4.1

Nucleic Acids

1. Definition of Nucleic Acids

  • Nucleic Acids: Polymers made from monomers known as nucleotides.
  • Unlike proteins which are assembled from amino acids, nucleic acids are composed of nucleotides.

2. Learning Objectives

  • Objective 4.1: Analyze the characteristics of nucleotides and the bonds linking them together in nucleic acids.

3. Structure of Nucleotides

  • Components of a Nucleotide (See Figure 4.1):

    • Phosphate Group: First component of the nucleotide.
    • Five-Carbon Sugar: Central component, provides structure; compared to alpha carbon in amino acids.
    • Nitrogenous Base: Contains nitrogen and serves as the component that varies between nucleotides.

  • Nucleotide Representation:

    • The sugar has five carbon atoms, numbered with numbers and primes ().
    • The base is attached to the 1' (one-prime) carbon.
    • The phosphate group is attached to the 5' (five-prime) carbon.

4. Types of Nucleotides

  • Ribonucleotides:

    • Contains ribose as the sugar.
    • The structure includes an —OH group on the 3' carbon and also an —OH group on the 2' carbon.

  • Deoxyribonucleotides:

    • Contains deoxyribose as the sugar.
    • The structure includes an —OH group only on the 3' carbon, and an —H (hydrogen) on the 2' carbon.

5. Nitrogenous Bases

  • Structural Groups: Nitrogenous bases fall into categories called purines and pyrimidines.

    • Purines: Adenine (A) and Guanine (G); consist of double rings formed from nine atoms.
    • Pyrimidines: Cytosine (C), Uracil (U, used in RNA), and Thymine (T, used in DNA); single ring composed of six atoms.

  • Distinct Nucleotide Types:

    • Total of eight nucleotides used to build nucleic acids:
    • Four ribonucleotides (with uracil)
    • Four deoxyribonucleotides (with thymine)

6. Models of Nucleotides

  • Making Models 4.1: Tips for drawing nucleotides.
    • Use shapes:
    • Circle for phosphate group.
    • Pentagon for sugar.
    • Hexagon for base.
    • Example: Draw one ribonucleotide and one deoxyribonucleotide, with covalent bonds and carbons labeled (2', 3', 5').

7. Chemical Evolution and Nucleotides

  • Discussion around the possibility that nucleic acids played a role in the chemical evolution of life.
  • Evidence lean towards the presence of nucleotides in prebiotic conditions.
  • Miller Experiment: Showed amino acids could be synthesized early in Earth's history.
  • Challenges described with identifying prebiotic synthesis of nucleotides.
    • Laboratory simulations confirm nitrogenous bases and sugars, including ribose, could be synthesized under early Earth-like conditions.

8. Deep Sea Hydrothermal Vent Evidence

  • Reactive minerals found in deep sea vents preferentially bind to ribose, suggesting a concentration of RNA's sugar in ancient environmental contexts.
  • Implications: A concentrated environment of ribose in early settings aligns with hypotheses surrounding life's evolution.

9. Polymerization of Nucleotides to Form Nucleic Acids

  • Condensation Reactions: Nucleotides polymerize by chemical reactions between hydroxyl groups of sugars and phosphate groups of other nucleotides.
    • This reaction releases a water molecule and forms a new covalent bond.
9.1 Phosphodiester Linkage
  • The bond formed in the polymerization process is known as a phosphodiester linkage (or bond).
  • Connection: Links the 3' carbon of one nucleotide to the 5' carbon of another nucleotide.
  • This mechanism can occur with both ribonucleotides (producing RNA) and deoxyribonucleotides (producing DNA).
  • Directional Nature: Nucleic acid strands have a sugar phosphate backbone that is directional, similar to peptide bonded backbones in proteins.

10. Primary Structure and Sequence of Nucleic Acids

  • In DNA or RNA, one end has an unlinked 5' phosphate, and the other has an unlinked 3' hydroxyl, marking the directionality of the macromolecule.
  • The sequence of the nucleotides constitutes the primary structure of the nucleic acid, generally represented using single-letter abbreviations:
    • Example: A sequence of six nucleotides in DNA could be represented simply by their base letters (A, T, C, G).
  • By convention, the sequence is always written from 5' to 3' direction, reflecting the synthesis direction in cells where nucleotides are added only to the 3' end.

11. Energy Requirements for Polymerization

  • Non-Spontaneity: The process of polymerization leads to decreased entropy, thus requiring an energy input to favor the reaction.
  • Nucleotide polymerization occurs in cells helped by enzymes as potential energy in nucleotides needs elevation.
  • Nucleotides can be activated by adding two additional phosphate groups, generating nucleoside triphosphates, which are essential for nucleic acid synthesis.
11.1 Activated Nucleotides
  • Example includes Adenosine Triphosphate (ATP) for RNA synthesis and Deoxyadenosine Triphosphate (dATP) for DNA synthesis.
  • Potential Energy Storage: The energy primarily resides in the bonds between phosphate groups, where hydrolysis of ATP will yield lower energy bonds, resulting in energy release that drives polymerization processes.

12. Conclusion and Further Study

  • The discussion around how phosphates raise the potential energy of a nucleotide via repelling like charges.
  • The significance of activated nucleotides extends beyond polymerization as they also support other cellular activities, requiring further exploration in later chapters.