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Sunday, February 13, 2011

Ap Bio. Chapers 18: Regulation of Gene Expression

Chapter 18
Regulation of Gene Expression
Overview: Conducting the Genetic Orchestra
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

Concept 18.1: Bacteria often respond to environmental change by regulating transcription
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.
Gene expression in bacteria is controlled by the operon model.

Operons: The Basic Concept
A cluster of functionally related genes can be under coordinated control by a single on-off “switch”.
The regulatory “switch” is a segment of DNA called an operator usually positioned within the promoter.
An operon is the entire stretch of DNA that includes the operator, the promoter, and the genes that they control.

The operon can be switched off by a protein repressor.
The repressor prevents gene transcription by binding to the operator and blocking RNA polymerase.
The repressor is the product of a separate regulatory gene.

The repressor can be in an active or inactive form, depending on the presence of other molecules.
A corepressor is a molecule that cooperates with a repressor protein to switch an operon off.
For example, E. coli can synthesize the amino acid tryptophan.

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.

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

Inducible enzymes usually function in catabolic pathways; their synthesis is induced by a chemical signal.
Repressible enzymes usually function in anabolic pathways; their synthesis is repressed by high levels of the end product.
Regulation of the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor.
Positive Gene Regulation
Some operons are also subject to positive control through a stimulatory protein, such as catabolite activator protein (CAP), an activator of transcription.
When glucose (a preferred food source of E. coli) is scarce, CAP is activated by binding with cyclic AMP.
Activated CAP attaches to the promoter of the lac operon and increases the affinity of RNA polymerase, thus accelerating transcription.

When glucose levels increase, CAP detaches from the lac operon, and transcription returns to a normal rate.
CAP helps regulate other operons that encode enzymes used in catabolic pathways.

Concept 18.2: Eukaryotic gene expression can be regulated at any stage
All organisms must regulate which genes are expressed at any given time.
In multicellular organisms gene expression is essential for cell specialization.
Differential Gene Expression
Almost all the cells in an organism are genetically identical.
Differences between cell types result from differential gene expression, the expression of different genes by cells with the same genome.
Errors in gene expression can lead to diseases including cancer.
Gene expression is regulated at many stages.

Regulation of Chromatin Structure
Genes within highly packed heterochromatin are usually not expressed.
Chemical modifications to histones and DNA of chromatin influence both chromatin structure and gene expression.
Histone Modifications
In histone acetylation, acetyl groups are attached to positively charged lysines in histone tails.
This process loosens chromatin structure, thereby promoting the initiation of transcription.
The addition of methyl groups (methylation) can condense chromatin; the addition of phosphate groups (phosphorylation) next to a methylated amino acid can loosen chromatin.

The histone code hypothesis proposes that specific combinations of modifications help determine chromatin configuration and influence transcription.
DNA Methylation
DNA methylation, the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some species.
DNA methylation can cause long-term inactivation of genes in cellular differentiation.
In genomic imprinting, methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development.
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
Regulation of Transcription Initiation
Chromatin-modifying enzymes provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery
Organization of a Typical Eukaryotic Gene
Associated with most eukaryotic genes are control elements, segments of noncoding DNA that help regulate transcription by binding certain proteins
Control elements and the proteins they bind are critical to the precise regulation of gene expression in different cell types

The Roles of Transcription Factors
To initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called transcription factors
General transcription factors are essential for the transcription of all protein-coding genes
In eukaryotes, high levels of transcription of particular genes depend on control elements interacting with specific transcription factors

Proximal control elements are located close to the promoter
Distal control elements, groups of which are called enhancers, may be far away from a gene or even located in an intron

An activator is a protein that binds to an enhancer and stimulates transcription of a gene
Bound activators cause mediator proteins to interact with proteins at the promoter

Some transcription factors function as repressors, inhibiting expression of a particular gene
Some activators and repressors act indirectly by influencing chromatin structure to promote or silence transcription

