1. Regulation of Gene Expression
Chapter 18

2. Operons Prokaryotes Only
Found in Prokaryotes (bacteria)
Cluster of genes of related function in one transcription unit
Genes are under coordinate control – have a single on/off “switch”
Composed of 3 parts:
Operator – in promoter;
controls the access of RNA
polymerase to the genes
Promoter – where RNA
polymerase attaches
Genes of the operon
Recall Beadle and Tatum’s Arginine Synthesis discovery

3. Regulatory Genes Prokaryotes Only
Located some distance from the operon it controls
Produce repressors which block the operator
Has it own promoter
Expressed continuously but at a low rate

4. Negative & Positive Gene Regulation Prokaryotes Only
Negative regulation
Attachment of a repressor to an operator blocking transcription of the operon genes
Ex) Repressible and Inducible operons
Positive Regulation
Attachment of an activator protein directly to the promoter (not the operator) stimulating transcription of the operon genes
Ex) CAP and cAMP

5. Negative Gene Regulation Repressible Operons (trp operon)
Typically anabolic – builds organic molecules
Usually on but can be repressed
Ex) Tryptophan (a.a.) synthesis
Operon is on if trp is not present in cell
If trp is present in cell, it will bind to the repressor, which will in turn bind to the operator, blocking transcription by RNA polymerase (trp = corepressor)

6. Negative Gene Regulation Inducible Operons (lac operon)
Typically catabolic – breaks down food molecules for energy
Usually off but can be activated (induced)
Ex) Lactose metabolism
If lactose is not present the repressor is active; operon off; no transcription for lactose enzymes
If lactose is present repressor is inactivated by a binding allolactose (inducer – isomer of lactose); operon on; transcription stimulated

7. Positive Gene Regulation
When glucose levels are low, E. coli will use lactose as an energy source
Low levels of glucose = high levels of cAMP
CAP (catabolite activator protein) is an activator protein which binds to the promoter of the lac operon
Activated when cAMP binds
Helps RNA polymerase bind to the DNA
Increases the rate of transcriptioin

8. Differential Gene Expression
Human cells probably express 20% of its genes at a given time
Highly differentiated cells such as mucle or nerve cells, express an even smaller fraction of their genes
The differences between cell types are not due to different genes being present, but to the expression of different genes by cells with the same genome
Gene expression (transcription) in eukaryotes can be regulated at many stages

9. Regulation of Chromatin Structure Differential Gene Expression
Histone acetylation
addition of acetyl groups (-COCH3) to histones; unpacks DNA slightly allowing access to the DNA for transcription
DNA methylation
adding methyl groups (-CH3) to the cytosine bases of DNA making genes less accessible for transcription

10. Regulation of Transcription Initiation Differential Gene Expression
Control elements help general transcription factors bind to the DNA
Distal control elements called enhancers are bound to the promoter region by proteins called activators and mediator proteins; in combination with the general transcription factors, they help increase the rate of (enhance) transcription
Activator proteins can be thought of as specific transcription factors

11. Regulation of Transcription Initiation Differential Gene Expression
Different types of cells produce different types of control elements (ie - activators)
Allows only the genes whose products are needed by the cell to be activated while the other genes stay dormant

12. Post-Transcriptional Regulation Differential Gene Expression
Alternative RNA splicing
Different mRNA molecules can be produced from the same primary transcript (pre-mRNA)
Depends on which mRNA segments are treated as exons and introns
Regulatory proteins specific to a cell type control intron-exon choices by binding to regulatory sequences within the pre-mRNA

13. Post-Transcriptional Regulation Differential Gene Expression
mRNA Degradation
Nucleotide sequences that determine the lifespan of mRNA are often found in the 3’ UTR
mRNA can survive for hours, days, or even weeks!
mRNA is digested by nuclease enzymes
Ex) mRNA’s for hemoglobin polypeptides in red blood cells are unusually stable and are translated repeatedly
Initiation of Translation
Regulatory proteins can bind to specific sequences in the 5’ UTR preventing the ribosome from attaching to the mRNA
Incomplete poly(A) tails (too short) can prevent ribosome binding; common in unfertilized eggs; poly(A) tails are completed at a specific time in embryonic development

14. Post-Translation Regulation Differential Gene Expression
Protein processing
Many proteins undergo chemical modifications that make them functional
Regulatory proteins are activated by phosphate groups
Proteins destined for the cell membrane require the addition of sugars (glycoproteins)
Digestive enzymes in lysosomes can’t be activated until they are actually in the lysosome!
Protein lifespan
Depending on the protein’s function, some must be degraded sooner than others
Cell attaches a ubiquitin protein to the protein, then proteasomes break down the protein

