🧬Biochemistry Unit 6 – Nucleotides and Nucleic Acids

What Are Nucleotides?

• Nucleotides are the fundamental building blocks of nucleic acids (DNA and RNA)
• Consist of three components: a nitrogenous base, a pentose sugar, and a phosphate group
• Play crucial roles in various biological processes, including genetic information storage, energy transfer, and cell signaling
• Serve as the monomeric units that polymerize to form the polynucleotide chains of DNA and RNA
• Exist in both free and polymerized forms within cells
• Free nucleotides, such as ATP and GTP, function as energy carriers and signaling molecules
• Polymerized nucleotides form the backbone of nucleic acids, with the nitrogenous bases carrying genetic information

Building Blocks: Nucleotide Structure

• Nucleotides are composed of three distinct parts: a nitrogenous base, a pentose sugar, and one or more phosphate groups
• Nitrogenous bases are heterocyclic aromatic compounds that come in two types: purines (adenine and guanine) and pyrimidines (cytosine, thymine, and uracil)
  • Purines have a double-ring structure, while pyrimidines have a single-ring structure
• Pentose sugar in nucleotides is either ribose (in RNA) or deoxyribose (in DNA)
  • Deoxyribose lacks a hydroxyl group at the 2' position compared to ribose
• Phosphate groups are attached to the 5' carbon of the pentose sugar and are responsible for the negative charge of nucleotides
• Nucleosides are formed when a nitrogenous base is attached to a pentose sugar via an N-glycosidic bond
  • Nucleotides are nucleosides with one or more phosphate groups attached to the sugar

Types of Nucleic Acids: DNA and RNA

• There are two main types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
• DNA is the primary genetic material in most organisms and is responsible for storing and transmitting genetic information
  • DNA is a double-stranded molecule with complementary base pairing (A-T and G-C)
• RNA is a single-stranded molecule that plays various roles in gene expression, regulation, and catalysis
  • RNA contains uracil (U) instead of thymine (T) as a nitrogenous base
• Both DNA and RNA are polymers of nucleotides joined by phosphodiester bonds between the 5' phosphate of one nucleotide and the 3' hydroxyl of another
• DNA is more stable than RNA due to its double-stranded structure and the absence of the 2' hydroxyl group in its sugar moiety
• RNA is more versatile than DNA, with various types (mRNA, tRNA, rRNA) serving different functions in the cell

DNA Structure and Function

• DNA is a double-stranded helical molecule composed of two antiparallel polynucleotide chains
• The two strands are held together by hydrogen bonds between complementary base pairs: adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C)
  • The base pairing follows the Watson-Crick model, with A-T forming two hydrogen bonds and G-C forming three hydrogen bonds
• The sugar-phosphate backbones of the two strands run in opposite directions (5' to 3' and 3' to 5'), creating an antiparallel structure
• The double helix structure of DNA is stabilized by base stacking interactions between adjacent nucleotides
• DNA's primary function is to store and transmit genetic information, serving as a template for its own replication and the synthesis of RNA
• The genetic information in DNA is encoded by the sequence of nucleotides, with each triplet of nucleotides (codon) specifying a particular amino acid
• DNA also plays a role in gene regulation through various mechanisms, such as promoter and enhancer sequences that control transcription

RNA Structure and Types

• RNA is a single-stranded nucleic acid that contains ribose sugar and the nitrogenous bases adenine (A), guanine (G), cytosine (C), and uracil (U)
• Unlike DNA, RNA is usually single-stranded and can fold into complex secondary and tertiary structures due to intramolecular base pairing
• There are three main types of RNA: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)
  • mRNA carries the genetic information from DNA to the ribosomes for protein synthesis
  • tRNA acts as an adapter molecule, translating the genetic code into amino acid sequences
  • rRNA is a component of ribosomes and catalyzes peptide bond formation during protein synthesis
• Other types of RNA include small nuclear RNA (snRNA), small interfering RNA (siRNA), and microRNA (miRNA), which play roles in gene regulation and RNA processing
• RNA can also function as a catalyst (ribozymes) and regulate gene expression through various mechanisms, such as RNA interference (RNAi)

