Nucleic Acids and Gene Expression Study Notes

Nucleic Acids and Gene Expression I

Biological Function of Nucleotides and Nucleic Acids

  1. Functions of Nucleic Acids:

    • Storage of Genetic Information (DNA): DNA is responsible for storing the genetic blueprint of organisms.
    • Transmission of Genetic Information (mRNA): mRNA carries genetic information from DNA to the ribosomes for protein synthesis.
    • Processing of Genetic Information (Ribozymes): Ribozymes are RNA molecules that catalyze biochemical reactions.
    • Protein Synthesis (tRNA and rRNA): Transfer RNA and ribosomal RNA are critical components of the protein synthesis machinery.

  2. Functions of Nucleotides:

    • Building Blocks of Nucleic Acids: Each nucleotide is a fundamental unit of nucleic acid structure.
    • Energy for Metabolism (ATP): Adenosine triphosphate (ATP) serves as a primary energy carrier.
    • Enzyme Cofactors (NAD+): NAD+ acts as an electron carrier in metabolic reactions.
    • Signal Transduction (cAMP): Cyclic adenosine monophosphate (cAMP) acts as a secondary messenger in signal transduction pathways.

Structure of Nucleic Acids and Nucleotides

  1. Nucleic Acids:

    • Large Molecules: Comprised of long chains of nucleotides.
    • Polymers of Nucleotides: Nucleic acids are polymers made up of multiple nucleotides.
    • Four Different Nucleotides: Each nucleic acid contains four distinct nucleotide types.

  2. Nucleotide Structure:

    • Three Parts of a Nucleotide:
      • Five-Carbon Sugar (Pentose): The sugar can be either deoxyribose (in DNA) or ribose (in RNA).
      • Phosphate Group (-PO4): Typically attached to the 5’ position of the sugar.
      • Nitrogenous Base: Can be either a Purine (A, G) or a Pyrimidine (C, T, U).
    • Nucleoside: A nucleoside is formed when a nitrogenous base is linked to a pentose sugar without a phosphate group.
    • Covalent Bonds: Nucleotides are connected through ester bonds (glycosidic bonds between the base and sugar) and phosphodiester bonds between sugars.

Nitrogenous Bases

  1. Classification:

    • Purines: Adenine (A) and Guanine (G), which have a two-ring structure, each containing two nitrogen atoms.
    • Pyrimidines: Cytosine (C), Thymine (T, in DNA), and Uracil (U, in RNA), which have a single-ring structure, each containing two nitrogen atoms.

  2. Content:

    • DNA Bases: A, G, C, T
    • RNA Bases: A, G, C, U

  3. UV Absorption: Nitrogenous bases absorb UV light at the range of 250–270 nm.

Pentose Sugar Type

  1. DNA: Contains deoxyribose.
  2. RNA: Contains ribose.

Phosphate Group

  1. Charge: Negatively charged at neutral pH.
  2. Attachment: Typically attached to the 5’ position of the sugar.
  3. Phosphorylation: Nucleic acids are synthesized using 5’-triphosphates such as ATP, GTP, TTP (or UTP for RNA), CTP.

Nucleic Acid Structure

  1. Backbone Composition:

    • Formed by phosphodiester bonds between the 3’-OH of one nucleotide and the 5’-phosphate of another.
    • Polarity and Directionality: Nucleic acids have a defined directionality, conventionally written 5’ to 3’.

  2. DNA Double Helix:

    • Complementary sequences of DNA form a double helix.
    • Established by Watson and Crick: Two antiparallel polynucleotide chains coiled in a right-handed helix around a common axis.
    • Base Pairing: The bases are oriented nearly perpendicular to the axis of the helix with A pairs with T (2 hydrogen bonds) and G pairs with C (3 hydrogen bonds).

  3. Stabilizing Interactions:

    • Hydrogen Bonds: Between complementary bases (A=T; G≡C).
    • Van der Waals Forces: Stabilization by base stacking within the DNA strand.

  4. Physical Dimensions:

    • 10 base pairs per turn, with 3.4 Å base separation, 34 Å in height per turn, and a diameter of 20 Å.

  5. Chargaff’s Rules:

    • For any species, there is a 1:1 ratio of guanine to cytosine, and adenine to thymine. This gives rise to the relations: A = T and G = C.

DNA Denaturation and Annealing

  1. Denaturation: The process involves the separation of the two strands of DNA, breaking hydrogen bonds while covalent bonds remain intact.

    • Causes: High temperature or changes in pH.
    • UV Absorbance: Increases as the bases unstack during denaturation (hypochromic effect).

