1. Chapter 15
Gene Control

2. I. Prokaryotic Gene Control
A. Conserves Energy and Resources by
1. only transcribing genes when necessary
a. don’t make mRNA for tryptophan
producing enzymes if tryptophan can
be absorbed from environment
2. only producing proteins when needed
a. don’t need lactose digesting enzymes
if no lactose is present

3. B. control enzymes already in cell : post-translation control
1. allosteric enzymes
a. activated
b. inhibited
2. feed back inhibition
a. end product of
anabolic path is
the inhibitor
3. adjustment to short
term changes

4. C. control production of enzymes: transcription control
1. control transcription of genes
a. repressors bind to operators and stop
transcription
b. enhancers bind to promotor to speed
2. slower/longer lasting effects: more stable environment

5. D. Negative control
1. negative slows or stops function
2. feed back inhibition (allosteric enzymes)
3. repressors blocking transcription (gene control)
E. positive control
1. SPEEDS up production
2. just allowing production does not count!!
3. Enhancers bound to promoter
4. allosteric activators

6. F. Operon model : clusters of functionally related genes controlled as a group (3 parts)
1. DNA code for the genes
2. promotor – stretch of DNA before genes
a. attracts RNA polymerase
b. needed to start transcription
3. operator – DNA sequence near promotor
a. binding site for repressor protein

7. G. Regulatory Genes : make repressors
found up stream from operon they regulate

8. H. trp Operon : trp = tryptophan amino acid
1. Repressible operon bcs it is normally active
2. genes make trp
3. low trp level in cell : operon active
a. repressor is inactive
b. promoter is open to RNA polymerase
c. genes to make trp are copied

9. 4. High trp level in cell : operon repressed
a. trp repressor is allosteric
1. binding to trp activates repressor
2. active repressor binds to operator
3. blocks RNA polymerase
4. genes not transcribed

10. I. Lac operon : lactose (galactose + glucose)
1. Inducible operon : usually off
a. repressor is active unless lactose bound to it
2. genes make
a. β-galactosidase cleaves lactose in 1/2
b. permiase membrane transport protein
for lactose
c. third gene
unknown

11. a. lactose binds to allosteric repressor i. inactivates repressor
3. presence of lactose:
a. lactose binds to allosteric repressor
i. inactivates repressor
ii. Repressor releases operator
iii. RNA polymerase copies all 3 genes

12. J. Positive control of lac operon
1. lac operon is an inducible operon
= can be activated
2. lac operon exhibits positive control
= can be speeded up
3. If glucose is present E. coli prefer to use it
a. lack of glucose causes E. coli to speed up
use of lactose
b. lack of glucose causes build up of cAMP
(cyclic AMP) = signal molecule
c. cAMP signals speed up operon translation

13. c. cAMP binds to regulatory protein CAP
catabolite activator protein
i. CAP becomes active
ii. CAP binds to start of promotor
iii. So promotor more attractive to RNA polymerase
iv. speeds up transcription
d. build up of glucose in cell causes lack of cAMP so CAP becomes inactivated

14. Prokaryotic Gene control review
Prokaryotic gene default setting is On/Off?
2 main points at which Prokaryotes regulate gene expression? Transcription/translation/post-translation?
Transcription control
regulatory proteins bind to…
regulatory protein that exerts negative control =
regulatory protein that exerts positive control =
Post-translation control:
regulatory molecule binds to…
regulatory molecule that exerts negative control =
regulatory molecule that exerts positive control =

15. Prokaryotic Gene control review
Prokaryotic gene default setting is On/Off?
2 main points at which Prokaryotes regulate gene expression? Transcription/translation/post-translation?
Transcription control
regulatory proteins bind to… DNA
regulatory protein negative control = repressor
regulatory protein positive control = activator
Post-translation control:
regulatory molecule binds to…allosteric site
regulatory molecule negative control = inhibitor
regulatory molecule positive control = activator

16. Repressible operons
a) repressor inactive w/o allosteric binding
b) normally on
c) usually anabolic
Inducible operons
a) repressor active unless bound
b) normally off
c) usually catabolic

17. II. Eukaryotic Gene Control
A. Gene expression regulated at many stages
1. Transcription control
a. chromatin structure regulation
b. transcription initiation control
2. Post-transcriptional control
a. RNA transcript processing
b. mRNA degradation
c. Translation initiation
3. Post-translational control
a. allosteric P, b. P processing, c. P degradation

