1. REGULATION OF GENE EXPRESSION
CHAPTER 18
REGULATION OF GENE EXPRESSION

2. I. Overview
Prokaryotes and eukaryotes alter gene expression in response to their changing environment
In multicellular eukaryotes, gene expression regulates development and is responsible for differences in cell types
RNA molecules play many roles in regulating gene expression in eukaryotes

3. II. Concept 16.1: Regulation of Transcription in Bacteria
Natural selection has favored bacteria that produce only the products needed by that cell
A cell can regulate the production of enzymes by feedback inhibition or by gene regulation
Changes in the environment and/or food sources can cause bacteria to switch genes on and off
Gene expression in bacteria is controlled by the operon model

4. Regulation of a Metabolic Pathway
Feedback Inhibition- inhibits the activity of the first enzyme in the metabolic pathway.
Regulation of Gene Expression- enzymes are controlled at the transcription level, by turning genes on/off.
Each cell type contains the same genome, but expresses a different subset of genes. (Ex: the genes that code for eyes, don’t express hair).
E.Coli must have tryptophan to survive. They try to conserve energy typically by obtaining trp from the host. When levels are absent/low, they begin to synthesize their own. This gene expression is regulated through 2 different mechanisms
2) The cell stops making the enzymes that catalyze the syntheses of tryptophan. In this case, it happens at the transcription level. The synthesis of messenger RNA coding for these enzymes. Switching off many of the genes in this metabolic pathway. Gene expression is controlled by operons- discovered in 1961 by Jacob and Monod.
The five genes that code for these enzymes are clustered together on the bacterial chromosome. A single promoter serves all five genes, which together is a transcription unit. Thus transcription of this gene actually produces 5 polypeptides that make up the enzymes in the tryptophan pathway. The cell can translate this into 5 different polypeptides because the transcription unit is punctuated with 5 different start and stop signals.
When enzymes that function together are coded for side by side in the genetic sequence, it makes it easier to turn them on or off in the promoter region. When tryptophan is needed, all of the enzymes needed to make it are turned on and synthesized at one time. This is called coordinate control.

6. A. Operons: The Basic Concept
1. The operon was discovered in 1961 by Francois Jacob and Jacques Monod and was proposed as a model for the control of gene expression in bacteria 2. A cluster of functionally related genes can be under coordinated control by a single on-off “switch” 3. The regulatory “switch” is a segment of DNA called an operator usually positioned within the promoter 4. An operon is the entire stretch of DNA that includes the operator, the promoter, and the genes that they control 5. The operon can be switched off by a protein repressor

7. 6. The repressor prevents gene transcription by binding to the operator and blocking RNA polymerase 7. The repressor is the product of a separate regulatory gene which is usually located away from the operon they control
Described by Jacob and Monod
The on/off switch for a particular segment of DNA is called the operator. Found in between the promoter and the exons.
Naturally this is switch is turned on, and RNA polymerase is allowed to bind to the promoter sequence. It can be switched off by a protein called the trp repressor.

8. 8. The repressor can be in an active or inactive form, depending on the presence of other molecules 9. A corepressor is a molecule that cooperates with a repressor protein to switch an operon off
Promoter includes TATA box which RNA polymerase recognizes.
This is the mRNA strand. Previously, there were other introns between the observed exons.
A repressor protein is specific for the operator of a particular operon. The repressor that turns off the trp operon has no affect on the other operons in the E. coli.
The repressor is coded by its own gene, called the regulatory gene (trpR) which is located upstream from the trp operon and has its own promoter. Regulatory genes are expressed continually at a low rate, leaving a few repressor molecules always present in cells. How then, is the operon not switched off permanently? These repressors have two forms: active inactive, without their corepressor, (Which in this case is the tryptohphan molecule) then they are inactive- so having a few in the cell will not stop production. When tryptophan accumulates in the cell, tryptophan binds with the repressor, which activates it- and it binds to the operator, turning the switch off, and inactivating the transcription unit that produces tryptophan. When trp is needed, it is pulled from the repressor, which reactivates the operator for trp production.