  2. Annealing: The reversible process where separated strands of DNA recombine to form a double helix.

Nucleic Acids and Gene Expression II

Central Dogma of Molecular Biology

  1. Flow of Genetic Information: The process begins with DNA, which replicates to form more DNA, is then transcribed into RNA, and finally translated into protein.
  2. Exceptions:
    • RNA Viruses: (e.g., tobacco mosaic virus) use RNA instead of DNA as genetic material, replicating by RNA-directed RNA polymerase.
    • Retroviruses: (e.g., HIV-1) convert their RNA genome into DNA using reverse transcriptase.

DNA Replication

  1. Mechanism: The process is semiconservative, where each parental strand serves as a template for new strands.

    • Catalysis: DNA synthesis is catalyzed by DNA polymerase.
    • Direction of Synthesis: New DNA strands are synthesized in the 5’ to 3’ direction.
    • Error Checking: DNA polymerase also performs proofreading; the approximate error rate is 1x10^-8/bp.

  2. Required Components:

    • DNA template, four deoxynucleoside triphosphates (dATP, dTTP, dGTP, dCTP), a primer (often RNA), a magnesium ion, and DNA polymerase.

Transcription

  1. Process by RNA Polymerase: Catalyzes synthesis of RNA from a DNA template.

    • Directionality: RNA is formed in the 5’ to 3’ direction from a 3’ to 5’ template.
    • Lack of Proofreading: Unlike DNA polymerase, RNA polymerase does not possess proofreading capabilities.

  2. Promoter Sites: Sites on DNA that bind RNA polymerase and initiate transcription.

    • Prokaryotic Promoters: Typically contain -10 (Pribnow box) and -35 regions.
    • Eukaryotic Promoters: Can include TATA boxes and CAAT boxes. Enhancers may also enhance transcription in eukaryotic cells.

  3. Termination of Transcription: In bacteria, RNA polymerase stops transcription upon encountering terminators, forming base-paired hairpin structures in RNA. Eukaryotic termination is less well characterized.

mRNA Processing (Eukaryotes Only)

  1. Pre-mRNA: The initial RNA transcript directly copied from DNA is termed precursor mRNA.
  2. Modifications Include:
    • 5’-Capping: Addition of a modified guanine nucleotide at the 5' end of the mRNA.
    • 3’-Polyadenylation: Addition of a poly(A) tail to enhance stability and export from the nucleus.
    • RNA Splicing: Removal of non-coding introns and joining of coding exons to produce mature mRNA.

Translation

  1. Process of Protein Synthesis: mRNA serves as the template for protein synthesis, conducted by ribosomes.

    • tRNA Function: Transfer RNA carries amino acids to ribosomes where they correspond to codons on the mRNA.
    • Ribosome Composition: Consists of ribosomal RNA and proteins, serving as the site for translation.

  2. Genetic Code: Composed of nucleotide sequences translated into amino acids.

    • Codons: Each set of three nucleotides represents a single amino acid. There are 64 codons, corresponding to 20 amino acids, making the code degenerate except for methionine (Met) and tryptophan (Trp).
    • Start Codon: AUG
    • Stop Codons: UAA, UAG, UGA.

  3. First Amino Acid: In bacterial proteins, it is formylmethionine (fMet); in eukaryotes, it is methionine (Met).

Conclusion

  • This comprehensive overview encapsulates the main biochemical and molecular biological aspects of nucleic acids and their role in gene expression, including the foundational mechanisms of replication, transcription, and translation.

Other Related Topics

Monosaccharides

  1. Chemical Composition: Monosaccharides have the general formula (CH2O)n. They can be classified further based on their carbon count (e.g., triose, tetrose, pentose, hexose).
  2. Examples:
    • Aldoses: Glucose, which contains an aldehyde group.
    • Ketoses: Fructose, which contains a ketone group.

D vs L Designation

  1. Asymmetric Carbons: The designation of sugars as D (right) or L (left) is based on the orientation around the last asymmetric carbon in the molecule.
  2. Natural Occurrence: Most naturally occurring sugars are D-isomers.

Common Monosaccharides

  1. Standard Sugars: Ribose (5-carbons), Glucose (6-carbons), Mannose, Galactose (epimers of glucose), Fructose (ketose form of glucose).

  2. Cyclization of Monosaccharides: Reaction of aldehydes or ketones with alcohols to form hemiacetals or hemiketals, leading to ring structures (e.g., pyranose, furanose).

Disaccharides and Polysaccharides

  1. Formation: Disaccharides are formed by glycosidic bonds between anomeric carbon and hydroxyl carbon.
  2. Common Names: Maltose (from glucose), Sucrose (glucose + fructose), and Lactose (glucose + galactose).
  3. Polysaccharides: Examples include starch, glycogen, cellulose; their structure can be homopolysaccharides or heteropolysaccharides with linear or branched configurations.