1. Chapter 18- Regulation of gene expression
You Must Know
Functions of 3 parts of an operon
Role of repressor genes on the operon
Impact of DNA methylation and histone acetylation on gene expression
Role of oncogenes, proto-oncogenes, and tumor suppressor genes

2. Bacteria (prokaryotes)
Characteristics
Peptidoglycan
Membrane, cell wall
Binary fission
Conjugation
Exchange of genetic material and information
F plasmid, F+ donates to F-
R plasmids- resistance

3. Bacteria Response to Environmental Change
Regulate Transcription
Bacteria are favored by Natural Selection
Reproduces quickly
Produce what it needs
Regulates enzymatic production by feedback inhibition or gene regulation
Gene expression by the operon model

4. Environmental Impacts on Bacteria
In our “gut”bacteria must respond to what we eat
Lacks tryptophan (aa in turkey that makes you sleepy) bacteria actives another pathway-feedback mechanism
You pig out on turkey, bacteria will stop manufacturing tryptophan- feedback inhibition

5. Bacteria in Colon Respond to what the host eats
Sounds like + and – feedback
Low tryptophan, must manufacture
High Tryptophan
Stop

6. Bacterial Genes Clustered into units called OPERONS 3 parts Operator
Controls RNA polymerase access to genes
Promoter
Where RNA polymerase attaches
Genes of the operon
DNA required for all enzymes produced buy the operon

7. Operon On switch for segment of DNA
Positioned in promoter or between the promoter and enzyme coding genes
Controls access point of RNA polymerase
Operator, promoter and genes they control is operon

8. Anatomy of an Operon Operator Controls access of RNA polymerase
Found within promoter or between promoter and protein coding genes of the operon

9. Operon
Promoter
RNA polymerase attaches

10. Genes of the Operon Entire stretch of DNA
Codes for all enzymes produced by the operon

11. Regulatory Proteins Located some distance from the operon
Produce repressor proteins to bind to the operator site
RNA polymerase
Blocked from the genes
Operon is OFF

12. Repressor Is the protein OFF switch Prevents gene transcription
Binds to the operator
Blocks RNA polymerase
Part of a separate regulatory gene
Can be active or not
Corepressor molecule works with repressor protein to switch off the operon

13. Repressible
Anabolic
Synthesize essential end products from raw materials
Suspend production of end product when it’s present conserves resources
On all the time, can be turned off

14. Repressible Operon

15. Bozeman
Lac Operon

16. Inducible Operon(enzymes)
Lactose
Normally off but can be activated
Catabolic
Repressor protein is active
Inducer binds to and inactivates the repressor protein
RNA poly can access

17. Inducible Operon

18. 2 Types of Operons Tryp Operon-Normally on Lac Operon Normally off
Repressible
Inducible
Tryp Operon-Normally on
Can be inhibited
Anabolic for building organic molecules
repressor protein is inactive.
Produced molecule can act as a corepressor and binds to the repressor protein and actives it
Binds to the operator site and shuts down the operator
Lac Operon
Normally off
Can be activated
Catabolic-breaking down macromolecules
Repressor protein is active
small molecule called inducer ginds to and inactivates the repressor
Repressor out of the operator site, RNA polymerase can access the genes of the operon

19. How do you regulate operons?
Feedback mechanisms inhibition
Anabolic (biosynthetic)
Shuts down synthesis of tryptophan
Regulate the expression of the genes encoding the protein
Control enzyme production during transcription
mRNA encoding
OPERON!!!

20. Positive Gene Regulation
When glucose (preferred source of food for E. coli) is scarce, CAP is activated by cyclic AMP-changes shape and binds to it
Activated CAP
Attaches to the promoter of the lac operon
Increases the affinity of RNA polymerase
Accelerates transcription
CAP detaches when glucose levels increase
Transcription back to normal
Positive Gene Regulation
Needs a stimulatory protein such as catabolite activator protein (CAP)
ACTIVATOR OF TRANSCRIPTION

21. What does this all mean? Survival!!!
If glucose is not present, lactose is broken down
Glucose is plentiful, CAP is inactive, enzyme activity slows down for other sugars

22. Eukaryotic Gene Expression
Regulated at many stages

23. What is the fundamental packaging of DNA?
Chromatin Structure
Genes within highly packed heterochromatin are usually not expressed
Nucleosomes
DNA bound to histone
Tighter the winding. Less access for transcription
Chemical modifications and DNA Chromatin
Methylation, acetylation

24. Eukaryotic Regulation of Gene Expression
Regulation of Chromatin Structure
Histone acetylation, DNA Methylation, Epigenetic inheritance
Regulation of Transcriptional Initiation
Control elements, general transcription factors, specific transcription factors, Enhancer
Combinatorial control, Nuclear architecture and gene expression
Post-Translation Regulation
RNA splicing, mRNA degradation