9. B. Repressible and Inducible Operons:
B. Repressible and Inducible Operons: Two Types of Negative Gene Regulation
1. Repressible Operon
2. Inducible Operon
*Both are examples of negative gene regulation
Both are inhibited or stimulated when a small specific molecule interacts with a regulatory protein.
Lac = lactose, this is what Jacob and Monod first did their research on.
They inhibit gene function in some ways.

10. B. Repressible and Inducible Operons:
B. Repressible and Inducible Operons: Two Types of Negative Gene Regulation
1. Repressible Operon
A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription
The trp operon is a repressible operon
By default the trp operon is on and the genes for tryptophan synthesis are transcribed
When tryptophan is present, it binds to the trp repressor protein, which turns the operon off
The repressor is active only in the presence of its corepressor tryptophan; thus the trp operon is turned off (repressed) if tryptophan levels are high

11. trp Operon--on

12. trp Operon--off

13. By itself, the lac repressor is active and switches the lac operon off
2. Inducible Operon
An inducible operon is one that is usually off; a molecule called an inducer inactivates the repressor and turns on transcription
The lac operon is an inducible operon and contains genes that code for enzymes used in the hydrolysis and metabolism of lactose
By itself, the lac repressor is active and switches the lac operon off
A molecule called an inducer inactivates the repressor to turn the lac operon on
Lactose is available to E.coli when the host drinks milk. Lactose (a disaccharide) is then broken down into its 2 sugars, galactose and glucose- with the help of an enzyme Beta-galactosidase. Typically only a few of these enzymes are available in the cell in the absence of lactose. But as lactose is added to the environment the enzyme increases a thousand-fold in about 15 minutes.
The gene for B-galactosidase is part of the lac operon, which includes two other genes for enzymes that function in lactose utilization. All coded in one transcription unit with the same operator and promoter. The regulatory gene, lac I is located outside of the operon and codes for a repressor protein that can switch on/off the lac operon by binding to the operator.
The difference between this and the repressor is that the repressor it is inactive by itself, but active when the something (the copressor) binds to it
Here, the pathway is usually off- no B-galactosidase is made, except when there is an inducer, in this case allolactase, an isomer of lactose that is formed in small amounts of lactose. When this enzyme binds to the repressor, it inactivates it, thus starting the transcription process and allowing the B-galactosidase to be made.
Both help the cell keep from wasting energy- one by not making an enzyme when there is nothing for it to break down, and one by not synthesizing amino acids when they are already present in the cell.

14. lac Operon--off

15. lac Operon--on

16. C. Inducible enzymes usually function in catabolic pathways; their synthesis is induced by a chemical signal D. Repressible enzymes usually function in anabolic pathways; their synthesis is repressed by high levels of the end product E. Regulation of the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor

17. F. Positive Gene Regulation
1. Some operons are also subject to positive control through a stimulatory protein, such as catabolite activator protein (CAP), an activator of transcription
2. When glucose (a preferred food source of E. coli) is scarce, CAP is activated by binding with cyclic AMP
3. Activated CAP attaches to the promoter of the lac operon and increases the affinity of RNA polymerase, thus accelerating transcription
4. When glucose levels increase, CAP detaches from the lac operon, and transcription returns to a normal rate
5. CAP helps regulate other operons that encode enzymes used in catabolic pathways
Both of the previous example exhibit negative control of genes, because the operons are switched off by the negative form of the proteins. Gene regulation is positive when a regulatory protein interacts directly with the genome to switch transcription on.
E.Coli use glucose over lactose, and enzymes necessary for glucose breakdown are constantly present. Only when glucose is in short supply, does it use lactose and generate the enzymes necessary for its breakdown.
cAMP accumulates when glucose is scarce and binds to an inactivated CAP (a regulatory protein- called an activator), which binds to the promoter region, starting the synthesis of glucose. When glucose concentrations in the cell increase, cAMP falls, which results in CAP pulling away from the promoter and slowing the production of glucose. (Glucose is still synthesized, although at much lower levels because RNA polymerase is poorly bound to the DNA strand.
When glucose is low (and lactose is present), cAMP Is high which activates cAMP. CAP then binds to DNA and causes snythesis of the enzymes needed to break down lactose. (B-galactosidase
When glucose is present, e.coli doesn’t need to break down lactose. High glucose = low cAMP, so CAP isnt active to help in transcription. Transcription still happens just at low levels.
The absence/presence of allolactose determines whether or not transcription happens at all. The amount of glucose (and the amount of cAMP) determines the rate of transcription if no repressor is present. Thus lac operon is under positive and negative gene control. (on/off switch and volume control)
CAP is also known to be involved in the expression of 100 other genes

