Nucleic acids.pptx

Nucleic acids -Nucleotides, nitrogenous bases, purines, pyrimidines, sugars, sugar pucker, nucleoside, functions of nucleotides, polynucleotide, Chargaff’s rules.

1. Nucleic acids Nucleotides, nitrogenous bases, purines, pyrimidines, sugars, sugar pucker, nucleoside, functions of nucleotides, polynucleotide, Chargaff’s rules.

2. Nucleic acids Was first discovered by Friedrich Miescher from the nuclei of the pus cells ( leukocytes) FROM THE DISCARDED SURGICAL BANDAGES AND CALLED IT NUCLEIN nuclein was later shown to be a mixture of a basic protein and a phosphorus- containing organic acid, now called nucleic acid There are 2 types of nucleic acids (polynucleotides) – ribonucleic acid(RNA) and deoxyribonucleic acid (DNA)

3. Nucleotides The monomeric units of nucleic acids are called nucleotides Nucleic acids therefore are also called polynucleotides Nucleotides are phosphate esters of nucleosides and made up of 3 components- A base that has nitrogen atom (nitrogenous base) A 5 carbon sugar A ion of phosphoric acid

4. Nitrogenous bases Are heterocyclic, planar and relatively water insoluble aromatic molecules. There are 2 general types of nitrogenous bases in both RNA and DNA, pyrimidines and purines Purine Pyrimidine

5. Purines and pyrimidines Purines- 2 different nitrogenous bases with a purine ring (composed of carbon and nitrogen) are found in DNA. The 2 common purine bases found in DNA and RNA are adenine (6-aminopurine) and guanine (6-oxy-2-aminopurine) Adenine has an amino group (-NH2) on the C6 position of the ring (carbon at position 6 of the ring ). Guanine has an amino group at C2 position and a carbonyl group at the C6 position

6. Purines and pyrimidines Pyrimidines- 2 major pyrimidine bases found in DNA are thymine (5-methyl-2,4-dioxypyrimidine) and cytosine (2-oxy-4-aminopyrimidine) and in RNA they are uracil (2,4-dioxypyrimidine) and cytosine. Thymine contains a methyl group at the C5 position with carbonyl groups at the C4 and C2 positions. Cytosine contains a hydrogen atom at the C5 position and an amino group at C4. uracil is similar to thymine but lacks the methyl group at the C5 position. Uracil is not usually found in DNA. It is the component of RNA

7. Purine and pyrimidine

8. Sugars Naturally occurring nucleic acids have 2 types of pentose sugars- ribose and deoxyribose sugars Ribose sugar is found in RNA. It is a 5 carbon monosaccharide with a hydroxyl group(-OH) on each carbon Deoxyribose sugar is found in DNA. It is 5 carbon monosaccharide, lacking one oxygen atom at 2` position The hydroxyl group (-OH) at 2` position of ribose sugar is replaced by a hydrogen (-H) The carbon atoms of the Ribose and Deoxyribose present in nucleoside or nucleotides are designated with a prime (`) mark to distinguish them from the backbone numbering in the nitrogenous base. Unprimed numbers refer to the atoms of the nitrogenous base

9. Sugars

10. Sugar pucker Pentose sugar is non-planar. This non planarity is termed as puckering. Pentose ring can be puckered in 2 basic conformations- envelope and twisted. In the envelope form- the 4 carbons of pentose sugar are nearly coplanar and the 5 th is away from the plane In twisted form- 3 atoms are coplanar and the other 2 lie away on opposite sides of this plane. Twisting the C2` and C3` carbons relative to the other atoms results in twisted forms of the sugar ring Sugar pucker can be endo or exo. C2` /C3` endo pucker means that C2`/C3` are on the same side as the base and C4`-C5` bond. Exo pucker describes shift in the opposite direction. Purines show a preference for the C2`- endo pucker conformational type whereas pyrimidines favor C3` -endo. In RNA we find predominantly the C3` - endo conformation