25. Chromatin Modification
Nucleus
Histone Modification
Histone Acetylation
Acetyl groups are attached to positively charged lysines in histone tails
Loosens chromatin
Promotes initiation of transcription

26. Chromatin Modifications
Nucleus
DNA Methylation
Addition of methyl groups (methylation)
Condenses chromatin
Reduces transcription
Addition of phosphate (phosphorylation) next to methylated amino acid loosens chromatin

27. Histone Code Hypothesis
Proposes that specific combinations of modifications, as well as the order in which they occur determines the chromatin configuration
Influences transcription

28. Chromatin Modifications
Epigenetic Inheritance
Chromatin modifications do not alter DNA sequence
Can be passed on to future generations
No change in nucleotide sequence
Saw this with the sepia eyes over-riding an X-linked trait

29. Transcription -Nucleus
DNA Control elements in enhancers
Bind specific transcription factors
Bend the DNA
Activators contact proteins at the promoter initiation transcription

30. RNA Processing In Nucleus
Alternate RNA splicing
primary transcript is edited, mis-sliced
mRNA degradation
Sequences in the 5’and 3’ end determines life span

31. Post-Translational Regulation-cytoplasm
Alternative RNA splicing
Protein processing and destruction
Proteasomes recognize proteins tagged with ubiquitin
Mutations making specific cell cycle proteins impervious to proteasomes can lead to cancer

32. Noncoding RNA in Gene Expression
Play multiple roles
1.5% of the human genome codes for protein
Regulation and expression by ncRNA (noncoding RNA)

34. Form and Function of MiRNA

35. MRNA impact by miRNA and RNAi
miRNA, RNAi, siRNA
Destroys double stranded foreign RNA (virus)
Degrades mRNA
Prevents translation
piRNA (piwiRNA)-induces formation of heterochromatin and prevents parasitic DNA or transposons

36. Translation
miRNA or siRNA can block the translation of specific mRNA’s
Can target specific mRNA’s for destruciton

37. Who cares? Scientists can use siRNA (small interfering) too
Cure disease with inappropriate gene expression

38. Impacts of differential gene expression on multicellular organisms
Cell division
Increase cell number
Cell differentiation
Specialization of cells
Morphogenesis
Organization into tissues and organs

39. Differential Gene expression
Leads to different cell types in multicellular organism
Cell division
Number of cells
Cell differentiation
specialization
Morphogenesis
Tissues and organs

40. What Controls differentiation and expression?
Cytoplasmic determinants
Maternal substances in the egg
Cell-cell signals
Molecules, growth factors
Determination
Cell-cell signals and is irreversible
Pattern formation
Hox

41. Cytoplasmic Determinants
Maternal substances in the egg that influence development
Induction
Determination
Signals that change the target cells causing cellular development by embryo

42. Determination Series of observable differentiation of a cell
Irreversible differentiation by cell-cell signals

43. Pattern Formation
Body plan as set up by cytoplasmic determinants and inductive signals
Hox gene
Molecular cues that control pattern formation are called positional information

46. Hox gene

47. Cancer Genetic changes that affect the cell cycle
Gene regulation goes bad

48. Cancer
Uncontrolled mitosis by a mutation in a gene whose products normally inhibit cell division

49. Oncogenes Genes that cause Cancer
Proto-oncogenes code for proteins for normal cell growth but can become oncogenes when a mutation occurs that increases the product of proto
How does a proto-oncogene become an oncogene?
1. movement of DNA
2. amplification of proto-onco
3. point-mutation of proto-onco

50. Tumor suppressor genes
Cells secrete products to inhibit cell division
BRACA1 and 2 (breast cancer gene) mutations in those genes increase risk
Functions of these genes:
Repair damaged DNA
Control adhesion of cells to eachother or extracellular matrix

51. Tumor Suppressor p53 gene
Named for the 53,000 dalton molecular wieght of its molecular product
Halts cell cycle-Guardian Angel of the Genome
Binds cyclin-dependent kinases
Turns on genes for DNA repair
Activates suicide genes-APOPTOSIS

53. Multistep model of Cancer Development

54. What happens when there is interference with normal cell-signaling pathways?
Ras protein- encoded by ras gene (rat sarcoma)
Relay switch in membrane for chemical cascade of kinases that stimulate cell cycle
Must be triggered by the RIGHT growth factor, hyperactive ras gene- increases cell division
P53 gene
Promotes synthesis of cycle-inhibiting proteins
Knock out P53- activates RAS protein

55. BRCA-1 and 2 Tumor suppressor genes Blood test to check for mutation
the long (q) arm of chromosome 17 at position 21.
BRCA-2- chromosome 13