18. Positive Gene Regulation

19. Gene Expression
Differential Gene Expression- the expression of different genes by cells with the same genome.
Gene expression typically refers to actions occurring in transcription, but regulation can happen at other stages in more complex organisms.
A typical human cell might express about 20% of its protein-coding genes at any given time. Highly differentiated cells, such as muscles or nerves, express an even smaller percentage of their genes. Almost all cells contain an identical genome (immune cells are an exception- discussed later). The genes expressed in each cell type are unique.
Each stage represents an opportunity for gene expression to be controlled. Note that prokaryotic cells do not have as many opportunities because they transcribe and translate simultaneously.
Gene expression most typically occurs in transcription- regulated in response to signals from outside the cell- such as hormones or other signaling molecules. The more complex the cell structure and function, the more opportunities for gene regulation (eukaryotes much more complex than prokaryotes)

20. Chromosomal Modification
Epigenetic Inheritance- inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence.
Ex: histone acetylation and DNA methylation
This includes the chromatin modifications just discussed- including histone acetylation and DNA methylation. Mutations in the DNA are permanent changes, but these changes can be reversed, by a process poorly understood. Different systems may work together and interact in a regulated way. In fruit flies it is believe that a histone-modifying enzyme recruits a DNA methylation enzyme to one region (or vice versa) and the two enzymes work together to silence a set of genes.
Epigenetic variation can help explain why one identical twin acquires a genetically based disease such as schizophrenia, but the other is normal although they have identical genomes. Alterations of normal patterns of DNA methylation are also observed in some cancers, where they are involved in incorrect gene expression. Thus enzymes that modify chromatin structure are a huge part of regulating transcription.

21. III. Other Means of Gene Regulation
In histone acetylation, acetyl groups are attached to positively charged lysines in histone tails which loosens chromatin structure, thereby promoting the initiation of transcription
Neutralizes the positive charge on the lysine which cause histones to not bind to neighboring nucleosomes. Causes chromatin to form a looser structure.
Deacetylation- removal of acetyl groups
Review DNA coiling. DNA + Proteins = Chromatin- wind together around histones to form nucleosomes. This helps pack DNA inside nucleus but also helps in gene expression.
The location of a gene’s promoter relative to nucleosomes and to sites where DNA attaches to chromosome scaffold or nuclear lamina can affect whether the gene is transcribed. Highly condensed chromatin (heterochromatin) is also not usually expressed. Chemical modifications to histones and DNA can change chromatin structure and gene expression.
Much evidence indicates that modifications to histones directly effects gene transcription. The histone tails stick out from nucleosome. They can be modified by enzymes by removal or addition of chemical groups.
Acetyl (COCH3) When chromatin is loosely wound, transcription proteins can access genes easier in an acetylated region. Therefore these enzymes that acetylate are very important components of transcription factor that bind to promoters and may help the initiation of transcription by potentially binding to and recruiting components of transcription machinery.
Some activators recruit proteins that acetylate histones near the promoters of specific genes- promoting transcription. Some repressors recruit proteins that deacetylate leading to reduced transcription or “silencing” Chromatin modification is one of the most common mechanisms of repression in eukaryotes.
Methyl and Phosphate groups can attach to amino acids in histone tails and promote chromatin condensation. Placing a methylated amino acid next to a phosphorylated amino acid though has the opposite effect. These findings have led to the proposal of the histone code hypothesis- specific combinations of modifications and the order they occur in help determine the chromatin configuration (remember pretty picture?) which ultimately influences transcription.
*occurs in plants, animals and fungi. Example: inactive X chromosome in women.
There are some exceptions to this rule. Removal of the methylated regions can turn on some of these genes. For some species, DNA methylation is essential for long-term inactivation of genes that occurs in cell differentiation. Once methylated, genes usually stay that way though cell divisions in a given individual. In DNA replication where one strand is already methylated, enzymes methylate the daughter strand after DNA replication. Methylation patterns are thus passed on

