1. Molecular Basis for Relationship between Genotype and Phenotype DNA RNA protein genotype function organism phenotype DNA sequence amino acid sequence transcription translation

3. Eukaryotic Gene Regulation - Transcription Expression of genes can be: - constitutively on (housekeeping genes... ~15,000 in humans) - regulated (temporally or spatially... up to 2000+ unique proteins in differentiated cell) Differentiation is a manifestation of genes being selectively turned off. Regulation of gene expression involves: - cis-acting regulatory elements - trans-acting transcription factors

4. Cis-acting Regulatory Elements Promoter - located near transcription-initiation site - binds RNA polymerase II Promoter-proximal Elements - located near promoter - binds proteins that assist RNA polymerase binding Distance-independent Elements - enhancers: increase transcription rates - silencers: decrease transcription rates

5. In all cells, constitutive expression of transcription factors that bind to upstream promoter elements ensures active transcription at all times. Promoter and Promoter-proximal Elements

6. Effect of point mutations on transcription rate of  -globin gene. In general, transcription rate is reduced when base sequence is changed in the core promoter and promoter-proximal elements. Promoter and Promoter-proximal Elements

7. Both enhancers and silencers affect transcription rate. Each has unique DNA sequence for the binding of regulatory proteins. Enhancer sequences contain multiple binding sites for trans-acting regulatory proteins. Enhancers could be located upstream from the promoter, downstream from the gene, or even within an intron of a gene. Distance-independent Cis-acting Elements

8. Interaction between regulatory proteins that bind to enhancer elements and promoter- proximal elements with RNA polymerase initiates transcription at appropriate levels. Architectural proteins allow bending of the DNA to bring all components together, both spatially and functionally. Distance-independent Cis-acting Elements

9. These proteins contain one or more functional domains: 1.Recognize DNA regulatory sequence 2.Interact with transcriptional apparatus proteins (RNA polymerase, proteins associated with RNA polymerase) 3.Interact cooperatively with other regulatory proteins bound to DNA sequence 4.Influence chromatin condensation 5.Act as sensor of intracellular physiological conditions Regulatory Proteins that Modulate Transcription

10. Transcription factors have: 1.DNA binding domain (interact with promoter-proximal elements or enhancers/silencers) 2.Transactivation domain (activate or repress transcription, involved in protein/protein interaction) Transcription Factors

11. Structural Families of Transcription Factors and Regulatory Proteins: Helix-Turn-Helix: Zinc-Finger: Leucine Zipper: Helix-Loop-Helix: Many homeotic genes code for TF's of this class. Many steroid hormone receptor protein TF's belong to this class. Proto-oncogenes such as c-jun and c-fos are genes that encode TF's of this class. Certain proto-oncogenes and genes involved in differentiation encode TF's of this class.

12. Structural Families of Transcription Factors and Regulatory Proteins: Zinc-Finger: Leucine Zipper: Helix-Loop-Helix: