Gene Regulation and Operons

The Lac Operon

• Discovered by Jacob and Monod in 1961.
• Regulates the production of enzymes needed to break down lactose.
• Operon is active when lactose is present, inactive when lactose is absent.
• Repressor protein binds to the operator, blocking RNA polymerase transcription when lactose is absent.
• Lactose binding to the repressor causes a conformational change, preventing it from binding to the operator and allowing transcription.
• Three enzymes are regulated as a single unit: LacZ (β-galactosidase), LacY (Galactose permease), LacA (Thiogalactoside transacetylase).

Gene Regulation in Eukaryotes

• Different cell types have different sets of genes expressed, despite having the same complete set (~37 trillion cells).
• Various mechanisms control gene expression, including DNA packing, transcription factors (TFs), alternative RNA splicing, microRNAs, and translation regulation.

Eukaryotic Transcription Complexes

• TFs are essential for gene expression timing, and 10% of the human genome functions as TFs.
• Enhancers are DNA sequences where TFs bind.
• TFs assist RNA polymerase in binding to the promoter to initiate transcription.
• Homeodomain proteins, coded by HOX genes, are crucial TFs in development.

Homeobox (HOX) Genes

• Regulate body plan along the "head-tail" axis.
• Essential for proper development in all organisms.
• For example, the HOX gene Ubx affects wing development, and turning it off causes a second pair of wings.

HOX Genes and Development

• Expressed in specific body regions during embryological development.
• Highly conserved across species, controlling body regions consistently.
• Contribute to the evolution of body plans during the Cambrian explosion.

Epigenetics

• The study of heritable changes in gene expression without DNA sequence alterations.
• Changes phenotype but not genotype.
• Environmental factors (diet) can change epigenomes.
• Epigenetic control involves methyl groups, acetyl groups, and small RNA molecules which can activate or repress genes.

RNA Interference (RNAi)

• RNA molecules suppress gene expression by destroying mRNA or blocking translation.
• Discovered by Craig Mello and Andrew Fire, who won the Nobel Prize in 2006.
• Used as a therapeutic tool to treat various diseases by silencing malfunctioning genes.
• RNAi enables researchers to deactivate specific genes and understand their functions.

Role of MicroRNAs (miRNA)

• Major role in regulating gene expression.
• siRNA (small interfering RNA) silences specific genes, while miRNA can silence multiple genes.

Transcription

• RNA polymerase unwinds DNA, binds to the promoter, and adds complementary base pairs to the template strand, creating mRNA.
• Template strand (antisense) is complementary to the mRNA strand, with thymine (T) replaced with uracil (U).

Post-Transcription

• Introns (non-coding regions) are removed via spliceosomes, leaving exons (coding regions).
• mRNA is capped with GTP at the 5' end and a poly-adenine tail at the 3' end, protecting it from degredation and signaling nuclear export.

Mutations: Damage and Repair

• Mutations can be caused by replication errors or mutagens.
• Mismatch repair uses DNA polymerase and other proteins to correct mismatched bases during replication.
• Base excision repair and nucleotide excision repair remove damaged bases.
• Homologous recombination and non-homologous end joining repair broken DNA strands.

Cell Division

• Karyotype: normal number of chromosomes in the nucleus of eukaryotic cells, consisting of 23 pairs – 22 pairs of autosomal chromosomes and 1 pair of sex chromosomes.
• Diploid cells contain two sets of chromosomes (46), while haploid cells contain one set (23).

Mitosis

• Occurs in somatic cells and involves replicating the full diploid chromosome complement.
• Stages:
  • Interphase: G1 (growth), S (DNA replication), G2 (growth and organelle replication).
  • Prophase: Chromosomes become visible, centrioles move to opposite poles.
  • Metaphase: Chromosomes line up at the center, spindle fibers attach to centromeres.
  • Anaphase: Sister chromatids separate.
  • Telophase: Chromosomes gather at opposite ends, lose rod shape, two nuclear membranes form.
  • Cytokinesis: Cell membrane pinches, divides in half, forming two new identical cells.

Meiosis

• Occurs in sex organs to produce haploid germ cells (sperm/egg).
• Stages:
  • Interphase: chromosomes duplicate.
  • Meiosis I:
    • Prophase: chromosomes pair up, crossing over.
    • Metaphase: chromosomes line up in pairs.
    • Anaphase: chromosomes separate.
    • Telophase and Cytokinesis: two non-identical diploid cells are formed.
  • Meiosis II:
    • Prophase, Metaphase, Anaphase, Telophase, and Cytokinesis: four non-identical haploid cells are formed.

Cancer

• Characterised by unchecked growth and division due to disrupted interphase checkpoints.
• Chemotherapy can interfere with cell division and replication, but can also damage normal cells.

Gene Regulation

• Controlling which genes are "on" or "off" for protein production.
• Operons are a mechanism of gene regulation in prokaryotes.
• Lac operon example:
  • Repressor binds to the operator, preventing transcription when lactose is absent.
  • Lactose binding to the repressor inactivates it, allowing transcription.

Prokaryotic Transcriptional Regulation

• Ability to change metabolic activities in response to the environment.
• Inducible control (Lac operon): repressor is inactivated by inducer.
• Repressible control (Trp operon): repressor is activated by the product.

DNA Structure and Function

• DNA: Deoxyribose Nucleic Acid. Carries genetic information in genes.
• RNA: ribonucleic acid. Copies of DNA for protein synthesis.
• DNA structure: double helix, sugar-phosphate backbone, with purines (adenine, guanine) pairing with pyrimidines (cytosine, thymine) via hydrogen bonds.

DNA Replication

• 5' to 3' direction.
• Helicase unwinds the DNA strands.
• Single-strand binding proteins keep the strands separated.
• Primase adds RNA primers.
• DNA polymerase adds complementary nucleotides to the 3' end, leading to elongation.
• Okazaki fragments are formed on the lagging strand, joined by ligase.

Packaging DNA

• Histones are proteins around which DNA is wrapped and is the first step in DNA packaging, forming a "beads on string" structure.
• Nucleosomes are more tightly wound histones and DNA.
• Chromatin is tightly wound nucleosomes forming a fiber.
• Chromosomes are supercoiled chromatin that only forms when cells are dividing.

Translation

• mRNA carries information to ribosomes where translation into proteins takes place.
• tRNA carries specific amino acids to the ribosome, guided by codons on the mRNA.

Central Dogma

• Proposed by Francis Crick.
• The flow of genetic information from DNA to mRNA to protein.

Genetic Code

• Information encoded in nucleotide base sequences of DNA.
• Translated into amino acids by codons (groups of three nucleotides).
• Amino acids form proteins in ribosomes.

Genes and Genetic Variation

• Genes are functional and physical units of heredity on chromosomes.
• Mutations are changes in the nucleotide sequences, which can be substitutions, insertions, or deletions.