Biomolecules: nucleotides
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1 Biomolecules: nucleotides
2 Nucleotides and nucleic acids Nucleic acids are linear hetero-polymers adapted to maintain and transmit the genetic information Depending on their sugar moiety they can be classified into: ribonucleic acids (RNA) and deoxy-ribonucleic acids (DNA) The building blocks of nucleic acids are complex molecules called nucleotides base Pi dribose
3 Nucleotides Each nucleotide is composed by three different chemical entities: 1 to 3 molecules of phosphoric acid 1 cyclic (deoxy)ribose molecule 1 nitrogenous aromatic base (aka nucleobase), chemically derived from (but not synthesized from) either purine or pyrimidine Purine Pyrimidine
4 The structure and nomenclature of the nucleobases: Only in RNA Only in DNA
5 Nucleotides The reactions leading to the formation of nucleotides belong to condensations: One of the 3 acid groups of phosphoric acid reacts with the alcoholic group in position C5' of (deoxy)ribose phosphoester bond (sometimes also in C3') The alcoholic group in beta-c1' of (deoxy)ribose reacts with the NH group either in position 9 (Purines) or 1 (Pyrimidines) N-glycosidic bond In the absence of a phosphate group, the ribose-base compound is called nucleoside At physiological ph, the phosphate groups are ionised, this explains the acidic behaviour of nucleotides (mono-, di-, triphosphate) and their preference to form salts with Mg2+
6 Nucleotides In order to avoid confusion in the numbering: all the C and N belonging to the base are numbered following the purine/pyrimidine convention All the C belonging to the sugar are added a prime (ex. C5', C2', etc) The only difference between ribonucleotides and deoxyribonucleotides lays in the substitution of the alcoholic group on C2' with a Hydrogen This will improve the stability towards hydrolysis of about 100-folds of DNA with respect to RNA
7 Nucleotides In order to avoid confusion in the numbering: all the C and N belonging to the base are numbered following the purine/pyrimidine convention All the C belonging to the sugar are added a prime (ex. C5', C2', etc) The only difference between ribonucleotides and deoxyribonucleotides lays in the substitution of the alcoholic group on C2' with a Hydrogen This will improve the stability towards hydrolysis of about 100-folds of DNA with respect to RNA
8 Hydrolysis of RNA
9 Functions of nucleotides Building blocks of RNA and DNA Transporters of energy (ATP, GTP) Transporters of electrons (FAD, NAD, NADP) Transporters of acyl groups (CoenzymeA) Signalling molecules (camp, c-di-gmp)
10 Functions of nucleotides Building blocks of RNA and DNA Transporters of energy (ATP, GTP) Transporters of electrons (FAD, NAD, NADP) Transporters of acyl groups (CoenzymeA) ATP It transfers energy in all living organisms The energy is stored in the phospho-anhydride bond and released when this group os transferred to another molecule (ΔG= kj/mol) Its intracellular concentration is quite low (5mM) but its daily production is about the same as the animal's weight
11 FAD (flavin adenine dinucleotide) In this co-enzyme of redox proteins one ADP is bound to riboflavin (Vitamin B2) Many organisms can synthesize riboflavin, men are not capable The redox reaction involves the acceptance/release of two electrons in two steps by the dimethyl-isoalloxazine ring Oxidised FAD has a bright yellow colour Reduced FADH2 has a pale yellow colour
12 FAD (flavin adenine dinucleotide) In this co-enzyme of redox proteins one ADP is bound to riboflavin (Vitamin B2) Many organisms can synthesize riboflavin, men are not capable The redox reaction involves the acceptance/release of two electrons in two steps by the dimethyl-isoalloxazine ring Oxidised FAD has a bright yellow colour Reduced FADH2 has a pale yellow colour
13 NAD NADP (nicotinamide adenine dinucleotide - phosphate) In this molecule ADP is bound to another ribose which is N-glycosilated to nicotinamide (a derivative of niacin, vitamine B3) Niacin can either be synthesized from Trp or taken from the diet, its deficiency causes Pellagra The redox centre is indeed on the nicotinamide ring, where a quaternary N acts as an electrons trap Both NAD+ and NADP+ transfer 2 electrons (one ion H-)