22. III. Other Means of Gene Regulation
In histone acetylation, acetyl groups are attached to positively charged lysines in histone tails which loosens chromatin structure, thereby promoting the initiation of transcription
Review DNA coiling. DNA + Proteins = Chromatin- wind together around histones to form nucleosomes. This helps pack DNA inside nucleus but also helps in gene expression.
The location of a gene’s promoter relative to nucleosomes and to sites where DNA attaches to chromosome scaffold or nuclear lamina can affect whether the gene is transcribed. Highly condensed chromatin (heterochromatin) is also not usually expressed. Chemical modifications to histones and DNA can change chromatin structure and gene expression.
Much evidence indicates that modifications to histones directly effects gene transcription. The histone tails stick out from nucleosome. They can be modified by enzymes by removal or addition of chemical groups.
Acetyl (COCH3) When chromatin is loosely wound, transcription proteins can access genes easier in an acetylated region. Therefore these enzymes that acetylate are very important components of transcription factor that bind to promoters and may help the initiation of transcription by potentially binding to and recruiting components of transcription machinery.
Some activators recruit proteins that acetylate histones near the promoters of specific genes- promoting transcription. Some repressors recruit proteins that deacetylate leading to reduced transcription or “silencing” Chromatin modification is one of the most common mechanisms of repression in eukaryotes.
Methyl and Phosphate groups can attach to amino acids in histone tails and promote chromatin condensation. Placing a methylated amino acid next to a phosphorylated amino acid though has the opposite effect. These findings have led to the proposal of the histone code hypothesis- specific combinations of modifications and the order they occur in help determine the chromatin configuration (remember pretty picture?) which ultimately influences transcription.
*occurs in plants, animals and fungi. Example: inactive X chromosome in women.
There are some exceptions to this rule. Removal of the methylated regions can turn on some of these genes. For some species, DNA methylation is essential for long-term inactivation of genes that occurs in cell differentiation. Once methylated, genes usually stay that way though cell divisions in a given individual. In DNA replication where one strand is already methylated, enzymes methylate the daughter strand after DNA replication. Methylation patterns are thus passed on

23. III. Other Means of Gene Regulation
B. DNA methylation, the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some species and can cause long-term inactivation of genes in cellular differentiation
Ex: genomic imprinting
Inactive DNA is typically more methylated than regions that are actively transcribed. Individual genes are usually more methylated in cells where they are not expressed
Methyl and Phosphate groups can attach to amino acids in histone tails and promote chromatin condensation. Placing a methylated amino acid next to a phosphorylated amino acid though has the opposite effect. These findings have led to the proposal of the histone code hypothesis- specific combinations of modifications and the order they occur in help determine the chromatin configuration (remember pretty picture?) which ultimately influences transcription.
*occurs in plants, animals and fungi. Example: inactive X chromosome in women.
There are some exceptions to this rule. Removal of the methylated regions can turn on some of these genes. For some species, DNA methylation is essential for long-term inactivation of genes that occurs in cell differentiation. Once methylated, genes usually stay that way though cell divisions in a given individual. In DNA replication where one strand is already methylated, enzymes methylate the daughter strand after DNA replication. Methylation patterns are thus passed on

24. III. Other Means of Gene Regulation
C. 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
There are many opportunities for regulation of genes during RNA processing (not available to prokaryotes).
Regulatory proteins specific to a cell type control intron-exon choices by binding to regulatory sequences in the primary transcript. While some genes only offer a few number of products, others offer many more. A drosophila gene has about 19,000 membrane protein options on one gene, about 94% of those (17,500) are actually synthesized. These are nerve cells with unique proteins that are cell surface markers.
Relative to the complexity, the human genome has a small number of genes (similar to a mustard plant or a soil worm), and one explanation points to alternative RNA splicing. It is believed that % of human genes undergo alternative splicing, providing many more proteins and combinations to explain human complexity.

