More Regulating Gene Expression Bonus 1 is due

More Regulating Gene Expression Bonus #1 is due 10/02

We looked at the mechanisms of gene expression, now we will look at its regulation. Combinations of 3 nucleotides code for each 1 amino acid in a protein.

Fig 15. 1 Why change gene expression? • Different cells need different components • Responding to the environment • Replacement of damaged/worn-out parts

Two points to keep in mind: 1. Cellular components are constantly turnedover. 2. Gene expression takes time: Typically more than an hour from DNA to protein. Most rapidly 15 minutes. Fig 15. 1

• Gene expression can be controlled at many points between DNA and making the final proteins. • Changes in the various steps of gene expression control when and how much of a product are produced. Fig 15. 1

In bacteria, transcription and translation occur simultaneously. So most regulation of gene expression happens at transcription. Fig 13. 22

Transcription initiation in prokaryotes: sigma factor binds to the -35 and -10 regions and then the RNA polymerase subunits bind and begin transcription Fig 12. 7

Fig 14. 3 Operon: several genes whose expression is controlled by the same promoter

Fig 14. 3 E. coli lactose metabolism

Fig 14. 4 In the absence of lactose, the lac operon is repressed.

Fig 14. 4 Lactose binds to the repressor, making it inactive, so that transcription can occur.

Fig 14. 5 Repression or induction of the lac operon

Fig 14. 3 There is more to lac gene expression than repression

Fig 14. 8 Glucose is a better energy source than lactose

Fig 14. 8 Low glucose leads to high c. AMP binds to CAP which increases lac operon transcription

High glucose leads to low c. AMP, CAP inactive, low lac operon transcription Fig 14. 8

Fig 14. 3 The lac operon: one example of regulating gene expression in bacteria

Overview of transcriptional regulation Fig 14. 1 and 15. 1

Gene Expression is controlled at all of these steps: • DNA packaging • Transcription • RNA processing and transport • RNA degradation • Translation • Post-translational Fig 15. 1 Fig 16. 1

Tightly packaged DNA is unavailable. DNA packaging changes as the need for different genes changes. Fig 10. 21

Different levels of DNA packaging Fig 10. 21

Histones can be posttranslationally modified, which affects their abililty to bind DNA.

Fig 12. 15 Acetylation (-COCH 3): post-translational modifications of the histones loosen DNA binding

Acetylation of histones ( -COCH 3) causes a loosening of the DNA/histone bond…unpackaging the DNA.

Fig 15. 13 DNA methylation

DNA methylation often inhibits transcription Fig 15. 14

Epigenetics: the inheritance of DNA modifications, including methylaton Fig 15. 15

Four-stranded DNA: cancer, gene regulation and drug development by Julian Leon Huppert Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences Triennial Issue of 'Chemistry and Engineering’ DOI: 10. 1098/rsta. 2007. 0011 Published: September 13, 2007

Four-stranded DNA forms between sequences of guanines…G-quadruplexes 4 strand DNA Fig 1

The Gquadruplexes can form from 4, 2, or 1 DNA strand. 4 strand DNA Fig 2

Fig 10. 11 During DNA replication, the ends of the DNA are not completely copied.

Fig 10. 11 Telomeres are non-gene DNA at the ends of DNA strands. Telomeres are shortened during DNA replication.

Fig 11. 25 Telomeres can be lengthened by telomerase.

The telomeric cap structure is one place where G-quadruplexes can be found

Fig 10. 11 Telomeres are non-gene DNA at the ends of DNA strands. Short telomeres will cause cells to stop replicating or cell death. The critical size is unknown.

Drugs that can block the action of telomerase, by binding the G-quadruplexes, are being investigated to treat cancer.

Fig 12. 13 Eukaryotic promoters often contain G-rich areas

G-quadruplex in promoters 4 strand DNA Fig 5

If the promoter is defined as 1 kbase upstream of the transcription start site: • Quadruplex motifs are significantly overrepresented relative to the rest of the genome, by almost an order of magnitude. • almost half of all known genes have a putative quadruplex-forming motif • By comparison, the TATA box motif—probably the best-known regulatory motif and a staple of undergraduate textbooks—is found in only approximately 10% of genes. Four-stranded DNA: cancer, gene regulation and drug development by Julian Leon Huppert in Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences Triennial Issue of 'Chemistry and Engineering’ DOI: 10. 1098/rsta. 2007. 0011 Published: September 13, 2007

Oncogenes, the genes involved in cancer, are especially rich in potentially regulatory quadruplexes— 69% of them have such motifs Four-stranded DNA: cancer, gene regulation and drug development by Julian Leon Huppert in Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences Triennial Issue of 'Chemistry and Engineering’ DOI: 10. 1098/rsta. 2007. 0011 Published: September 13, 2007

G-quadruplex ligands TMPy. P 4 BRACO-19 Down regulates telomerase and some oncogene transcription G-quadruplex telomestatin Specifically binds to telomeres, naturally occurring in Streptomyces anulatus 4 strand DNA Fig 6

Model of specific G-quadruplex ligand binding to G-quadruplex and a specific DNA sequence 4 strand DNA Fig 7

Gene Expression is controlled at all of these steps: • DNA packaging • Transcription • RNA processing and transport • RNA degradation • Translation • Post-translational Fig 15. 1 Fig 16. 1

More Regulating Gene Expression Bonus #1 is due 10/02