Nucleotides and Nucleic Acids

Chapter 8: Nucleotides and Nucleic Acids

Biological Functions of Nucleotides and Nucleic Acids

  • Nucleotide Functions:

    • Energy for Metabolism: ATP (adenosine triphosphate) serves as the energy currency of the cell.

    • Enzyme Cofactors: NAD+ (Nicotinamide adenine dinucleotide) is crucial in redox reactions.

    • Signal Transduction: cAMP (cyclic adenosine monophosphate) acts as a secondary messenger in signal transduction pathways.

  • Nucleic Acid Functions:

    • Storage of Genetic Information: DNA holds the genetic blueprint that guides the development and functioning of living organisms.

    • Transmission of Genetic Information: mRNA (messenger RNA) carries genetic information from DNA to ribosomes for protein synthesis.

    • Processing of Genetic Information: Ribozymes, RNA molecules with catalytic activity, play roles in processes like splicing.

    • Protein Synthesis: tRNA (transfer RNA) and rRNA (ribosomal RNA) are essential for translating mRNA into protein.

Nucleotides and Nucleosides

  • Definition:

    • Nucleotide: A nucleotide is composed of a nitrogenous base, a pentose sugar (ribose or deoxyribose), and one or more phosphate groups.

    • Nucleoside: A nucleoside consists of a nitrogenous base bonded to a pentose sugar without any phosphate group.

Structures of Common Nucleotides

  • General Structure:

    • Nitrogenous base can be a purine (adenine, guanine) or pyrimidine (cytosine, thymine, uracil).

    • Pentose sugar has specific positions for hydroxyl (-OH) groups: 2’, 3’, and 5’.

  • Phosphate Group:

    • Typically attached to the 5' position of the sugar.

    • Nucleic acids are synthesized from nucleoside 5'-triphosphates (ATP, GTP, TTP, CTP).

    • Contain one phosphate group per nucleotide.

Other Nucleotides and Their Structural Variations

  • Monophosphate Groups in Different Positions:

    • Adenosine 5'-monophosphate (AMP) has the phosphate group at the 5’ position.

    • Adenosine 2’-monophosphate and adenosine 3’-monophosphate have phosphate groups at alternative positions.

Pentose Sugar in Nucleotides

  • Types:

    • B-D-ribofuranose (found in RNA)

    • B-2'-deoxy-D-ribofuranose (found in DNA)

  • Conformations: Different puckered conformations of the sugar ring are present in these nucleotides.

Nucleobases

  • Characteristics:

    • Nitrogenous bases are derivatives of purines or pyrimidines; they are heteroaromatic and absorb UV light (250-270 nm).

Pyrimidine Bases:

  • Cytosine: Found in both DNA and RNA.

  • Thymine: Found only in DNA, good H-bond donor.

  • Uracil: Found only in RNA, similar to thymine.

  • pKa Values:

    • Cytosine (N3) = 4.5

    • Thymine (N3) = 9.5

    • Neutral at pH 7.

Purine Bases:

  • Adenine and Guanine: Found in both RNA and DNA, with significant H-bonding abilities.

  • pKa Values:

    • Adenine (N1) = 3.8

    • Guanine (N7) = 2.4

    • Neutral at pH 7.

N-glycosidic Bonds

  • The pentose sugar is attached to the nucleobase via a N-glycosidic bond:

    • Formation: The bond forms to the anomeric carbon of the sugar in the β configuration.

    • Positions: N1 for pyrimidines and N9 for purines.

    • Stability: Stable toward hydrolysis, but can be cleaved under acidic conditions.

Conformation Around N-Glycosidic Bond

  • Rotation: Relatively free rotation occurs around the N-glycosidic bond in free nucleotides.

  • Torsion Angle: Defined by the sequence of atoms:

    • For purines: O4'-C1'-N9-C4

    • For pyrimidines: O4'-C1'-N1-C2

    • Syn Conformation: Angle near 0°

    • Anti Conformation: Angle near 180°

    • Anti conformation predominant in B-DNA.

Tautomerism of Nucleobases

  • Prototropic Tautomers: Structural isomers that differ in the location of protons (e.g., keto-enol tautomerism common in ketones).

