Total pyrimidines: 50.1% Purine Pyrimidine
Structure of DNA • James D. Watson and Francis H. C. Crick proposed a structure for DNA in 1953. • Watson and Crick's structure was based on: •Chargaff's observations •X-ray crystallographic data of Maurice Wilkins and Rosalind Franklin •Model building
2-deoxyribose 2-deoxyribose A T Base Pairing • Watson and Crick proposed that A and T were present in equal amounts in DNA because of complementary hydrogen bonding.
Base Pairing • Watson and Crick proposed that A and T were present in equal amounts in DNA because of complementary hydrogen bonding.
2-deoxyribose 2-deoxyribose G C Base Pairing • Likewise, the amounts of G and C in DNA were equal because of complementary hydrogen bonding.
Base Pairing • Likewise, the amounts of G and C in DNA were equal because of complementary hydrogen bonding.
The DNA Duplex • Watson and Crick proposed a double-stranded structure for DNA in which a purine or pyrimidine base in one chain is hydrogen bonded to its complement in the other. • •Gives proper Chargaff ratios (A=T and G=C) • •Because each pair contains one purine and one pyrimidine, the A---T and G---C distances between strands are approximately equal. • •Complementarity between strands suggests a mechanism for copying genetic information.
Fig. 26.4 • Two antiparallel strands of DNA are paired by hydrogen bonds between purine and pyrimidine bases.