Molecular Biology: DNA Structures and Functions

Primary Structure of DNA/RNA

• Nucleic acids are linear sequences of nucleotides linked by phosphodiester bonds.
• Phosphodiester bonds bridge the 3' and 5' positions of the sugar moiety.
• Directionality runs from 5' to 3'.
• Oligonucleotides/polynucleotides are short/long chains of nucleotides.
• The backbone consists of phosphate and pentose sugar.
• Nucleotide monophosphates (NMPs) are basic building blocks of nucleic acids while nucleoside triphosphates (NTPs) are the activated precursors for synthesis.
• Example DNA sequence: 5'-ATGCGGCTATTGTA-3'
• Example RNA sequence: 5'-UGCGGCUAUUGUA-3'

Secondary Structure of DNA

• Erwin Chargaff's findings:
  • Base composition varies between species.
  • Base composition is consistent within a species, regardless of tissue or environment.
  • The number of adenine residues equals the number of thymine residues (A=T).
  • The number of guanine residues equals the number of cytosine residues (G=C).
  • The sum of purines (A+G) equals the sum of pyrimidines (T+C).
• Right-handed double helix.
• Two helical DNA chains wound around a common axis.
• Antiparallel orientation: Chains run in opposite directions (5' to 3' and 3' to 5').
• Base-pairing via hydrogen bonds (A-T = 2 bonds, G-C = 3 bonds).
• Hydrophilic sugar-phosphate backbone on the outside.
• Hydrophobic bases stacked inside.
• Major and minor grooves on the DNA surface due to the offset pairing of the strands.

DNA Denaturation and Renaturation

• DNA's secondary structure is sensitive to pH, temperature and ionic strength (salt).
• Denaturation: separation of DNA strands due to high temperature or other factors.
• Melting temperature (Tm): temperature at which half of the DNA in a solution is denatured.
• Renaturation: reformation of the double helix structure under favorable conditions (cooling, neutralization of pH, or dilution of denaturants).

DNA Replication

• DNA replicates in a semi-conservative way.
• Pre-existing parent strands separate. Each strand acts as a template for the biosynthesis of a new complementary strand.

Roles of DNA

• Encodes genetic information for cell growth, function, and reproduction.
• The amino acid sequence of proteins and nucleotide sequences of RNA are specified by the DNA sequence.
• Double-stranded helix structure with an internal structure.

DNA Size/Organization

• A cell's DNA is condensed into chromosomes to fit inside the cell.
• Chromatin: fibers of proteins (histones) and DNA which make up the chromosome.
• Histones (proteins) tightly associate with DNA, forming nucleosomes.
• Non-histone proteins assist in chromosome structure or regulate gene expression.

Gene

• A segment of DNA that codes for a protein or RNA.
• Prokaryotic genes are often continuous, while eukaryotic genes have introns (non-coding sequences) and exons (coding sequences). Exons, expressed regions, are the coding areas of a gene.
• Example: Genes for ovalbumin and β hemoglobin subunit have exons and introns.

Types of RNA

• Messenger RNA (mRNA): Carries genetic code from DNA to ribosomes for protein synthesis.
• Transfer RNA (tRNA): Carries amino acids to ribosomes, matching them to mRNA codons.
• Ribosomal RNA (rRNA): Part of the ribosome, the protein synthesis machinery.

Secondary Structures of RNA

• Single-stranded RNA folds back through complementary base pairing.
• Common secondary structures include stems (stem-loops), loops, bulges, and junctions.
• Example: tRNA has specific secondary structures critical for its function.
• Example: rRNA has complex secondary structures needed during protein synthesis.