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
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
Nucleosides The classical structural definition is that a nucleoside is a pyrimidine or purine N-glycoside of D-ribofuranose or 2-deoxy-D-ribofuranose. The purine or pyrimidine part of a nucleoside is referred to as a purine or pyrimidine base.
O H3C NH O N HOCH2 O HO Pyrimidine nucleosides Thymidine Thymidine occurs in DNA
NH2 N N O HOCH2 O HO OH Pyrimidine nucleosides Cytidine Cytidine occurs in RNA; its 2-deoxy analog occurs in DNA
O NH O N HOCH2 O HO OH Pyrimidine nucleosides Uridine Uridine occurs in RNA
NH2 N N N N HOCH2 O HO OH Purine nucleosides Adenosine Adenosine occurs in RNA; its 2-deoxy analog occurs in DNA
O N NH N NH2 N HOCH2 O HO OH Purine nucleosides Guanosine Guanosine occurs in RNA; its 2-deoxy analog occurs in DNA
Nucleosides in DNA Base Sugar Nucleoside Adenine (A) Deoxyribose Adenosine Guanine (G) DeoxyriboseGuanosine Cytosine (C) DeoxyriboseCytidine Thymine (T) DeoxyriboseThymidine
Nucleosides in RNA Base Sugar Nucleoside Adenine (A) ribose Adenosine Guanine (G) riboseGuanosine Cytosine (C) riboseCytidine Uracil (U) riboseUridine
Functions of Nucleosides In addition to their roles as the subunits of nucleic acids, nucleotides perform some other functions. As carriers of chemical energy: ATP, GTP, CTP. As components of enzyme factors: NAD+, FAD. As chemical messengers: cyclic AMP or cAMP, cGMP.
Nucleotides Nucleotides are phosphoric acid esters of nucleosides. Nucleic acids consist of nucleotides that have a sugar, nitrogen base, and phosphate nucleoside Base PO4 Sugar
Nucleoside [structure of deoxyadenosine] Nucleotide
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 phosphorylation
Chemistry of Nucleotides Formation of ADP from AMP and ATP from ADP by the addition of a phosphate group forming a phosphoric anhydride linkage. Note that the reaction is a dehydration synthesis.
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.
O NH2 N NH N N N NH2 N CH2 O N N CH2 O O O OH O O OH P P O O HO 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 guanosinemonophosphate (cGMP) Cyclic adenosine monophosphate (cAMP)
Nucleotides in DNA and RNA DNA dAMPDeoxyadenosinemonophosphate dGMPDeoxyguanosinemonophosphate dCMPDeoxycytidinemonophosphate dTMPDeoxythymidinemonophosphate RNA AMP adenosine monophosphate GMP guanosinemonophosphate CMP cytidinemonophosphate UMP uridinemonophosphate
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. A polynucleotide of about 50 or fewer nucleotides is called an oligonucleotide.
free 5' end A T G free 3' end The trinucleotide ATG phosphodiester linkages between 3' of one nucleotide and 5' of the next
Nucleic Acid Nucleic acids are polynucleotides • Nucleic acids are linear polymers of nucleotides linked 3' to 5' by phosphodiester bonds. • Two types: • Ribonucleic acid (RNA) and • Deoxyribonucleic acid (DNA)
Nucleic Acid • The nature, properties and function of the two nucleic acids depend on the exact order of the purine and pyrimidine bases in the molecule. • This sequence of specific bases is termed the primary structure. • The purine and pyrimidine bases of DNA carry genetic information whereas the sugar and phosphate groups perform a structural role. • Interestingly enough, the human body contains about 0.5 g of DNA !
Structure of Nucleic Acid Polymers of four nucleotides Linked by alternating sugar-phosphate bonds RNA: ribose and A, G, C, U DNA: deoxyribose and A,G,C,T nucleotide nucleotidenucleotidenucleotide base base base base sugar sugar P sugar P sugar P P
Structure of Nucleic Acid 3,5-phosphodiester bond 3 5
Structure of Nucleic Acid RNA: 3',5'-phosphodiester bridges link nucleotides together to form polynucleotide chains. The 5'-ends of the chains are at the top; the 3'-ends are at the bottom.
Structure of Nucleic Acid DNA: 3’,5’-phosphodiester bridges link nucleotides together to form polynucleotide chains. The 5’-ends of the chains are at the top; the 3’-ends are at the bottom.
Nucleic Acid Structure… Shorthand notation for DNA. The bases are at the top. The vertical line is the sugar numbered top to bottom. The 5' end is to the left and the 3' end to the right. a and b are cleavage sites for nucleases. Linkage is a phosphodiester bond, each P has a (-) charge.
Double Helix of DNA DNA contains two strands of nucleotides H bonds hold the two strands in a double-helix structure A helix structure is like a spiral stair case Bases are always paired as A–T and G-C Thus the bases along one strand complement the bases along the other