Biology Chapter on Nucleotides and DNA Structure

Nucleotide Structure

• Nucleotides consist of a 5-carbon sugar (deoxyribose), a phosphate group, and a nitrogenous base (adenine, thymine, cytosine, or guanine).

Chargaff’s Rule

• Erwin Chargaff discovered that adenine equals thymine and cytosine equals guanine, demonstrating equal proportions of purines (A and G) and pyrimidines (C and T).

DNA Structure Contributions

• Linus Pauling identified helical structures in proteins in 1951.
• Rosalind Franklin and Maurice Wilkins used X-ray diffraction to reveal DNA’s helical structure with nitrogen bases inside and a sugar-phosphate backbone outside.
• James Watson and Francis Crick proposed the double helix structure of DNA in 1953, featuring antiparallel complementary strands.

Genetic Material Organization

• Genes are specific DNA sequences coding for proteins and RNA molecules.
• Most of an organism's genome consists of non-coding regions.
• Prokaryotic cells, such as Escherichia coli, have a circular, double-stranded DNA chromosome that is tightly packed.
• Eukaryotic cells have linear, double-stranded DNA organized with histones into nucleosomes.

Prokaryotic DNA

• E. coli contains a circular DNA molecule that has to be tightly packed within the nucleoid through coiling and supercoiling.
• DNA supercoiling is controlled by topoisomerase I and II enzymes.
• Prokaryotes may contain plasmids, small DNA molecules with non-essential genes.
• Prokaryotic genomes primarily consist of gene regions and regulatory sequences that activate certain genes.

Eukaryotic DNA

• Eukaryotic cells bear double-stranded linear DNA compacted in the nucleus, involving various levels of organization with histones forming nucleosomes.
• Telomeres at chromosome ends protect against degradation.

DNA Replication

• Involves producing two identical DNA molecules during the cell cycle.
• Proposed models include semi-conservative, conservative, and dispersive.
• Meselson and Stahl used density gradient centrifugation to support the semi-conservative model, demonstrating DNA strands containing one old and one new strand.

Prokaryotic Replication

• Occurs with a single circular DNA and begins at one origin, proceeding bidirectionally.
• Replication involves initiator proteins and helicase to unwind DNA, forming replication forks.

Steps of DNA Replication

• Initiation: Unwinding starts at the origin, with helicase breaking hydrogen bonds.
• Elongation (Leading Strand): DNA polymerase III builds a complementary strand in the 5′ to 3′ direction.
• Elongation (Lagging Strand): Synthesized in short Okazaki fragments; requires RNA primers and involves DNA polymerase III.
• Termination: Completion of new DNA strands leads to separation and dismantling of replication machinery.

Errors in DNA Replication

• Human cells replicate DNA quickly (error rate ~1 in 1 billion).
• Errors can lead to mutations from base mispairing or strand slippage.

Error Correction during Replication

• DNA polymerase I and II possess proofreading abilities to correct errors.
• Mismatch repair proteins address deformities in newly synthesized DNA.

Genetic Code

• DNA base sequences dictate the genetic code, with triplet sequences coding for specific amino acids.
• The sequence of amino acids determines protein structure.

Central Dogma of Genetics

• Genetic information flows from DNA to RNA to protein; this flow is one-directional and irreversible.

Protein Synthesis

• Entails transcription, RNA processing, and translation.

Transcription Process

• RNA strands are synthesized from DNA templates at the promoter and terminator regions.
• RNA polymerase links nucleotides into RNA after unwinding DNA.

RNA Processing

• Pre-RNA molecules undergo splicing to remove introns, allowing mature RNA to exit the nucleus.

Translation

• Initiation: Links mRNA, tRNA, and ribosomal subunits; initiator tRNA attaches at the start codon.
• Elongation: Involves sequential addition of amino acids.
• Termination: Triggered by stop codons, releasing polypeptide and ribosomal complex.

Applications of DNA Technology

• Medicine: Diagnosis of diseases, gene therapy for conditions like heart disease and cancer, production of pharmaceuticals.
• Forensics: DNA fingerprinting with simple tandem repeats; analysis of variable genome regions.
• Environmental: Genetically engineered organisms for waste treatment and pollution cleanup.
• Agricultural: Transgenic organisms for enhanced productivity and disease resistance.

Polymerase Chain Reaction (PCR)

• Amplifies specific DNA segments, producing billions of copies quickly.
• Essential in genetic testing for conditions such as Huntington's, cystic fibrosis, and HIV.