15. Regulation by Noncoding RNAs
Recall that only 1.5% of our DNA codes for proteins and another small fraction codes for rRNAs and tRNAs
We believed the rest of the DNA was untranscribed and was basically junk
However, we have discovered that a lot of that junk DNA actually codes for noncoding RNAs (non-protein-coding)
These noncoding RNAs regulate mRNA translation and chromatin configuration

16. Types of Noncoding RNAs
MicroRNAs (miRNAs) (1993)
Bind to complimentary sequences in mRNAs
Once bound, it can cause degradation of the mRNA or block translation
May regulate the expression of up to 1/3 of ALL human genes!
Small interfering RNAs (siRNAs)
Similar function as miRNAs but can also remodel chromatin structure
Responsible for forming heterochromatin which blocks transcription

17. From fertilized egg to multicellular organism
Differential Gene Expression Leads to Different Cell Types in Multicellular Organisms
From fertilized egg to multicellular organism
Cell division – increase in the number of cells
Differentiation – cells becoming specialized in structure and function
Morphogenesis – the organization of cells into tissues and organs

18. Differentiation
Cytoplasmic determinants – maternal substances in the egg that influence the course of early development; unevenly distributed in the unfertilized egg cell
Ex) mRNA, proteins, and organelles
As mitotic divisions occur, the nuclei of the new cells are exposed to different cytoplasmic determinants depending on which portion of the zygotic cytoplasm that was received, thus allowing certain genes to be turned on

19. Differentiation
Cell-cell signals from a cell may influence neighboring cells, a process called induction
The observable differentiation of cells is called determination

20. These transcription factors are activators for enhancers control elements (remember activators = specific transcription factors)

21. Differentiation
Pattern formation sets up the body plan and is a result of cytoplasmic determinants and inductive signals; determines head/tail, left/right, and front/back; uneven distribution of substances called morphogens play a role in establishing these axes
Experiment by Nüsslein-Volhard & Wieschaus– a mother’s bicoid gene product is essential for establishing the anterior end of the embryo (morphogen gradient hypothesis)

22. A set of diseases in which cells escape from the control mechanisms that normally limit their growth
Cancer

23. Genes Associated with Cancer
Genes for growth factors, their receptors, and the intracellular molecules of cell signaling pathways
Mutations in any of these genes can lead to cancer
These mutations are likely caused by environmental influences such as
Chemical carcinogens
X-rays, UV, and other high-energy radiation
Certain viruses
Papillomavirus (HPV) – cervical cancer
Epstein-barr virus – many kinds; Burkitt’s lymphoma
HTLV-1 virus – adult leukemia

24. Cancer Genes
Proto-oncogenes – code for proteins that stimulate normal cell growth and division
Can convert into an oncogene (cancer gene) if one of the following occur:
There is an increase in the protein product
There is a change in the activity of the protein product

25. Proto-oncogenes  Oncogenes
Movement of DNA within the genome
chromosome fragments and rejoins incorrectly (translocation)
if the proto-oncogene ends up near an active promoter it may be transcribed more often

26. Proto-oncogenes  Oncogenes
Amplification of a proto-oncogene
increases in the number of copies of the proto-oncogene increases the products

27. Proto-oncogenes  Oncogenes
Point mutations in a control element, promoter, or the proto-oncogene itself
either causes increased expression of the gene or a protein product more active or more resistant to degradation

28. Cancer Genes Tumor-suppressor genes produce:
Proteins that repair DNA damage
Prevents the accumulation of mutations which can lead to cancer
Proteins that are components of cell-signaling pathways that inhibit the cell cycle
Proteins that control the adhesion of cells to each other or to the extracellular matrix
Recall that anchorage dependence is crucial for normal cell growth

30. Luckily…
More than one somatic mutation is generally needed to produce all of the changes we discussed leading to full-fledged cancer cells (typically about 6 or more)
This is why the incidence of cancer increases with age (more time for mutations to accumulate)

31. Cancer in Families
An individual inheriting an oncogene or a mutant allele of a tumor-suppressor gene is one step closer to accumulating the necessary mutations for cancer to develop
This is why we say if you have the breast cancer gene, you are at a greater risk of developing breast cancer
In reality, you have a mutation in the BRCA1 or BRCA2 tumor-suppressor gene which is involved in DNA repair
Inheriting one mutant BRCA1 allele puts a woman at a 60% probability of developing breast cancer compared to a 2% probability for a woman homozygous normal for the gene
Minimizing exposure to DNA-damaging agents reduces your risk: UV radiation, chemicals in cigarettes, etc.