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
i. CAP becomes active
ii. CAP binds to start of promotor
iii. Makes 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. https://smartsite. ucdavis

15. 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

16. 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

17. 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

19. 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

20. 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

21. 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

22. 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

23. 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

24. 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

26. 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

27. 5.coordination of functionally related genes
a. related genes have same control element sequences
b. bind same transcription factors
c. environmental signal triggers TF and the bind to all the matching control elements in the genome
d. activate all the related genes

28. 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 lack poly-A tail so no initiation
c. global control : lack of initiation factor (egg)

29. 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

30. 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

31. G. Monitoring gene expression
1) in situ hybridization (see if gene is transcribed)
a. fluorescent DNA probe added to solution around embryo
b. probe hybridizes & concentrates in cells that have complementary mRNA
2) reverse transcriptase – PCR (RT-PCR)
a. used to see how much mRNA is present
b. make cDNA
c. do PCR for genes of interest
d. run electrophoresis to see what cells have it
3) RNA sequencing : sequence cDNA

32. In situ hybridization fruit fly embryo