Control of Gene Expression and Cloning

Definition of Gene Expression: This is the overall process by which information flows from genes to proteins, representing the transition from genotype to phenotype.
Functions of Gene Expression Control:
- Enables cells to produce specific kinds of proteins exactly when and where they are required.
- Facilitates cell differentiation and development in multicellular organisms.

General Characteristics:
- Regulation involves turning genes on and off.
- Prokaryotes do not undergo development; consequently, these cells lack "master genes."
- Regulation helps prokaryotes respond to environmental changes and adjust their metabolism accordingly.
The Operon Model:
- Definition: A cluster of genes with related functions along with specific DNA control sequences.
- Components within an operon are transcribed together.
- Prokaryotes primarily control gene expression by adjusting the rate of transcription.
The lac Operon in E. coli:
- Components: The operon includes a promoter, two operators, and three specific genes (gene 1, gene 2, and gene 3).
- Mechanism in the Absence of Lactose:
  1. A repressor protein binds to the two operators.
  2. This binding physically prevents RNA polymerase from attaching to the promoter.
  3. Transcription of the operon genes does not occur.
- Mechanism in the Presence of Lactose:
  1. When lactose is present, some is converted into a form that binds to the repressor protein.
  2. This binding alters the shape of the repressor, causing it to release the operators.
  3. RNA polymerase can then successfully bind to the promoter.
  4. The RNA polymerase transcribes the operon genes into mRNA.

Overview: The "switches" turning genes on or off are molecules or processes that trigger or inhibit individual steps of expression. Control occurs at six major levels:
Level 1: DNA Accessibility:
- Focuses on whether the DNA is accessible for transcription.
- DNA that is tightly wound around proteins called histones cannot be transcribed.
Level 2: Transcription Initiation:
- Focuses on whether the gene will be transcribed.
- Regulated by proteins called transcription factors, which can either activate or block the transcription process.
Level 3: RNA Processing:
- Focuses on whether the transcript will be processed.
- Only mature mRNAs are permitted to leave the nucleus.
Level 4: Translation Regulation:
- Focuses on whether the mRNA will be translated into a protein.
- MicroRNAs (miRNAs) can bind to mRNA and block its translation.
- Enzymes in the cytoplasm can also degrade mRNAs before translation occurs.
Level 5: Post-Translational Modification:
- Focuses on whether the protein will be modified.
- Many polypeptides require modification after translation (e.g., cleaving or adding chemical groups) to become functional.
Level 6: Protein Degradation:
- Focuses on whether the protein will be degraded.
- Proteins are intentionally degraded by the cell when they are no longer needed.

Terminology:
- Zygote: A fertilized egg cell resulting from the union of a female gamete (egg/ovum) and a male gamete (sperm).
The Process of Development:
- Mitosis: Alone, mitosis would only produce a large ball of identical cells.
- Differentiation: Necessary to produce a functional organism.
- Embryonic Development Components: Cell division, cell differentiation, and morphogenesis.
Genetic Equivalency:
- All cells within a complex multicellular organism contain the identical DNA; there is no loss or gain of DNA during differentiation.
- Variety in cell types (e.g., liver cells vs. skin or muscle cells) is determined by the specific combination of genes turned on (expressed) or off (repressed).
Control by Homeotic Genes:
- Development is driven by cascades of homeotic gene expression.
- Homeotic Gene: A gene encoding a product that causes other genes to be expressed.
- Function: They define the overall body plan and complete intricate tasks, such as the formation of an eye.

X Chromosome Inactivation (Barr Body):
- This process is initiated in early embryonic development when the embryo consists of approximately $200$ cells.
- Mechanism: Heavy methylation leads to the inactivation of most genes on one of the X chromosomes; non-coding RNA also sticks to the inactivated chromosome.
Dosage Compensation: This ensures that males and females have the same effective dose of genes found on the X chromosome.
Patchwork Mosaicism:
- Females are a mosaic of cell clumps: some where the maternal X is inactivated and some where the paternal X is inactivated.
- Example: The tortoiseshell pattern in female cats.
  - One X chromosome carries the allele for orange fur.
  - The other X chromosome carries the allele for black fur.
  - Random inactivation leads to specific populations of cells producing orange or black fur, resulting in the adult pattern.

Definition: The process of making an exact copy of a gene, a cell, a tissue, or an entire organism.
Biological Basis: Since all somatic cells possess a full set of the genetic code, it is theoretically possible to grow an entire new organism from a single cell.
Plant Cloning:
- Common practices include taking cuttings.
- Tissue Culture Process: Cells are removed from a mother plant (e.g., an orchid), placed in a growth medium as single cells, prompted to undergo cell division in culture, and grown into young plants and finally adults.
Animal Cloning Methods:
- Somatic Cell Nuclear Transplant (SCNT):
  - Replace the nucleus of an egg cell or zygote with a nucleus removed from an adult donor body (somatic) cell.
  - The process involves minimal nutrients in the medium and pulses of electric currents.
- Reproductive Cloning: The resulting embryo is implanted into a surrogate mother, and a clone of the donor is born.
- Therapeutic Cloning: Embryonic stem cells are removed from the embryo and grown in culture, where they are induced to form specialized cells for therapeutic use.

Notable Cloned Animals:
- Dolly the Sheep: Cloned in 1996; she gave birth to her first lamb, Bonnie, on April 13th, 1998.
- Andi: A rhesus monkey.
- Copy Cat (CC): The first cloned cat.
- Snuppy: The first cloned dog.
- Millie, Christi, and Carrel: Cloned pigs.
Potential Applications:
- Breeding superior livestock.
- Restoring extinct species.
- Developing genetically identical animals for scientific research.
- Increasing the population of endangered species.

Sources of Stem Cells:
- Embryos (Embryonic Stem Cells or ES cells).
- Blood collected from the umbilical cord and placenta at birth.
- Adult tissues (Adult Stem Cells).
Adult Stem Cells vs. ES Cells:
- Adult stem cells are further along the road to differentiation than ES cells.
- They can give rise to only a few related types of specialized cells.
- They function to generate replacements for some of the body's cells.
Ethics: Adult stem cells are considered less ethically problematic than ES cells because no embryonic tissue is involved in their harvest.