Nucleotides and Nucleic Acids Overview

Nucleoside 5'-Triphosphates Are Carriers of Chemical Energy

• Nucleoside 5'-triphosphates are critical for metabolism due to their high-energy phosphoric anhydride bonds
• The bases in nucleotides serve as recognition units
• Cyclic nucleotides act as signal molecules and regulators of cellular processes
• ATP is essential for energy metabolism
• GTP drives protein synthesis
• CTP drives lipid synthesis
• UTP drives carbohydrate metabolism

The Structure of a Nucleic Acid Chain Can Be Simplified

• Nucleic acid chains are represented by the sequence of their bases

3',5'-Phosphodiester bridges link nucleotides together to form polynucleotide chains.

• The 5'-ends of the chains are at the top; the 3'-ends are at the bottom.

What Are the Different Classes of Nucleic Acids?

• DNA exists in one form and has one primary purpose
• RNA exists in three (or four) types and has three (or four) purposes
  • Ribosomal RNA (rRNA) forms the structural and functional basis of ribosomes
  • Messenger RNA (mRNA) carries the genetic code for protein synthesis
  • Transfer RNA (tRNA) carries amino acids to the ribosomes for protein synthesis
  • Other types include small nuclear RNA and small non-coding RNAs

The Structure of DNA

• Each phosphodiester bridge in a nucleic acid backbone has a negative charge
• Nucleosides consist of a base bonded to a sugar
• DNA contains the bases adenine (A), thymine (T), guanine (G), and cytosine (C)
• Nucleic acids are conventionally written in the 5'-to-3' direction

Base Pairing in DNA

• Guanine pairs with cytosine (G:C)
• Adenine pairs with thymine (A:T)
• The base pairs have similar shapes
• Hydrogen bonds hold the base pairs together

Chargaff's Rules

• The A:T and G:C ratios are nearly 1:1 in different organisms
• The A:G ratio varies between organisms

Stability of the Double Helix

• Base stacking contributes to the stability of the double helix due to hydrophobic interactions
• Van der Waals forces also stabilize stacked base pairs

DNA Replication

• DNA replication involves the unwinding of the double helix and separation of the two strands
• Each strand serves as a template for the synthesis of a new complementary strand
• DNA polymerase catalyzes the addition of nucleotides to the growing strand in a 5'-to-3' direction
• The process is semiconservative, meaning that each new helix contains one parental strand and one newly synthesized strand

RNA

• RNA is less susceptible to hydrolysis by dilute base than DNA due to its shorter glycosidic bond
• Hydrolysis of RNA by dilute base involves:
  • An OH- abstracts a proton from the C'2 hydroxyl group
  • The charged oxygen attacks the positive phosphorus, breaking the phosphodiester bond
  • The cyclic nucleotide is hydrolyzed by water to form a mixture of 2'- and 3'-monophosphate derivatives

Gene Expression

• Gene expression is the process of converting genetic information from DNA into functional molecules
• It involves two steps:
  • Transcription: DNA is transcribed into mRNA
  • Translation: mRNA is translated into proteins

Types of RNA

• Messenger RNA (mRNA): serves as a template for protein synthesis
• Transfer RNA (tRNA): carries amino acids to the ribosome for protein synthesis
• Ribosomal RNA (rRNA): forms the major component of ribosomes and acts as a catalyst for protein synthesis

RNA Polymerase

• RNA polymerase synthesizes RNA from a DNA template
• It does not require a primer
• The process involves the elongation of the RNA strand in a 5'-to-3' direction using ribonucleoside triphosphates (ATP, GTP, UTP, and CTP)
• The reaction is driven by pyrophosphate hydrolysis

Transcription

• Transcription begins at promoter sites and ends at terminator sites
• Promoter sites are regions on DNA that bind RNA polymerase and determine the start of transcription
• Terminator sequences are regions that signal the end of transcription

Promoter Sites

• Prokaryotes: Pribnow box (-10 region), -35 region
• Eukaryotes: TATA box (Hogness box), CAAT box

Transcription Termination

• Prokaryotes: terminator sequences or rho protein
• Eukaryotes: less well-defined, may involve specific sequences or protein factors
• Terminator sequences often involve a stem-loop structure followed by a sequence of U residues

Complementarity Between DNA and RNA

• The base sequence of mRNA is complementary to the template strand of DNA
• Uracil (U) in RNA replaces thymine (T) in DNA

Key Characteristics of DNA Synthesis

• Requires four deoxynucleoside 5'-triphosphates and Mg2+
• Occurs on a pre-existing DNA template
• Requires a primer to initiate synthesis
• Chain elongation proceeds in the 5'-to-3' direction
• Many DNA polymerases have nuclease activity to remove mismatched nucleotides

Viral RNA Genomes

• Some viruses have RNA genomes that are replicated by RNA-directed RNA polymerases
• Retroviruses have single-stranded RNA genomes that are converted to DNA by reverse transcriptase

Hypochromism

• Hypochromism is the decrease in UV absorbance at 260 nm when DNA is in a double-stranded form
• This phenomenon is due to stacking interactions between base pairs
• It is an indication of the double helix formation

X-Ray Diffraction of DNA

• X-ray diffraction studies provided essential information about DNA structure
• They revealed that DNA is a double helix with a helical structure

Importance of Chargaff's Discovery

• Chargaff's discovery of the equivalence of A and T, and G and C, was essential for understanding DNA structure
• It supported the idea of base pairing in DNA and provided evidence for the Watson-Crick model

Semiconservative Replication

• DNA replication is semiconservative, meaning each new DNA molecule contains one parental strand and one newly synthesized strand