25. Transcription

26. INSERT FIGURE 18.10
In eukaryotes, the rate of gene expression can be strongly increased or decreased by the binding of specific transcription factors, either activators or repressors. To the control elements of the enhancers.
Protein mediated bending of DNA enables enhances to influence a promoter hundreds or thousands of nucleotides away. These interactions help assembled the transcription initiation complex on the promoter.
Activator proteins bind to distal control elements grouped as an enhancer in the DNA. This enhancer has three binding sites, each called a distal control element.
A DNA-bending protein brings the bound activators closer to the promoter. General transcription factors, mediator proteins, and RNA polymerase II are nearby.
The activators bind to certain mediator proteins and general transcription factors helping them form an active transcription initiation complex on the promoter.
Study in mice reveals that proteins regulating a gene contact promoter and enhancer 50,000 nucleotides away.
Repressors can bind directly to control element DNA (in enhancers or proximal control) blocking activator, or turn off transcription even when activators are bound.
Activators- factors that bind and enhance transcription of a gene.

27. Control of transcription depends on binding Activators to DNA control elements. Each enhancer has about 10 control elements, each can only bind to one or two specific transcription factors. A specific combination of control elements must be expressed in order to regulate a given gene. (Control elements are coded by repeats off short nucleotide sequences- there are about a dozen total control elements). Even with only 12 control elements- there are a lot of combinations, and they can only be activated by a specific activator that may only be present at certain times and certain cell types.
Liver and lens cells both have genes for making albumin and crystallin. Only liver cells make albumin (blood protein) and lens cells make crystallin (protein cell in eye) The transcription factors made in each cell determine which genes are expressed. All of the activators of a high level expression of a gene are present only in the specific cell type where that protein is needed.
In the event that two cells have all of the same control elements, there are also repressors that can turn off a signal.

28. Coordinate Control in Eukaryotes
Genes with the same control elements are activated by the same chemical signals. (Not by a common operator, as in prokaryotes).
In bacteria, all genes in trp pathway are under one promoter and one operon. With a few exceptions, that is the not the case in eukaryotes. Genes coding for the same pathway may be scattered all over various chromosomes in eukaryote cells. In order for each region to be expressed, it is dependent on recognition of a set of control factors. All genes involved in one pathway would show the same set of control factors. When their activators are present, they would bind to all of the control factors and promote transcription on each segment of the DNA in that pathway. This is analogous to mailmen and the red flag, indicating there is mail to pick up.
Image: Each chromosome has its own territory, but in regions where territories meet, chromatin loops overlap. Recent research indicates that this may be a transcription factory that is specialized for a common function. This is thought to be a part of readying genes for transcription.

29. Regulation of Transcription Initiation
Control Elements- segments of noncoding DNA that serve as binding sites for transcription factors (proteins that regulate transcription).
Proximal Control Elements (near promoter) vs. Distal Control Elements called Enhancers (upstream or downstream of a gene or within an intron)
Chromatin modifying enzymes are the initial control for gene expression by making a region of DNA more or less able to bind to transcription machinery RNA Polymerase)
Transcription initiation complex assembles on promoter RNA polymerase II then proceeds to transcribe gene, synthesizing a primary transcript. RNA processing then occurs (cap, tail, intron/exon splicing) to produce mature RNA
Control elements and the factors they bind are critical for gene regulation in different cell types.
Some transcription factors are required for all protein-coding genes, and are frequently called general transcription factors. Only a few of those bind to a DNA sequence such as the TATA box, but most bind proteins, including each other and RNA polymerase II. These protein interactions are critical to initiation of transcription. Only when the complete initiation complex is assembled can polymerase begin transcription. These general transcription factors only lead to a low rate of transcription and production of a few RNA transcripts.
IN eukaryotes, specific transcription factors interact with control elements and aid in high levels of transcription of particular genes at the appropriate time and place.
A gene may have multiple enhancers each active at a different time or in an different cell type or location. Each enhancer is only associated with one gene.

30. Post Transcriptional Regulation
mRNA Degradation- nucleotide sequences (in UTR) determine how long mRNA remains intact. By degrading mRNA, expression is blocked.
Initiation of Translation- by preventing the attachment of mRNA on ribosomes, translation is blocked.
Can occur when regulatory proteins bind to sequences in UTR, when poly-A tail isn’t sufficient in length, or when translation initiation factors are deactivated.
mRNA Degradation
-the life span of mRNA is different in different cells. Typically in prokaryotes they are degraded quickly (couple minutes). Some stable mRNA molecules (such as that for hemoglobin) can last a few weeks. in the UTR at 3’ end. (in experiments, scientists have transferred them between short and long lasting molecules). By degrading mRNA, this blocks its expression.
Initiation of Translation
-(5’ cap and tail are really important in binding to ribosomes). In many eggs during embryonic development, the poly-A tail isnt of sufficient length for transcription. An enzyme later adds more adenine allowing translation to begin. Translation of all mRNA may be regulated by activating/deactivating a translation initiation factor protein. This helps start translation of mRNA stored in eggs after fertilization. In plants and algae this can occur when light triggers the reactivation of the proteins after a period of darkness.

