Nucleic Acids

Learning Objectives

  • Describe the subunits of DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) and explain the mechanisms of how their nucleotides bond through phosphodiester linkages to form the nucleic acid structures.

  • Understand the complex properties and multifaceted functions of DNA, including its role in heredity, regulation, and the storage of genetic information. Explore how DNA is meticulously packaged within the cell, focusing on structures unique to eukaryotes, prokaryotes, and how viruses utilize their genetic material differently.

  • Distinguish between the different types of RNA (mRNA, rRNA, tRNA), delve into the specific functions of each type, and explain their roles in the process of transcription and translation in protein synthesis.

Case Study: HIV and AZT

  • Background: Client exhibited symptoms characteristic of AIDS (Acquired Immunodeficiency Syndrome) due to HIV (Human Immunodeficiency Virus) infection, a virus that targets the immune system, specifically CD4 T cells, leading to severe immune compromise.

  • AZT (Zidovudine): An antiretroviral medication that acts as a nucleoside reverse transcriptase inhibitor (NRTI). AZT mimics the natural nucleoside thymidine, thus interfering with viral replication by preventing the conversion of viral RNA into DNA within the host cells. This mechanism is crucial in managing HIV infection and delaying the progression to AIDS.

Central Dogma of Molecular Biology

  • Information flow: The central dogma illustrates the flow of genetic information from DNA → RNA → Protein, highlighting the essential processes of transcription (the synthesis of RNA from DNA) and translation (the synthesis of proteins from RNA).

  • Role of RNA: RNA functions as a crucial intermediary between the genetic blueprint contained in DNA and the machinery that synthesizes proteins, acting as a messenger carrying instructions from the nucleus to the cytoplasm where proteins are made.

Biomolecules: DNA and RNA

  • DNA:

    • Composed of chains of deoxyribonucleotides (dATP, dTTP, dGTP, dCTP), structured in a double helix formation.

    • DNA is double-stranded, residing within the nucleus of eukaryotic cells, where it is organized into chromatin that facilitates genome regulation and expression.

  • RNA:

    • Made up of chains of ribonucleotides (ATP, CTP, GTP, UTP), which can fold into various shapes contributing to its diverse functions.

    • Typically single-stranded, RNA is transcribed in the nucleus and later translated in the cytoplasm or associated with the rough endoplasmic reticulum, indicating its role in protein production.

DNA vs. RNA

  • DNA:

    • Serves as the primary genetic information source in all living organisms (humans, animals, plants, bacteria, and viruses).

    • In eukaryotic cells, DNA is housed within membrane-bound nuclei; prokaryotic cells contain DNA primarily in the cytoplasm, and organelles like mitochondria and chloroplasts feature prokaryotic-like DNA structures.

Viruses

  • Viruses have the unique ability to utilize either DNA or RNA as their genetic material; they do not possess the cellular machinery for replication and, thus, must hijack host cells' biochemical pathways to reproduce.

  • For example, bacteriophages are viruses specifically known to infect bacterial cells, utilizing them for the replication of their genetic material and propagation of the viral progeny.

Plasmids

  • Plasmids are small, circular DNA molecules found in bacterial cells that replicate independently from chromosomal DNA.

  • They are commonly involved in antibiotic resistance mechanisms and are pivotal tools in genetic engineering and biotechnology for the cloning and expression of genes.

History of DNA Discovery

  • Significant milestones in the discovery of DNA include:

    • 1865: DNA was first isolated, marking the initial understanding of genetic material.

    • 1944: Oswald Avery's experiments established DNA as the "transforming principle" in bacterial transformation, news that laid the groundwork for genetics.

    • 1952: The Hershey-Chase experiment demonstrated, through the use of radioisotopes, that DNA is indeed the genetic material.

    • 1953: Key contributions from James Watson, Francis Crick, Rosalind Franklin, and Maurice Wilkins elucidated the double-helix structure of DNA, foundational to understanding genetic information storage and replication.

Nucleotide Structure

  • A nucleotide consists of three components:

    • A nitrogenous base (adenine, guanine, cytosine, or thymine in DNA; uracil replaces thymine in RNA).

    • A sugar molecule (deoxyribose in DNA and ribose in RNA).