  • Lactam-Lactim Tautomerism: Specific to certain heterocycles, existing predominantly as lactam forms at neutral pH.

UV Absorption of Nucleobases

  • Absorption at 250-270 nm due to p → p* electronic transitions, which allows effective photoprotection of genetic material without fluorescence.

Molar Extinction Coefficient Data:

  • Molar extinction coefficients ($ ext{€}_{260}$)

    • AMP: 15,400

    • GMP: 11,700

    • UMP: 9,900

    • dTMP: 9,200

    • CMP: 7,500.

Nomenclature of Nucleotides and Nucleic Acids

  • Purines:

    • Adenine: Nucleoside = Adenosine; Nucleotide = Adenylate.

    • Guanine: Nucleoside = Guanosine; Nucleotide = Guanylate.

  • Pyrimidines:

    • Cytosine: Nucleoside = Cytidine; Nucleotide = Cytidylate.

    • Thymine: Nucleoside = Thymidine; Nucleotide = Thymidylate.

    • Uracil: Nucleoside = Uridine; Nucleotide = Uridylate.

Deoxyribonucleotides Structure and Symbols:

  • Structure aspects include pentose sugar and nitrogenous base. Familiarity needed for names and symbols like (dA, dAMP) for Deoxyadenylate.

Ribonucleotides Structure and Symbols:

  • Learn symbols (one-letter and three-letter codes): A (Adenosine), G (Guanosine), C (Cytidine), U (Uridine).

Minor Nucleosides and Their Functions

  • 5-Methylcytosine: Common in eukaryotes, marks DNA for degradation of foreign DNA.

  • N6-Methyladenosine: Found in bacteria, indicates active genes.

  • Inosine: Occurs in the anticodon wobble position of tRNA, expands the genetic code.

  • Pseudouridine: Prevalent in tRNA and rRNA, stabilizes tRNA structure and aids in rRNA folding.

Polynucleotides

  • Formation: Formed via phosphodiester linkages, creating a negatively charged backbone.

  • DNA Stability: More stable than RNA which degrades quickly.

  • Directionality: Polymers are linear, with distinct 5' and 3' ends; read sequence from 5' to 3'.

Hydrolysis of RNA

  • RNA hydrolysis occurs rapidly under alkaline conditions and is catalyzed by RNase enzymes.

  • Enzyme Examples:

    • RNase P: A ribozyme involved in processing tRNA precursors.

    • Dicer: Cleaves double-stranded RNA into oligonucleotides for viral protection.

Hydrogen-Bonding Interactions

  • Base Pairing: Key interactions in DNA include:

    • Adenine (A) pairs with Thymine (T)

    • Cytosine (C) pairs with Guanine (G)

  • Watson-Crick Base Pairs: Dominant interaction type in double-stranded DNA.

DNA Structure Discovery

  • The double helix structure was elucidated by Watson and Crick in 1953, indicating scientific collaboration's importance.

Major and Minor Grooves

  • Structural features of the double-helix provide space for protein binding and affecting gene regulation.

DNA Characteristics

  • Complementarity: Strands have complementary sequences and run antiparallel.

  • Replication Mechanism:

    • Strand separation is the first step towards replication. Each serves as a template, catalyzed by DNA polymerases.

    • Resulting DNA molecule consists of one parent and one daughter strand.

mRNA Characterization

  • mRNA synthesized from DNA templates contains ribose and uracil, coding for proteins, with variations in coding capabilities (monocistronic vs polycistronic).

Complex RNA Structures

  • RNA exhibits intricate structures, allowing for functions such as regulatory roles in gene expression.

DNA Denaturation and Annealing

  • Denaturation: Hydrogen bonds break, allowing strands to separate; can occur under heat or pH changes and can be reversible.

Factors Affecting DNA Denaturation

  • Tm (melting temperature) affected by GC content, length, and ionic strength; AT-rich regions melt at lower temperatures.

Molecular Mechanisms of Mutagenesis

  • Spontaneous Mutagenesis: Occurs through deamination and depurination, leading to significant genetic changes.

    • Modification correction mechanisms are crucial for cellular function.

Radiation-Induced Mutagenesis

  • UV light can induce pyrimidine dimerization leading to significant DNA damage; ionizing radiation causes strand breaking, which cells struggle to repair.