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

3. Eukaryotic Gene Regulation - Transcription
Eukaryotes have 3 different RNA Polymerases.
Eukaryotic RNA transcripts are processed:
- 5’ capping
- Splicing out of introns
- 3’ polyadenylation
Eukaryotic RNA polymerase II:
- counterpart to prokaryotic RNA polymerase
- much larger than prokaryotic counterpart
* RNA synthesis
* coordinate processing events

4. 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

5. 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

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

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

8. Distance-independent Cis-acting Elements
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.

9. Distance-independent Cis-acting Elements
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.

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

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

12. 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.

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