11. Sugar pucker

12. Nucleoside Sugar and nitrogenous base join to form nucleoside The bond between the sugar and the base is called N- glycosidic bond The nitrogenous base lies above the plane of the sugar when the structure is written in the standard orientation. That is the configuration of the N- glycosidic linkage is β The base is free to rotate around the glycosidic bond. Due to rotation of the glycosidic bond, two different conformations are possible. The 2 standard conformations of the base around the glycosidic bond are syn and anti. Pyrimidines tend to adopt the anti conformation almost exclusively,bacause of steric interference between O2 and C5` in the syn conformation, whereas purines are able to assume both forms

13. Nucleosides

14. Nucleosides

15. Nucleotides The nucleotides are phosphoric acid esters of nucleosides, with phosphate at position C-5`. A nucleotide can therefore be called a nucleoside-5`-phosphate The nucleotide can have one, two or three phosphate groups at the C-5` position and are called nucleoside monophosphates, di phosphates and tri phosphates

16. Nucleotides

17. Functions of nucleotides Are primarily responsible for the formation of polynucleotides (nucleic acids( of the cell- RNA and DNA. Polynucleotides are informational macromolecules. They store, transmit and translate genetic information. However, they also are required for numerous other important functions within the cell. These functions are- Formation of energy currency like ATP, GDP Act as a precursor for several important coenzymes such as NAD+, NADP+, FAD and coenzyme A Serving as a precursor for secondary messengers like cyclic AMP (cAMP), cGMP ATP is a chemical link between catabolism and anabolism . It is the energy currency of living cells. It acts as a donor of high energy phosphate. ATP consists of adenosine moiety to which 3 phosphoryl groups (-PO3 2-) are sequentially linked via phosphoester bond followed by 2 phosphoanhydride bonds, referred to as a high energy bond. The active form of ATP is usually a complex of ATP with Mg2+/ Mn2+

18. Structure of ATP

19. Naming nucleosides and nucleotides Purines Pyrimidines Adenine(A) Guanine (G) Cytosine (C) Uracil(U) /thymine (T) Nucleoside RNA DNA Adenosine deoxyadenosine Guanosine deoxy guanosine Cytidine deoxycytidine Uridine deoxyuridine Nucleotides in RNA DNA adenylate deoxyadenylate guanylate deoxyguanylate cytidylate deoxycytidylate uridylate deoxyuridylate Nucleoside monophosphate AMP GMP CMP UMP/ TMP Nucleoside diphosphate ADP GDP CDP UDP /TDP Nucleoside triphosphate ATP GTP CTP UTP/TTP

20. Polynucleotides Are polymers of nucleotides which are formed by the condensation of nucleotides The condensation reaction occurs between the alcohol of a 5`- phosphate of one nucleotide and the 3`- hydroxyl of the second, with the elimination of H2O The linkage between 2 nucleotides is known as phosphodiester bond. Each nucleotide that has been incorporated into the polynucleotide is known as a nucleotide residue. The phosphates of polynucleotides are acidic, so at physiologically pH , polynucleotides are polyanions All nucleotides in the polynucleotide chain have the same relative orientation. The formation of phosphodiester bonds in DNA and RNA exhibits directionally. The primary structure of DNA and RNA (linear arrangements of the nucleotides) proceeds in the 5` 3` direction. The common representation of the primary structure of DNA /RNA molecules is to write the nucleotide sequences from left to right synonymous with the 5` 3` direction The order in which nucleotides occur in the polynucleotide describes the primary structure. By convention the sequence of nucleotide residues in the nucleic acid is written, left to right, from the 5` end to 3` end. The interchain/ intrachain base-pairing of complementary nucleotides gives the secondary structure of a nucleic acid. The 3D arrangement of nucleic acid- i.e. the arrangement of the molecule in space refers to tertiary structure of a nucleic acid

21. Polynucleotides

22. Chargaff’s rules Erwin Chargaff proposed 2 rules which is termed as Chargaff’s rules These rules played an important role in the discovery of the double helix structure of DNA RULE 1-in any double stranded DNA the number of guanine units equals the number of cytosine units and the number of adenine units equals the number of thymine units. RULE 2 – the composition of DNA varies from one species to another. Hence, in dsDNA The molar ration of A and T equals to 1. similarly the molar ration of G to C equals to 1 The sum of purines(A and G) equals that of the pyrimidines (C and T) The percentage of C+G does not necessarily equal the percentage of A+T