Nucleotide Synthesis and Breakdown

• Nucleotide synthesis occurs through two main pathways: de novo synthesis and salvage pathways
• De novo synthesis involves the formation of nucleotides from simple precursor molecules, such as amino acids and ribose-5-phosphate
  • The synthesis of purine nucleotides begins with the formation of inosine monophosphate (IMP), which is then converted to AMP and GMP
  • Pyrimidine nucleotide synthesis starts with the formation of uridine monophosphate (UMP), which is then converted to CTP and TTP (via dUMP)
• Salvage pathways recycle preformed nucleobases and nucleosides, conserving energy and resources
  • Examples include the conversion of hypoxanthine to IMP by hypoxanthine-guanine phosphoribosyltransferase (HGPRT) and the conversion of uracil to UMP by uracil phosphoribosyltransferase (UPRT)
• Nucleotide breakdown is essential for maintaining balanced nucleotide pools and preventing the accumulation of excess nucleotides
  • Nucleotidases and phosphatases remove phosphate groups from nucleotides, while nucleosidases and phosphorylases cleave the N-glycosidic bond between the base and the sugar
• Disorders of nucleotide metabolism can lead to various health problems, such as gout (caused by excessive uric acid production) and immunodeficiencies (resulting from impaired purine synthesis)

Nucleic Acid Replication and Transcription

• Replication is the process by which DNA makes an identical copy of itself during cell division
  • DNA replication is semiconservative, with each strand of the original double helix serving as a template for the synthesis of a new complementary strand
• Replication begins at specific sites called origins of replication and proceeds bidirectionally, with the help of enzymes such as DNA polymerases and helicases
  • DNA polymerases synthesize new DNA strands in the 5' to 3' direction, using the parental strands as templates
  • Helicases unwind the double helix, separating the two strands to allow access for the replication machinery
• Transcription is the process by which RNA is synthesized using DNA as a template
  • RNA polymerase catalyzes the formation of RNA from the DNA template, with the help of transcription factors that regulate the process
• Transcription occurs in three stages: initiation, elongation, and termination
  • During initiation, RNA polymerase binds to the promoter region of the gene and begins synthesizing the RNA transcript
  • Elongation involves the progressive addition of nucleotides to the growing RNA chain
  • Termination occurs when the RNA polymerase reaches a specific termination signal, releasing the completed RNA transcript
• The RNA transcript undergoes post-transcriptional modifications, such as splicing and capping, before being translated into a protein or serving its function as a non-coding RNA

Cool Applications in Biotech and Medicine

• Nucleic acid-based therapies, such as antisense oligonucleotides and small interfering RNAs (siRNAs), can be used to target specific genes and modulate their expression
  • Antisense oligonucleotides bind to complementary mRNA sequences, preventing their translation or inducing their degradation
  • siRNAs trigger the RNA interference (RNAi) pathway, leading to the cleavage of target mRNAs and gene silencing
• Gene editing technologies, such as CRISPR-Cas9, allow for precise modification of DNA sequences
  • CRISPR-Cas9 uses a guide RNA to direct the Cas9 endonuclease to a specific DNA sequence, where it creates a double-strand break that can be repaired by the cell's DNA repair mechanisms
  • This technology has the potential to correct genetic disorders, create disease-resistant crops, and develop novel therapies
• DNA sequencing technologies have revolutionized our understanding of genetics and genomics
  • Next-generation sequencing (NGS) platforms enable high-throughput, parallel sequencing of millions of DNA fragments, allowing for rapid and cost-effective genome sequencing
  • Sequencing data can be used for various applications, such as personalized medicine, evolutionary studies, and disease diagnosis
• Nucleic acid-based diagnostic tools, such as PCR and DNA microarrays, are widely used for the detection and identification of pathogens, genetic disorders, and cancer biomarkers
  • PCR amplifies specific DNA sequences, enabling the detection of even small amounts of target DNA
  • DNA microarrays contain thousands of DNA probes that can hybridize to complementary sequences in a sample, allowing for the simultaneous analysis of multiple genes or genetic variants
• Nucleic acid-based vaccines, such as mRNA vaccines, have shown promise in the fight against infectious diseases and cancer
  • mRNA vaccines deliver genetic instructions for the production of specific antigens, eliciting an immune response without the need for live or attenuated pathogens
  • The rapid development and success of mRNA vaccines against SARS-CoV-2 have highlighted the potential of this technology for responding to emerging threats and pandemics