1. Regulation of Gene Expression
CHAPTER 18

2. Bacterial Genome & Replication
Section 18.1 : Bacteria can respond to environmental change by regulating gene transcription
Bacterial Genome & Replication
double-stranded, circular DNA located in the nucleoid region
many bacteria also have plasmids – smaller circles of DNA with a few genes
reproduce by binary fission
therefore, most bacteria in a colony are genetically identical
genetic diversity can arise as a result of mutation especially when reproductive rates are high (short generation spans)

3. Metabolic Control in Bacteria
adjust the activity of enzymes already present via chemical cues
(ex) feedback inhibition
adjust the amount of enzyme being made by regulating gene expression
basic mechanism is described in the operon model

4. Operons
operator
gene A
gene B
gene C
gene D
promoter
made up of an operator, promoter, & a set of functionally related genes
operator = segment of DNA that acts like an on/off switch for transcription; positioned w/in promoter or between promoter & genes
promoter = site where RNA polymerase binds to DNA & begins transcription
set of genes = transcription unit

5. Example: trp operon

6. lac operon
repressor protein requires a small molecule called an inducer to make the repressor inactive (the repressor ‘unblocks’ the path)

7. Section 18.2 : Gene expression can be regulated at any stage

8. Regulation at Structural Levels of DNA
a single linear DNA double helix averages about 4 cm in length
DNA associates with proteins that condense it so it will fit in the nucleus
DNA-protein complex = chromatin
chromatin looks like “beads on a string” when unfolded
“beads” = nucleosomes made up of histones (proteins)
“string” = DNA

9. Structural Levels of DNA

10. chromatin fiber (30 nm) chromatin fiber (300 nm) chromosome
created by interactions between adjacent nucleosomes and the linker DNA
chromatin fiber (300 nm)
created when the 30 nm chromatin fiber forms loops called looped domains attached to a protein scaffold made of nonhistones
chromosome
forms when the 300 nm chromatin fiber folds on itself

11. Regulation of Chromatin Structure
compactness of chromatin helps regulate gene expression
heterochromatin – highly compact so it is inaccessible to transcription enzymes
euchromatin – less compact allowing transcription enzymes access to DNA
chemical modifications that can alter chromatin compactness:
histone acetylation (-COCH3) neutralizes the histones so they no longer bind to neighboring nucleosomes causing chromatin to have a looser structure

12. DNA Methylation
addition of methyl groups to DNA bases (usually cytosine) inactivates DNA
methylation patterns can be passed on
after DNA replication, methylation enzymes correctly methylate the daughter strand
accounts for genomic imprinting in mammals – expression of either the maternal or paternal allele of certain genes during development
(NOTE: inheritance of chromatin modifications that do not involve a change in the DNA sequence is called epigenetic inheritance)

13. Regulation at Transcription
Regulation at level of transcription results in differential gene expression
Most common way that gene expression is regulated

14. Regulation of Transcription Initiation
general transcription factors – proteins that form a transcription initiation complex on the promoter sequence (ex: TATA box) allowing RNA polymerase to begin transcription
control elements – segments of noncoding DNA that help regulate transcription by binding certain proteins
proximal control elements
distal control elements (enhancers) - interact with specific transcription factors:
activators –stimulate transcription by binding to enhancers
repressors - inhibit transcription by binding directly to enhancers or by blocking activator binding to enhancers or other transcription machinery

15. activators bind to enhancer with 3-binding sites
a DNA-bending protein brings the bound activators closer to the promoter
activators bind to general transcription factors & mediator proteins, helping them to form a functional transcription initiation complex
activators can also promote histone acetylation & repressors can promote histone deacetylation

16. Enhancer Promoter Albumin gene Control elements Crystallin gene
Fig
Enhancer
Promoter
Albumin gene
Control
elements
Crystallin gene
LIVER CELL
NUCLEUS
LENS CELL
NUCLEUS
Available
activators
Available
activators
Albumin gene
not expressed
Figure Cell type–specific transcription
Albumin gene
expressed
Crystallin gene
not expressed
Crystallin gene
expressed
(a) Liver cell
(b) Lens cell

17. Regulation of RNA splicing
In alternative RNA splicing, different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns

18. Exons DNA Troponin T gene Primary RNA transcript RNA splicing mRNA or
Fig
Exons
DNA
Troponin T gene
Primary
RNA
transcript
Figure Alternative RNA splicing of the troponin T gene
RNA splicing
mRNA or

19. Regulation of Protein Lifespan
After translation, various types of protein processing, including cleavage and the addition of chemical groups, are subject to control
Proteasomes are giant protein complexes that bind protein molecules and degrade them

20. Proteasome and ubiquitin to be recycled Ubiquitin Proteasome
Fig
Proteasome
and ubiquitin
to be recycled
Ubiquitin
Proteasome
Protein to
be degraded
Ubiquitinated
protein
Protein
fragments
(peptides)
Protein entering a
proteasome
Figure Degradation of a protein by a proteasome

21. 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

22. Section 18.4 : A program of differential gene expression leads to different cell types in a multicellular organism

23. Embryonic Development
Zygote transforms as a result of 3 processes:
cell division
Number of cells increases through mitosis
cell differentiation
process by which cells become specialized in structure & function
morphogenesis
Organization of cells into tissues and organs
*Cell differentiation arises primarily from differences in gene expression not from differences in the cells’ genomes*
- Differentiation and morphogenesis are controlled by both cytoplasmic determinants and cell to cell signals

24. Cytoplasmic Determinants
maternal substances in the egg that influence the course of early development
distributed unevenly to new cells produced by mitotic division of the zygote
the set of cytoplasmic determinants a cell receives helps regulate gene expression

25. Cell to Cell Signals
communication between cells can induce differentiation
Process is called induction

26. Determination
the events that lead to the observable differentiation of a cell
at the end of this process, an embryonic cell is irreversibly committed to its final fate (determined)
marked by the expression of genes for tissue specific proteins, which act as transcription factors for genes that help define cell type

27. Pattern Formation
development of a spatial organization in which the tissues and organs of an organism are all in their characteristic places
begins in early embryo when the major axes of the organism are established
molecular cues (positional information) that control pattern formation are provided by cytoplasmic determinants & inductive signals

28. Identity of Body Parts controlled by homeotic genes
turned on by segment-polarity gene products
specify the types of appendages and other structures that each segment will form
(why are homeotic genes found in clusters?)

29. Example of a homeotic gene : PAX-6

30. Section 18.5 : Cancer results from genetic changes that affect cell cycle control
The gene regulation systems that go wrong during cancer are the very same systems involved in embryonic development
Cancer can be caused by mutations to genes that regulate cell growth and division
Tumor viruses can cause cancer in animals including humans
Oncogenes are cancer-causing genes
Proto-oncogenes are the corresponding normal cellular genes that are responsible for normal cell growth and division