1. Introns and Exons
DNA is interrupted by short sequences that are not in the final mRNA
Called introns
Exons = RNA kept in the final sequence

2. Gene Regulation
Ability of an organisms to control which genes are present in response to the environment

3. Prokaryotic cells turn genes on and off by controlling transcription.
A promotor is a DNA segment that allows a gene to be transcribed.
An operator is a part of DNA that turns a gene “on” or ”off.”
An operon includes a promoter, an operator, and one or more structural genes that code for all the proteins needed to do a job.
Operons are most common in prokaryotes.
The lac operon was one of the first examples of gene regulation to be discovered.
The lac operon has three genes that code for enzymes that break down lactose.

4. The lac operon acts like a switch.
The lac operon is “off” when lactose is not present.
The lac operon is “on” when lactose is present.

5. Trp operon
lac operon

6. Points of control
The control of gene expression can occur at any step in the pathway from gene to functional protein
1. packing/unpacking DNA
2. transcription
3. mRNA processing
4. mRNA transport
5. translation
6. protein processing
7. protein degradation

7. 1. DNA packing as gene control
Degree of packing of DNA regulates transcription
tightly wrapped around histones
no transcription
genes turned off
heterochromatin
darker DNA (H) = tightly packed
euchromatin
lighter DNA (E) = loosely packed H E

8. DNA methylation Methylation of DNA blocks transcription factors
no transcription
 genes turned off
attachment of methyl groups (–CH3) to cytosine
C = cytosine
nearly permanent inactivation of genes
ex. inactivated mammalian X chromosome = Barr body
Methylation results in a human disease called fragile X syndrome; FMR-1 gene is silenced by methylation.

9. Histone acetylation Acetylation of histones unwinds DNA
loosely wrapped around histones
enables transcription
genes turned on
attachment of acetyl groups (–COCH3) to histones
conformational change in histone proteins
transcription factors have easier access to genes

10. Fig
Methylation of H19 inactivates transcription
(involved in expression of insulin like growth factor)

11. Fig a
Chromatin remodeling
Acetylation of histones enhances access to promoter region and facilitates transcription.

12. Epigenetic Inheritance
Although the chromatin modifications just discussed do not alter DNA sequence, they may be passed to future generations of cells
The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance

13. 2. Transcription initiation
Control regions on DNA
promoter
nearby control sequence on DNA (TATA box )
binding of RNA polymerase & transcription factors
“base” rate of transcription
enhancer
distant control sequences on DNA
binding of activator proteins
“enhanced” rate (high level) of transcription

14. Model for Enhancer action
Enhancer DNA sequences
distant control sequences
Activator proteins
bind to enhancer sequence & stimulates transcription
Silencer proteins
bind to enhancer sequence & block gene transcription
Much of molecular biology research is trying to understand this: the regulation of transcription.
Silencer proteins are, in essence, blocking the positive effect of activator proteins, preventing high level of transcription.
Turning on Gene movie

15. Transcription complex
Activator Proteins
• regulatory proteins bind to DNA at distant enhancer sites
• increase the rate of transcription
Enhancer Sites
regulatory sites on DNA distant from gene
Enhancer
Activator
Activator
Activator
Coactivator B F E
RNA polymerase II A
TFIID H
Coding region
T A T A
Core promoter
and initiation complex
Initiation Complex at Promoter Site binding site of RNA polymerase

16. Promoter Activators Gene DNA Enhancer
Fig
Promoter
Activators
Gene
DNA
Distal control
element
Enhancer
TATA
box
General
transcription
factors
DNA-bending
protein
Group of
mediator proteins
RNA
polymerase II
Figure 18.9 A model for the action of enhancers and transcription activators
RNA
polymerase II
Transcription
initiation complex
RNA synthesis

17. 3. Post-transcriptional control
Alternative RNA splicing
variable processing of exons creates a family of proteins

18. RNA processing is also an important part of gene regulation in eukaryotes.
mRNA processing includes three major steps.
Introns are removed and exons are spliced together.
A cap is added.
A tail is added.

19. Regulation by alternative splicing
Calcitonin gene-related peptide

20. 4. Regulation of mRNA degradation
Life span of mRNA determines amount of protein synthesis
mRNA can last from hours to weeks
RNA processing movie

21. 5. Control of translation
Block initiation of translation stage
regulatory proteins attach to 5' end of mRNA
prevent attachment of ribosomal subunits & initiator tRNA
block translation of mRNA to protein
Control of translation movie

22. 6-7. Protein processing & degradation
folding, cleaving, adding sugar groups, targeting for transport
Protein degradation
ubiquitin tagging
proteasome degradation
The cell limits the lifetimes of normal proteins by selective degradation. Many proteins, such as the cyclins involved in regulating the cell cycle, must be relatively short-lived.
Protein processing movie

23. Concept 18.3: Noncoding RNAs play multiple roles in controlling gene expression
Only a small fraction of DNA codes for proteins, rRNA, and tRNA
A significant amount of the genome may be transcribed into noncoding RNAs
Noncoding RNAs regulate gene expression at two points: mRNA translation and chromatin configuration

24. RNA interference NEW! Small interfering RNAs (siRNA)
short segments of RNA (21-28 bases)
bind to mRNA
create sections of double-stranded mRNA
“death” tag for mRNA
triggers degradation of mRNA
cause gene “silencing”
post-transcriptional control
turns off gene = no protein produced
siRNA

25. Action of siRNA siRNA mRNA degraded functionally turns gene off
Hot…Hot new topic in biology
Action of siRNA
dicer enzyme
mRNA for translation
siRNA
double-stranded miRNA + siRNA
breakdown enzyme
(RISC)
mRNA degraded
functionally turns gene off

26. Gene Regulation 7 6 protein processing & degradation
1 & 2. transcription
- DNA packing
- transcription factors
3 & 4. post-transcription
- mRNA processing
- splicing
- 5’ cap & poly-A tail
- breakdown by siRNA
5. translation
- block start of translation
6 & 7. post-translation
- protein processing
- protein degradation 5 4
initiation of translation
mRNA processing 2 1
initiation of transcription
mRNA protection
mRNA splicing 4 3

27. Cancers result from a series of genetic changes in a cell lineage
The incidence of cancer increases with age because multiple somatic mutations are required to produce a cancerous cell
As in many cancers, the development of colon cancer is gradual

28. Eukaryotic Gene Regulation
Hox genes – controls differentiation of genes
Responsible for general body pattern of most animals
Order of genes is order of body parts

30. Review questions
What does DNA polymerase do? What does Helicase do? What does ligase do? Match the bases below. 5’ – A T C G T A – 3’ List 3 differences between RNA/DNA. What are the 3 types of RNA? Where does RNA go after it is made? Transcribe the DNA below. A T C G T A

31. What does RNA attach to when it leaves the nucleus
What does RNA attach to when it leaves the nucleus? Amino Acids are the building block of ________. What type of RNA brings an amino acid? When does translation stop? Where is the codon located? Anticodon? What is a codon? Translate the mRNA strand below. A G C G A G Translate the DNA strand below ATG CTA TGCA