    • 1-3 phosphate groups, which define the nucleotide's role as a monomer in forming nucleic acid chains.

  • Nomenclature: The combination of sugar and base forms a nucleoside; nucleotides are produced upon the addition of one or more phosphate groups (mono-, di-, or tri-).

Sugars in DNA and RNA

  • DNA contains deoxyribose sugar, which is characterized by the absence of a hydroxyl group (-OH) on the 2’ carbon, thereby providing stability and making it less reactive compared to RNA.

  • RNA incorporates ribose, featuring a hydroxyl group on the 2’ carbon; this extra oxygen atom contributes to RNA's reactivity and functional diversity.

Nitrogenous Bases

  • The nitrogenous bases are categorized into:

    • Pyrimidines: Cytosine (C) and Thymine (T) in DNA, and Cytosine (C) and Uracil (U) in RNA.

    • Purines: Adenine (A) and Guanine (G), structurally characterized by their double-ring structure. A helpful mnemonic to remember purines is “Purines Are Giants.”

Base Pairing

  • In DNA, base pairing occurs as follows: A pairs with T forming two hydrogen bonds, while G pairs with C forming three hydrogen bonds, making G-C pairs more stable due to their higher bond count.

  • In RNA, Uracil (U) replaces Thymine (T) and pairs with Adenine (A), maintaining the fidelity of base-pairing rules vital for accurate transcription and translation.

DNA/RNA Bonding

  • Nucleotides are joined by strong covalent phosphodiester bonds between the 3’ and 5’ carbons of adjacent nucleotides, resulting in a stable sugar-phosphate backbone.

  • DNA boasts a negatively charged phosphate backbone, which plays a crucial role in attracting histone proteins and regulating the accessibility of the genetic material during processes such as transcription and replication.

DNA Structure

  • The DNA double helix exhibits a unique structure characterized by its winding shape and the presence of major and minor grooves that are accessible for protein binding and interaction, crucial for transcription and replication processes.

  • The antiparallel nature of DNA strands (5’ to 3’ and 3’ to 5’) is essential for the replication and transcription processes, guiding the synthesis direction of new strands.

DNA Packaging

  • DNA in eukaryotic cells is extensively packed to fit into the nucleus; this packaging is facilitated via complex interactions with histone proteins, resulting in a characteristic "beads on a string" appearance due to the formation of nucleosomes.

  • Nucleosomes are composed of histone proteins (H2A, H2B, H3, H4) and an additional H1 histone associated with the linker DNA, organizing the genetic material efficiently for both storage and access for cellular machinery.

Chromatin Structure

  • Histones, rich in arginine (Arg) and lysine (Lys), possess a net positive charge that contributes to their affinity for negatively charged DNA, facilitating effective binding.

  • Post-translational modifications, such as methylation and acetylation of histones, can markedly influence the interactions between DNA and histones, thus affecting gene expression and chromatin structure.

Types of RNA

  1. mRNA (messenger RNA): Carries genetic instructions from DNA for protein synthesis. It undergoes processing involving intron splicing, addition of a 5' guanosine cap, and a poly-A tail before exporting from the nucleus for translation.

  2. rRNA (ribosomal RNA): Combines with ribosomal proteins to form functional ribosomes, with eukaryotic ribosomes being 80S in size, essential for translating mRNA into protein.

  3. tRNA (transfer RNA): Transfers specific amino acids to ribosomes during translation; it possesses an anticodon that is complementary to mRNA codons, thus ensuring proper amino acid insertion during protein synthesis.

Viral Replication

  • Viruses exploit the cellular machinery of their host for their own replication as they lack the capability to independently reproduce. They typically employ mechanisms of hijacking host proteins and pathways.

  • Retroviruses (such as HIV) have unique replication cycles in which they reverse transcribe their RNA genome into DNA using an enzyme called reverse transcriptase, integrating into the host genome and evading immune responses.

Question Review

  • In terms of nucleotide pairing strength, G-C pairs are stronger due to the presence of three hydrogen bonds compared to the two hydrogen bonds in A-T pairs.

  • The backbone of both RNA and DNA is composed of alternating phosphate and sugar molecules, which provide structural integrity and facilitate the formation of the nucleic acid strands.