18. B. Chromatin structure control
1. Heterochromatin – Chromatin that remains tightly compacted even in interphase
a. genes not transcribed
2. acetylation –
a. acetyl group (-COCH3) bonded to histone
b. loosens up chromatin winding
c. promotes transcription
3. DNA methylation –
a. –CH3 bonds to DNA blocking transcription
b. methylated regions passed on to daughter
cells

20. C. Initiation control (transcription)
1. control elements : non-coding DNA up-stream from promotor that bind transcription factor proteins
a. distal control elements are far up-stream
i. often act as enhancers (DNA)
b. proximal control elements : near promotor

21. 2. transcription factors: proteins
a. needed for transcription initiation
b. general transcription factors (GTF)
needed for all transcription of genes
i. GTFs bind each other & RNA Polym. II
to form initiation complex
ii. Initiation complex binds to control
elements near promotor: start transcription

22. iii. One protein of the GTF will bind to a
section of promotor called the TATA box.
(fig 14.9 and 15.10)
iv. General Transcription Factor complexes
allow slow transcription of gene
f. Specific Transcription Factors
needed for
rapid transcription of gene

23. 3. Vocabulary in order to have a clue on 15.2
a. Things that are part of the DNA
i. control elements : binding site for
transcription factors
ii. Enhancers : distal (far) control elements, can be activated or repressed by transcription factor proteins
iii. TATA box : section of the promoter’s code
iv. promoter : just upstream from start of gene, where RNA polymerase binds to start transcription

24. b. Things that are proteins
i. Transcription factor : regulatory protein binds control elements
a. general transcription factors
allow transcription
b. activators speed transcription
c. repressors slow transcription
ii. Mediator proteins : form link between regulatory proteins and DNA

25. 4. Distal control elements = enhancers
a. may be up or down stream
b. each gene can have many enhancers
i. each active under different conditions
ii. Or active in different cell types
iii. Each enhancer works with only one gene
c. transcription factors called activator proteins bind to enhancer control elements
i. fold DNA so that the activator protein/enhancer complex binds to initiation complex to speed up transcription

27. d. repressor transcription factors interfere with the activator transcription factors to slow transcription
i. by binding to distal control elements and keeping activators out
ii. By binding to activator proteins

28. 5.coordination of functionally related genes
a. related genes have same DNA sequences in one of their control elements
b. one general transcription factor can activate all the genes
c. environmental signal triggers production of the GTF that then finds and binds to all related CE.

29. D. Post-transcription Control
1. RNA processing
a. alternative splicing
b. poly A tail length
c. cap designation
2. mRNA degradation
a. specialized RNAs can degrade mRNA
3. Translation initiation control
a. proteins bond to mRNA prevent initiation
b. egg mRNA
c. global control : lack of initiation factor (egg)

30. E. Post Translation Control : Protein Processing/degradation
1. Allosteric control or activation by phosphate
2. protein processing
a. inactive form cut to activate (pro-insulin)
b. glycoproteins, lipoproteins
3. selective degradation
a. ubiquitin = protein attached to proteins tags them for destruction

31. F. Non-coding RNA (ncRNA)
1)Don’t code for proteins
a) microRNAs (miRNAs)
i. complexes w/ proteins
ii. binds to complementary mRNA
iii stops translation or trigger degradation
b) small interfering RNA (siRNA)
i. turn off gene expression
ii. Used in knock-out experiments
c) ncRNA affect heterochromatin formation

32. G. Monitoring gene expression
1) To see which cells are using a gene do…
in situ hybridization (in situ = in place)
a. need to detect mRNA made from that gene
b. hybridization = bonding complementary bases to a template
c. the mRNA from the gene of interest = template
d. complementary strand = probe (DNA or RNA)
c. fluorescent dye added to probe
d. probe added to solution around embryo
b. probe hybridizes to target mRNA & concentrates in cells that are using the gene of interest

33. In situ hybridization fruit fly embryo

34. 2) reverse transcriptase – PCR (RT-PCR)
a. used to see how much mRNA is present
b. isolate mRNA and use reverse transcriptase to make cDNA (complimentary DNA)
c. use PCR and electrophoresis to determine how much mRNA was present
3) RNA sequencing : sequence cDNA