DNA Replication and Gene Expression

DNA Replication

• Definition: The biological process of producing two identical replicas of DNA from one original DNA molecule.

• Key Terms:

  • S-phase: The synthesis phase of the cell cycle during which DNA replication occurs.
  • Nucleotide: Basic structural unit of DNA and RNA, consisting of:
  • Phosphate group
  • Deoxyribose or ribose sugar
  • Nitrogenous base
  • DNA Polymerase: Enzyme that synthesizes DNA molecules from deoxyribonucleotides.
  • Template Strand: The strand of DNA used by DNA polymerase to synthesize a new complementary strand.
  • 5' to 3' Direction: Orientation of nucleotide addition where new nucleotides are added to the 3' hydroxyl group of the growing chain.
  • Primer: Short nucleic acid sequence providing a free 3' hydroxyl group for DNA polymerase initiation.
  • Complementary Base Pairing: Specific hydrogen bonding between bases:
  • DNA: Adenine (A) with Thymine (T), Guanine (G) with Cytosine (C)
  • RNA: A with Uracil (U), G with C

• Enzymes Involved in Replication:

  • DNA Helicase: Unwinds the double helix at the replication fork.
  • Leading Strand: Synthesized continuously in the 5' to 3' direction towards the replication fork.
  • Lagging Strand: Synthesized discontinuously in short fragments (Okazaki fragments) in the 5' to 3' direction away from the fork.
  • Okazaki Fragment: Short segments of DNA synthesized on the lagging strand.
  • DNA Ligase: Joins sugar-phosphate backbones of DNA fragments, e.g., Okazaki fragments.
  • Telomere: Repetitive DNA sequences at chromosome ends, protecting them from deterioration.
  • Telomerase: Adds repetitive DNA sequences to chromosome ends, preventing shortening after replication.
  • Topoisomerase: Alters supercoiling of DNA, relieving torsional stress during replication/transcription.

• DNA Repair Mechanisms:

  • Mismatch Repair (MMR): Corrects replication errors (insertion/deletion of bases, misincorporation).
  • Base Excision Repair (BER): Removes damaged or modified single bases.
  • Nucleotide Excision Repair (NER): Removes bulky DNA lesions (e.g., UV-induced pyrimidine dimers).

• Gene Expression:

  • Process by which information from a gene is used in synthesizing a functional gene product (usually a protein).

• Processes of Gene Expression:

  • Transcription: Synthesis of RNA from a DNA template.
  • Translation: Synthesis of a protein from an mRNA template.
  • RNA Polymerase: Enzyme synthesizing RNA from a DNA template.
  • Promoter: DNA sequence signaling the beginning of a gene and binding for RNA polymerase.

Lac Operon

• Definition: A cluster of genes in bacteria involved in lactose metabolism, regulated by the presence/absence of lactose.

• Key Components:

  • Operator: DNA sequence binding a repressor protein to control operon transcription.
  • Repressor Protein: Binds to operator sequence and inhibits gene transcription.
  • Transcription Factors: Proteins binding to specific DNA sequences, controlling transcription rates.
  • Enhancer Sequence: DNA sequence that binds activator proteins, increasing gene transcription (distant from promoter).

• Chromatin: Complex of DNA and proteins (histones) forming chromosomes in eukaryotic cells.

  • Nucleosome: Basic repeating unit of chromatin (DNA wound around histone core).
  • Histone Acetylation: Addition of acetyl groups to histones, associated with open chromatin and increased gene expression.
  • DNA Methylation: Addition of a methyl group to cytosine base in DNA, linked with transcriptional repression.
  • CpG Sequence: DNA region where cytosine is followed by guanine; often targets for DNA methylation.
  • DNA Methyltransferase (DNMT): Enzyme that transfers a methyl group to DNA.

• Nucleotide Structure:

  • Nucleoside: Nitrogenous base linked to a sugar (ribose or deoxyribose).
  • Nucleotide: Nucleoside with one or more phosphate groups.
  • Pyrimidine: Nitrogenous base with a single-ring structure (C, T, U).
  • Purine: Nitrogenous base with a double-ring structure (A, G).
  • PRPP (Phosphoribosyl Pyrophosphate): Activated sugar key in purine and pyrimidine nucleotide synthesis.
  • CPS II (Carbamoyl Phosphate Synthetase II): Enzyme catalyzing first committed step in pyrimidine biosynthesis.
  • OMP (Orotidine Monophosphate): Pyrimidine biosynthesis intermediate.
  • UMP (Uridine Monophosphate): Pyrimidine nucleotide precursor.
  • THF (Tetrahydrofolate): Coenzyme from folic acid carrying one-carbon units essential for purine and thymine synthesis.
  • IMP (Inosine Monophosphate): First purine nucleotide synthesized, precursor for AMP and GMP.
  • Ribonucleotide Reductase: Enzyme reducing ribonucleotides to deoxyribonucleotides.