IMED1002 - Nucleotides

Monomer of Nucleic acids (DNA and RNA)

nucleotide

Heredity

Passing of traits from parents to offspring

Nucleotides

nitrogenous base + pentose monosaccharide + phosphate

- are negatively charged

Phosphate

- simple molecule - phosphorus and oxygen atoms only

- at physiological pH (7-7.5), the hydroxyl groups are completely dissociated... H+ readily dissociate

- Hence phosphate has a net charge of -2

Pentose Monosaccharides

- Pentose sugars have 5 carbon atoms. In nucleotides there is either ribose or deoxyribose

- when free in solution, ribose exists as a straight chain aldehyde in equilibrium with a ring furan form

Deoxy/ribose in a nucleotide form

- it exists as a ring form

- C atoms are numbered 1 to 5. They are also designated 1', 2' etc. to distinguish them from C in the nitrogenous bases

Nitrogenous Bases

- Bases are heterocyclic aromatic amines and fundamental to coding information of nucleic acids

- Two categories of bases (Purines and Pyrimidines):

PURINES: Purine, Adenine (A), Guanine (G)

PYRIMIDINES: Pyrimidine, Cytosine (C), Uracil (U, RNA only), Thymine (T, DNA only)

Properties of Nitrogenous Bases

- hydrophobic and relatively insoluble in water at cellular pH

- Double bonded: significant because it results in bases being highly cojugated molecules. The electrons are no longer localised over only 2 atoms but spread over several - 'delocalisation'

Resonance

many atoms of the ring gives most bonds a partial double bond character

Difference between Purine and Pyrimidine

purine: 2 rings

pyrimidine: 1 ring

significance of double bonds in bases

- results in bases being highly conjugated molecules.

- The e- are no longer localised over only 2 atoms but spread over several = "delocalisation"

Result of Resonance

- resonance results in stabilisation

- double bonds of bases make pyrimidine bases planar and purines nearly planar

- electron sharing in benzene ring makes it very stable and explains why it does not undergo addition reactions like other alkenes

- ethylene undergoes addition

- benzene undergoes substitution

Absorption Spectra of Nucleotides

- due to resonance, all bases absorb UV light

- strong absorption at around 260nm wavelength

Bond between ribose and base

glycosidic bond = nucleoside, add phosphate to get nucleotide

Linkages in nucleosides and nucleotides

Condensation reaction is involved. Base + sugar + phosphate = nucleotide (great diagram in slide 21 of Lecture 7)

Nucleoside

nitrogenous base + sugar

Nucleoside and Nucleotide naming scheme (not super important to follow)

- for nucleoside: for purines, add "osine" to root. e.g if base is Adenine, nucleoside is Adenosine. For pyrimidines add "idine" to root. e.g Cytosine becomes Cytidine

- for nucleotide: for purines, add "ylate" to root. e.g if base is Adenine, nucleotide is Adenylate. For pyrimidines, add "idylate" to root. e.g Cytosine becomes Cytidylate

Deoxyribonucleotides

- deoxyribonucleoside monophosphates

- can add one or two additional phosphate groups to get diphosphate and triphosphate e.g dAMP, dADP, dATP

Ribonucleotides

- Ribonucleoside monophosphates

- can add one or two additional phosphate groups

Methylation

- bases may be modified by a process called methylation

- e.g methylation of cytosine

Minor Bases

- methylated forms of major bases

- e.g in tRNA

Unique cyclic structure of cells

- cells can have nucleotides where the P group is not on the 5'C and that form cyclic structures (great diagram on page 26)

Other roles in Nucleotides

- not only information storage - making RNA and proteins

- metabolic - ATP is the cellular energy "currency"

- cofactors in biochemical reactions - NAD+

- cell signalling - cAMP