31. Post-Transcriptional Regulation
Chemical modifications to polypeptides to make them functional.
Transport to target destinations.
Length of time for protein to function in the cell.
When cells are marked for destruction, a protein called ubiquitin is attached to the protein surface.
Proteosomes- complexes that recognize ubiquitin and degrade marked proteins.
Often eukaryotic polypeptides must be processed to yield functional protein molecules. Cleavage of the initial insulin polypeptide forms the active hormone. Many proteins undergo chemical modifications to make them functional. Many regulatory proteins have addition of phosphates and surface proteins require the addition of sugars (glycoproteins).
Cannot function if not in target destination
Regulation could occur at any of these steps.
Mutations make some cell cycle proteins (cyclins) impervious to proteosome degradation and can lead to cancer.

32. Noncoding RNA- Sec. 18.3
Protein coding DNA = 1.5% of human genome. Very small percent of non-coding DNA codes for genes of rRNA/tRNA. Significant amount of genome may be transcribed into noncoding RNA (ncRNA)
ncRNA can be small and large, and is regulated at several points in the pathway of gene expression- in translation and chromosomal modification.

33. Noncoding RNA
MicroRNA (miRNA)- bind to complementary mRNA and degrades or prevents translation.
miRNA is made from longer RNA precursors that fold back on themselves forming a double stranded hairpin held together by hydrogen bonds. Single stranded.
Hairpin cut from precursor, trimmed by enzyme (called a dicer) into a short double stranded fragment about 22 pairs nucleotides long. One strand degraded, the other (miRNA) forms a complex with one or more proteins and miRNA allows complex to bind to mRNA molecule with 7-8 complementary nucleotides. miRNA either degrades the target mRNA or blocks its translation. It is estimated that half of all human genes are regulated by miRNAs.

34. Noncoding RNA
RNA Interference- injecting double-stranded RNA molecules into a cell turns off expression of a gene with the same sequence as the RNA.
Small Interfering RNA (siRNA)- similar to miRNA in size and function.
RNA interference due to siRNA- similar in size and function to miRNA- generated by same cellular machinery and associate with same proteins, producing similar results. Difference is the precursor molecules for each. miRNA strand formed from single hairpin, multiple siRNA formed from a long, linear double-stranded RNA molecule.
Some viruses have double stranded RNA- that can turn off expression of genes (viral or nonviral)
Many species also produce their own long, double stranded RNA precursors to siRNAs. These RNAs can interfere with gene expression – by remodeling chromatin structure- turning it into highly condensed chromatin that is not easily transcribed.

35. Genetic Programming for Embryonic Development- Sec. 4
Cell Division- zygote gives rise to a large number or identical cells.
Cell Differentiation- become specialized in structure and function and organize into tissues and organs.
Morphogenesis- “creation of form”
The differences observed come from three interrelated processes
Differentiation- a particular 3D arrangement
Each of these activities depend on the genes an organism expresses and proteins it produces- but they have the same genome in each cell, thus differential expression results from gene regulation in each cell type.
This occurs because materials placed into the egg by the mother set up a sequential program of gene regulation carried out as the cells divide. This makes cells become different from one another in a coordinated way.

36. Differential Gene Expression
Cytoplasmic Determinants- maternal substances in the egg that influence the course of development. (non-homogenous)
This includes RNA and proteins, organelles, etc coded by the mothers DNA- not homogenous in the cell. During early cell division these particulates are distributed to various cells. The nuclei of these forming cells may be exposed to different cytoplasmic determinants. The combination of these determinants help determine a cell’s developmental fate by regulating expression of the cell’s genes during the course of cell differentiation.