A particular combination of control elements can activate transcription only when the appropriate activator proteins are present

Coordinately Controlled Genes in Eukaryotes
Unlike the genes of a prokaryotic operon, each of the coordinately controlled eukaryotic genes has a promoter and control elements
These genes can be scattered over different chromosomes, but each has the same combination of control elements
Copies of the activators recognize specific control elements and promote simultaneous transcription of the genes
Mechanisms of Post-Transcriptional Regulation
Transcription alone does not account for gene expression
Regulatory mechanisms can operate at various stages after transcription
Such mechanisms allow a cell to fine-tune gene expression rapidly in response to environmental changes
RNA Processing
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

mRNA Degradation
The life span of mRNA molecules in the cytoplasm is a key to determining protein synthesis
Eukaryotic mRNA is more long lived than prokaryotic mRNA
The mRNA life span is determined in part by sequences in the leader and trailer regions
Initiation of Translation
The initiation of translation of selected mRNAs can be blocked by regulatory proteins that bind to sequences or structures of the mRNA
Alternatively, translation of all mRNAs in a cell may be regulated simultaneously
For example, translation initiation factors are simultaneously activated in an egg following fertilization
Protein Processing and Degradation
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

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
Effects on mRNAs by MicroRNAs and Small Interfering RNAs
MicroRNAs (miRNAs) are small single-stranded RNA molecules that can bind to mRNA
These can degrade mRNA or block its translation

The phenomenon of inhibition of gene expression by RNA molecules is called RNA interference (RNAi)
RNAi is caused by small interfering RNAs (siRNAs)
siRNAs and miRNAs are similar but form from different RNA precursors

Chromatin Remodeling and Silencing of Transcription by Small RNAs
siRNAs play a role in heterochromatin formation and can block large regions of the chromosome
Small RNAs may also block transcription of specific genes
Concept 18.4: A program of differential gene expression leads to the different cell types in a multicellular organism
During embryonic development, a fertilized egg gives rise to many different cell types
Cell types are organized successively into tissues, organs, organ systems, and the whole organism
Gene expression orchestrates the developmental programs of animals
A Genetic Program for Embryonic Development
The transformation from zygote to adult results from cell division, cell differentiation, and morphogenesis

Cell differentiation is the process by which cells become specialized in structure and function
The physical processes that give an organism its shape constitute morphogenesis
Differential gene expression results from genes being regulated differently in each cell type
Materials in the egg can set up gene regulation that is carried out as cells divide

Cytoplasmic Determinants and Inductive Signals
An egg’s cytoplasm contains RNA, proteins, and other substances that are distributed unevenly in the unfertilized egg
Cytoplasmic determinants are maternal substances in the egg that influence early development
As the zygote divides by mitosis, cells contain different cytoplasmic determinants, which lead to different gene expression

The other important source of developmental information is the environment around the cell, especially signals from nearby embryonic cells
In the process called induction, signal molecules from embryonic cells cause transcriptional changes in nearby target cells
Thus, interactions between cells induce differentiation of specialized cell types
Sequential Regulation of Gene Expression During Cellular Differentiation
Determination commits a cell to its final fate
Determination precedes differentiation
Cell differentiation is marked by the production of tissue-specific proteins

Myoblasts produce muscle-specific proteins and form skeletal muscle cells
MyoD is one of several “master regulatory genes” that produce proteins that commit the cell to becoming skeletal muscle
The MyoD protein is a transcription factor that binds to enhancers of various target genes

Pattern Formation: Setting Up the Body Plan
Pattern formation is the development of a spatial organization of tissues and organs
In animals, pattern formation begins with the establishment of the major axes
Positional information, the molecular cues that control pattern formation, tells a cell its location relative to the body axes and to neighboring cells

Pattern formation has been extensively studied in the fruit fly Drosophila melanogaster
Combining anatomical, genetic, and biochemical approaches, researchers have discovered developmental principles common to many other species, including humans
The Life Cycle of Drosophila
In Drosophila, cytoplasmic determinants in the unfertilized egg determine the axes before fertilization
After fertilization, the embryo develops into a segmented larva with three larval stages

