1. Control of Gene Expression
Chapter 16

2. Many levels of control Transcription initiation (most common)
Post transcription modification
Pre-translation
Protein degredation

3. Translation initiation
RNA must be able to bind to DNA at the gene promotor
Regulatory proteins
Bind to specific sequences
100’s have been identified
Either block transcription or stimulate it

4. Prokaryotes vs. Eukaryotes
Prokaryotes: Regulation is a direct function of the need to adjust to changing environment
Eukaryotes:
Maintenance of homeostasis
Compensate for physiological changes
Growth and development regulation (fixed genetic program)
Apoptosis

5. Major Groove The nucleotides hydrogen donors
and acceptors are accessible through the major groove

6. DNA Binding motifs DNA binding domain
Functionally distinct region in the DNA binding motif the specifically bind to DNA in a set location

7. Helix-Turn-Helix

8. Homeodomain motif

9. Zinc Finger

10. Leucine Zipper Motif

11. Prokaryotic regulation
Positive control: increases frequence of initiation
Activators
Stimulate initiation of transcription
Negative control: decreases frequency of initiation
Repressors
Bind to operators
Require effector molecules
Allosteric proteins
Active site binds to DNA; allosteric site binds to effector

12. Operons Multiple genes Single transcription unit
Often same metabolic pathway

13. Repression lac operon: negatively regulated by lac repressor
presence of lactose causes removal of repressor from lac operon
trp operon: positively regulated by trp repressor
Presence of tryptophan causes the binding of repressor from trp operon

14. lac operon
Effector: allolactose

15. Glucose repression Prevents repressor from binding
Allows repressor binding

16. trp operon

17. Eukaryotic gene regulation
Complicated by chromatin structure
Amount of DNA
Complex developmental programs
Multiple tissues

18. Transcription factors
General
Necessary for assembly of transcription apparatus
Recruitment of RNA polymerase II to a promoter
Initiation complex
TFIID (recognizes and binds to TATA box)
Several other transcription factors and transcription-associated factors (TAFs)

19. Specific transcription factors
Tissue or time dependent
Stimulate higher levels of transcription
Have a domain organization
DNA Binding domain
Activating domain (interacts with transcription apparatus)
Interchangable

20. Binding sites Promoters Enhancers
Binding sites for general transcription factors
Mediated binding of RNA pol II
Enhancers
Binding sites for specific transcription factors
Act over large distances
DNA forms a loop

22. In Summary Activators: Coactivators: General factors
Specific transcription factors
Bind to enhancers at distance sites
Increase rates of transcription
Coactivators:
Transmit signals from activators proteins to the general factors
General factors
Position RNA polymerase at start of protein coding sequence

23. Eukaryotic Chromatin structure
Nucleosomes may block binding
of transcription factors

24. Histone modifications
Modified to block promotors
Chromatin remodeling complex
Large complexes of proteins
Modify hitsones and DNA
Changes chromatin
Repositions nulceosomes

25. Histone modifications
Methylation
Addition of methyl group (CH4) to cytosine
Found on most inactive mammalian genes
Blocks “accidental” transcription of inactive genes
Prevents transcription activators from binding to DNA

26. Histone Modifications
Acetylation
Makes DNA accessible to transcription factors
“Histone code”
Control of chromatin structure
Access to transcription sequences on DNA

28. Post-transcription Regulation
RNA interference
Double stranded RNA
Gene silencing: Strong inhibition of genes

29. Dicer
miRNAs: bind directly to
mRNA and prevent
translation

30. Alternative slicing Different tissues Different timing in cells
Calcitonin CGRP
Different tissues, different functions, same transcription unit

31. RNA editing Apolipoprotein B 5-HT Serotonin APOB100: only in the liver
LDL
APOB48: only in small intestine
“edited” form of APOB100
Alteration of mRNA changing a codon for glutamine to stop
5-HT Serotonin
Multiple edits
12 different isoforms

33. mRNA transport
mRNA transcript cannot move through nuclear pore while splicing enzymes are attached
Transcript must be recognized by nuclear pore receptors
Poly A tail
Only 5% of total mRNA transcripts reach cytoplasm

34. Degradation of mRNA mRNA half life 3 min: prokaryotic mRNA transcripts
10 hours: eukaryotic B-globin transcripts
1 hour: eukaryotic regulatory genes
Targeted for degradation
Enables levels of regulatory proteins to be altered quickly in response to changes

35. Protein degradation
Turnover of eukaryotic proteins is essential to cell function
Chemical alteration
Incorrect folding
Aggregation into complexes
Parkinson’s disease
Mad cow disease
Alzheimer dementia
Decreased need for
particular protein

36. Proteases Breaking peptide bonds Lysosome
Nonspecific
Need to protect necessary proteins; remove “bad” proteins

37. Ubiquitin Added in chain to target protein Ubiquitin ligase
Requires ATP
Polyubiquinated: signal for destruction

38. Proteasome
Nonmembrane
organelle