14 NAD NADP (nicotinamide adenine dinucleotide - phosphate) In this molecule ADP is bound to another ribose which is N-glycosilated to nicotinamide (a derivative of niacin, vitamine B3) Niacin can either be synthesized from Trp or taken from the diet, its deficiency causes Pellagra The redox centre is indeed on the nicotinamide ring, where a quaternary N acts as an electrons trap Both NAD+ and NADP+ transfer 2 electrons (one ion H-)
15 CoA (coenzyme A) This transporter has a central role in the metabolism since it transfers acyl groups (2 C atoms) to acceptors It is made by adeosine-3'-phosphate-5'-diphosphate linked to pantothenic acid and beta-mercaptoethylamine (b-mea) This thiol derivative is the carrier of acyl groups The thiol-ester bond has a stored energy greater than that of ATP (ΔG= 31.5 kj/mol) It is involved in the metabolism of FA Acetyl group b-mea ADP-3'P Pantothenic acid
16 Synthetic analogues of nucleotides Heterocycles synthesized to interfere with DNA replication used in chemotherapy Examples: 5-F-uracil used in anti-cancer therapy Acyclovir used against herpes viruses AZT used against HIV
17 Nucleic acids: DNA and RNA The genetic information must be stably stored in small volumes for long times The same information must be available to be read and used: Transcription is the process in which DNA is copied into RNA Translation is the process in which mrna is converted into proteins The information in DNA and RNA must be accessible to proteins and/or other nucleic acids The offspring must have the same set of instructions of the parents: Replication of DNA in a semiconservative way
18 Nucleic acids structure Nucleic acids are polymers of nucleotides in which the phosphate group bridges the 5'OH of the n position to the 3'OH of the (n-1) position phosphodiester bond The scaffold is the linear sugar-phosphate polyanion The sequence of the bases is the information free heteropolymer The heteropolymer is directional: 5' terminus: first residue with a 5'-phosphate group not involved in any other bonds 3' terminus: last residue carrying a free 3'OH group The sequence is always written 5' 3' since this is the way it is polymerized
19 Base pairing The bases can form directional hydrogen bonds in pairs: A with T (and T with A) in DNA only A with U (and U with A) in RNA only C with G (and G with C) in both DNA and RNA Several factors limits all the possible pairing to the above mentioned: the size of the rings (Pu-Pu is too large, while Py-Py is too narrow when two filaments are coupled) A:T can make 2 H-bond; G:C can make three The polarity of H-bond in corresponding positions of these couples is matching (ex. T has a C=O facing a NH2 of A acceptor facing donor, while G has a C=O in that position) A:U is possible since the only difference between the two bases (extra CH3 in C3 of U) is off the side involved in Hbonds
20 Base pairing
21 Keto-enol tautomerism The bases can undergo spontaneously tautomerism of C=O into C-OH, this is specially true for T (panel a) and G (panel b), but can also happen to C and U The interconversion of the two forms involves the movement of a proton and the shifting of bonding electron DNA double helix is only compatible with all the bases in their keto-form Within this frame, the most important tautomerism is the conversion of T, since its enol-form can only pair with G (3 Hbonds) and not with A induced mutation
22 DNA structure DNA is the nucleic acid of chromosomes It is always made by two paired filaments running in opposite direction This results into a double helix in which each filament is the template of the next generation's replicative event The complementarity is given by the reciprocal base pairing A small repertoir of base pairing is fundamental to keep errors to a minimum in both replication and transcription /translation
23 RNA structure RNA is always present as a single filament, but folds into itself in a larger variety of shapes, which includes short helical regions in which base-pairing can occur (stem-loop regions) RNA can be classified based on its function: mrna (the string directly relating DNA to protein) no fixed tertiary structure trna (adaptor molecule carrying aa to the ribosome) specific L-shape almost independent of the sequence rrna (structural and functional constituent of the ribosome) complex structure to host accessory scaffolding proteins and regulatory factors
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