Genetic Analysis of Early Development: Scientific Inquiry
Edward B. Lewis, Christiane Nüsslein-Volhard, and Eric Wieschaus won a Nobel 1995 Prize for decoding pattern formation in Drosophila
Lewis demonstrated that genes direct the developmental process

Nüsslein-Volhard and Wieschaus studied segment formation
They created mutants, conducted breeding experiments, and looked for corresponding genes
Breeding experiments were complicated by embryonic lethals, embryos with lethal mutations
They found 120 genes essential for normal segmentation
Axis Establishment
Maternal effect genes encode for cytoplasmic determinants that initially establish the axes of the body of Drosophila
These maternal effect genes are also called egg-polarity genes because they control orientation of the egg and consequently the fly

One maternal effect gene, the bicoid gene, affects the front half of the body
An embryo whose mother has a mutant bicoid gene lacks the front half of its body and has duplicate posterior structures at both ends

This phenotype suggests that the product of the mother’s bicoid gene is concentrated at the future anterior end
This hypothesis is an example of the gradient hypothesis, in which gradients of substances called morphogens establish an embryo’s axes and other features

The bicoid research is important for three reasons:
–    It identified a specific protein required for some early steps in pattern formation
–    It increased understanding of the mother’s role in embryo development
–    It demonstrated a key developmental principle that a gradient of molecules can determine polarity and position in the embryo
Concept 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

Types of Genes Associated with Cancer
Cancer can be caused by mutations to genes that regulate cell growth and division
Tumor viruses can cause cancer in animals including humans

Oncogenes and Proto-Oncogenes
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

Proto-oncogenes can be converted to oncogenes by
Movement of DNA within the genome: if it ends up near an active promoter, transcription may increase
Amplification of a proto-oncogene: increases the number of copies of the gene
Point mutations in the proto-oncogene or its control elements: causes an increase in gene expression
Tumor-Suppressor Genes
Tumor-suppressor genes help prevent uncontrolled cell growth
Mutations that decrease protein products of tumor-suppressor genes may contribute to cancer onset
Tumor-suppressor proteins
Repair damaged DNA
Control cell adhesion
Inhibit the cell cycle in the cell-signaling pathway
Interference with Normal Cell-Signaling Pathways
Mutations in the ras proto-oncogene and p53 tumor-suppressor gene are common in human cancers
Mutations in the ras gene can lead to production of a hyperactive Ras protein and increased cell division

Suppression of the cell cycle can be important in the case of damage to a cell’s DNA; p53 prevents a cell from passing on mutations due to DNA damage
Mutations in the p53 gene prevent suppression of the cell cycle

The Multistep Model of Cancer Development
Multiple mutations are generally needed for full-fledged cancer; thus the incidence increases with age
At the DNA level, a cancerous cell is usually characterized by at least one active oncogene and the mutation of several tumor-suppressor genes

Inherited Predisposition and Other Factors Contributing to Cancer
Individuals can inherit oncogenes or mutant alleles of tumor-suppressor genes
Inherited mutations in the tumor-suppressor gene adenomatous polyposis coli are common in individuals with colorectal cancer
Mutations in the BRCA1 or BRCA2 gene are found in at least half of inherited breast cancers

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

Explain how DNA methylation and histone acetylation affect chromatin structure and the regulation of transcription
Define control elements and explain how they influence transcription
Explain the role of promoters, enhancers, activators, and repressors in transcription control

Explain how eukaryotic genes can be coordinately expressed
Describe the roles played by small RNAs on gene expression
Explain why determination precedes differentiation
Describe two sources of information that    instruct a cell to express genes at the appropriate time

Explain how maternal effect genes affect polarity and development in Drosophila embryos
Explain how mutations in tumor-suppressor genes can contribute to cancer
Describe the effects of mutations to the p53 and ras genes

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