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CHAPTER 18

REGULATION OF GENE EXPRESSION

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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

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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

Regulation of a Metabolic Pathway

A. Feedback Inhibition- inhibits the activity of the first enzyme in the metabolic pathway.

B. Regulation of Gene Expression- enzymes are controlled at the transcription level, by turning genes on/off.

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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

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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

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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

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B. Repressible and Inducible Operons: Two Types of Negative Gene Regulation

1. Repressible Operon2. Inducible Operon

*Both are examples of negative gene regulation

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B. Repressible and Inducible Operons: Two Types of Negative Gene Regulation

1. Repressible OperonA repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription

The trp operon is a repressible operonBy 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

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trp Operon--on

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trp Operon--off

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2. Inducible OperonAn 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

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lac Operon--off

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lac Operon--on

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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

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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

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Positive Gene Regulation

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.

Chromosomal Modification

Epigenetic Inheritance- inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence. Ex: histone acetylation and DNA methylation

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III. Other Means of Gene Regulation

A. 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

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III. Other Means of Gene Regulation

A. In histone acetylation, acetyl groups are attached to positively charged lysines in histone tails which loosens chromatin structure, thereby promoting the initiation of transcription

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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 differentiationEx: genomic imprintingInactive DNA is typically more methylated than regions that are actively transcribed. Individual genes are usually more methylated in cells where they are not expressed

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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

Transcription

INSERT FIGURE 18.10

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).

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)

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.

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.

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)

Noncoding RNA

• MicroRNA (miRNA)- bind to complementary mRNA and degrades or prevents translation.

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.

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”

Differential Gene Expression Cytoplasmic

Determinants- maternal substances in the egg that influence the course of development. (non-homogenous)

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.

Differential Gene Expression

Determination- events that lead to the observable differentiation of a cell.

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D. Oncogenes are cancer-causing genesProto-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

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.

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.

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You should now be able to:

1. Explain the concept of an operon and the function of the operator, repressor, and corepressor

2. Explain the adaptive advantage of grouping bacterial genes into an operon

3. Explain how repressible and inducible operons differ and how those differences reflect differences in the pathways they control

4. Describe 3 other means of gene regulation5. Define oncogenes, proto-oncogenes, and homeotic genes

Warm Up Exercise

Explain how DNA methylation and histone acetylation affect transcription of genes.

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?

Warm Up Exercise

Explain the effect of cytoplasmic determinants on cells and cell differentiation.

Describe what is meant by the term “embryonic lethals”?