37. Differential Gene Expression
Inductive Signals- signals from other nearby embryonic cells that cause a change in gene expression- sending a cell down a specific developmental path.
Cells releasing chemicals that signal nearby cells to change their gene expression. (maybe by binding to an inducer, operon, etc)
These signaling molecules send a cell down a specific developmental path by causing changes in its gene expression that eventually results in observable cellular changes. (these signals can include contact with cell-surface molecules on other cells, and binding of growth factors secreted by neighboring cells) Also signals can come from proteins that are expressed by the embryos own genes.

38. Differential Gene Expression
Determination- events that lead to the observable differentiation of a cell.
Once a cell has undergone determination, an embryonic cell is irreversibly committed to its final fate, even if placed in a different location. The outcome of determination is that cells are marked by the expression of genes for tissue specific proteins. These proteins are only found in specific cell types and give the cell its characteristic structure and function.
Embryonic precursor cells have potential to develop into different cell types, but specific conditions (namely, transcription factors) cause them to become muscle cells.
Signals from other cells activate master regulatory gene, which produces a specific transcription factor. This cell is now called a myoblast and is committed to becoming a skeletal muscle cell.
The muscle protein transcription factor stimulates the genes to produce faster and activates other genes for muscle transcription factors which activate genes for muscle proteins. They turn inactivate the cell cycle
These nondividing myoblasts fuse to become mature multinucelated muscle cells, aka: muscle fiber.
Master regulatory genes make protein products that commit cells to becoming a special type. Mechanism of determination is therefore expression of one of the master regulatory genes.

39. D. Oncogenes are cancer-causing genes
Proto-oncogenes are the corresponding normal cellular genes that are responsible for normal cell growth and division
Conversion of a proto-oncogene to an oncogene can lead to abnormal stimulation of the cell cycle
E. Homeotic genes are any of the master regulatory genes that control placement and spatial organization of body parts in animals, plants, and fungi by controlling the developmental fate of groups of cells

40. Pattern Formation Homeotic Genes- determine pattern formation.
Embryonic Lethals- mutations with phenotypes causing death at the embryonic stage.
Maternal Effect Gene- when mutant in mother, results in mutant phenotype in offspring, regardless of offspring’s own genotype.
Morphogens- establish an embryo’s axis and other features of its form.
cytoplasmic determinants also tell a cell positional information-location relative to body axis. In drosophila, cyto det provide information for the placement of anterior-posterior, dorsal-ventral, and right-left axis.
In the ovary, egg is surrounded by follicle cell and nurse cell which provides nutrients and mRNA and other substances needed for development.
Homeotic genes control pattern formation in late embryo, early larval, and adult (like it tadpole, fruit flies, humans, etc)
It is the mothers genes that determine how the anterior-posterior body axis is set up in the developing egg
mRNA or protein products of maternal effect genes are placed in egg while still in mother’s ovary. When mother has mutation, whe makes a defective gene and eggs are defective- when fertilized they fail to develop properly
Mutations in maternal effect genes are usually embryonic lethals as well.
These maternal mRNAs that code for early genes are later destroyed, involving the use of microRNA

41. Cancer Control
p53 Gene- codes for a transcription factor that promotes synthesis of cell-cycle inhibiting proteins.
Mutation is this gene usually leads to excessive cell growth and cancer.
Tumor-Suppressor Genes- code for proteins that help prevent uncontrolled cell growth.
Doesn’t stop cell cycle
Stimulates growth through absence of suppression
P53 is normal- tumor suppressor proteins repair DNA damage, control cells adhesion to one another, components of cell signaling.

43. You should now be able to:
Explain the concept of an operon and the function of the operator, repressor, and corepressor
Explain the adaptive advantage of grouping bacterial genes into an operon
Explain how repressible and inducible operons differ and how those differences reflect differences in the pathways they control
Describe 3 other means of gene regulation
Define oncogenes, proto-oncogenes, and homeotic genes

44. Warm Up Exercise
Explain how DNA methylation and histone acetylation affect transcription of genes.

45. Warm Up Exercise
Draw a diagram that represents how Alternative RNA Splicing can code for two different proteins.
How is a protein targeted for degradation, and what cellular component is responsible for degrading it?

46. Warm Up Exercise
Explain the effect of cytoplasmic determinants on cells and cell differentiation.
Describe what is meant by the term “embryonic lethals”?