Chapter 18 Regulation of Gene Expression

Differential gene expression

differences between cell types results from differential gene expression, the expression of different genes by cells with the same genome. Abnormalities in gene expression can lead to diseases including cancer. Gens expression is regulated at many stages. Almost all cell sin an organism are genetically identical.

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

charges of histone protein and DNA

histone protein have an overall positive charge, and the DNA has a negative charge. The positive charge in histone proteins allow them to interact tightly with negatively charged DNA, thus inhibiting transcription. to disrupt this interaction, the histone proteins would have to be made more negatively charged.

Combination control of gene activation

a particular combination of control elements can active transcription only when the appropriate activator proteins are present.

Two types of negative gene regulation

Repressible and Inducible Operons

Inducer

A molecule called inducer inactivates the repressor to turn the lac operon on.

Operon model

One mechanism for control of gene expression in bacteria is the operon model.

Activator

Some operons are also subject to positive control through a stimulator protein, such as catabolite activator (CAP), an activator of transcription.

Nuclear Architecture and Gene Expression

Loops of chromatin extend from individual chromosome territories into specific sites in the nucleus Loops from different chromosomes may congregate at particular sites, some of which are rich in transcription factors and RNA polymerases These may be areas specialized for a common function

Regulatory gene

The repressor is the product of a separate regulatory gene.

steps of eukaryotic gene expression

1. unpacking of DNA. 2. Transcription of gene 3. processing of RNA 4. Export of mRNA 5. Breakdown of mRNA 6. Translation of mRNA 7. Breakdown of protein. 8. Activation of protein

Gene regulation

A cell can regulate the production of enzymes by feedback inhibition or by gene regulation

On-Off switch

A cluster of functionally related genes can be coordinately controlled by a single "on-off switch"

Operon

An operon is the entire stretch of DNA that includes the operator, the promoter, and the genes they control.

Control elements

Associated with most eukaryotic genes are multiple control elements, segments of noncoding DNA that serve as binding sites for transcription factors that help regulate transcription. Control elements and the transcription factors they bind are critical to the precise regulation of gene expression in different cell types.

Regulation of transcription initiation

Chromatin-modifying enzymed provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery.

Coordinately controlled genes in eukaryotes

Co-expressed eukaryotic genes are not organized in operons (with a few minor exceptions) 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

HW notes

DNA methylation is a mechanism used by eukaryotes to do what? Inactivate genes- involving the attachmment of methyle groups to certain bases, is a mechanism for the long-term inactivation of genes during development. Enzyme complexes that break down protein are called Proteasomes. The nuclear membrane's role in the regulation of gene expression involves Regulating the transport of mRNA to the cytoplasm. function of spliceosome- RNA processing. Protein-phosphorylation enzymes' role in the regulation of gene expression involves. DNA-protein complexes that look like beads on a string in the chromatin are the nucleosomes. Activators are not composed of DNA sequence but promoter-proximal elements, enhancers and silencers are. Last event in transcription initiation to likely occurs is RNA polymerase binds to the promoter of the gene.

Enhancer

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

HW definition notes

Operon- a stretch of DNA consisting of an operator, a promoter, and genes for a related set of proteins, usually making up an entire metabolic pathway. Operon 2nd DEF- operon is a region of DNA that codes for a series of funtionally related genes under the control of the same promoter. Genes of an operon- is/are arranged sequentially after the promoter. Promoter- is a specific nucleotide sequence in DNA that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place. Regulator Gene- codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes. Repressor- is a protein that inhibits gene transcription. In prokaryotes, this protein binds to the DNA in or near the promoter. Inducer- is a specific small molecule that binds to a bacterial regulatory protein and changes its shape so that it cannot bind to an operator, thus switching an operon on. RNA polymerase- the molecule binds to promoters in bacteria and transcribes the coding regions of the genes. Allosteric regulation- in allosteric regulation, a small molecule binds to a large protein and causes it to change its shape and activity. lac structural genes expressed efficiently with No glucose, and High lactose. lacZ gene- This gene encodes an enzyme, b-galactosidase, which cleaves lactose into glucose and galactose. b-galactosidase- enzyme that converts ATP to cAMP

Differential expression of genes

Prokaryotes and eukaryotes precisely regulate gene expression in response to environmental conditions. In multicellular eukaryotes, gene expression regulates development and is responsible for differences in cell types. RNA molecules play any roles in regulation gene expression in eukaryotes.

Operator

The "switch" is a segment of DNA called an operator usually positioned within the promoter.

Epigenetic inheritance

The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance. Although the chromatin modification just discussed do not alter DNA sequence they may be passed to future generations of cells.

initiation of translation and mRNA degradation

The initation of translation of selected mRNAs can be blocked by regulatory proteins that bind to sequences or structures of the mRNA. Alternatively, tranlation of all mRNAs in a cell may be regulated simultaneously. For example, translation initiation factors are simultaneously activated in an egg following fertilization. The life span of mRNA molecules in the cytoplasm is a key to determining protein synthesis. Eukaryotic mRNA is more long lived than prokayrotic mRNA. Nucleotide sequences that influence the lifespan of mRNA in eukaryotes reside in the untranslated region (UTR) at the 3'end of the molecule.

Repressor

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 can be in a active or inactive form, depending on the presence of other molecules.

Roles of Transcription factors

To initiate transcription, eukaryotic RNA polymerase requires the assistance of 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.

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

cyclic AMP (cAMP)

When glucose (a preferred food source of E. coli) is scarce, CAP is activated by binding with cyclic AMP (cAMP). 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.

Histone acetylation

acetyl groups are attached to positively charged lysines in histone tails. This 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.

Two domains of activators

activators have two domains, one that binds DNA and a second that activates transcription Bound activators facilitate a sequence of protein-protein interactions that result in transcription of a given gene.

Protein processing and degradation

after translation, various types of protein processing, including cleavage and the addition of chemical groups, are subject to control. The length of time each protein function is regulated by selective degradation Cells mark proteins for degradation by attaching ubiquitin to them This mark is recognized by proteasomes, which recognize and degrade the proteins

Eukaryotic gene expression

all organisms must regulate which genes are expressed at any given time. In multicellular organisms regulation of gense expression is essential for cell specialization.

Activator

an activator is a protein that binds to an enhancer andn stimulates transcription of a gene.

Regulatory transcription and Basal transcription factors

basal transcription factors bind to the promoter but regulatory transcription factors bind to to promoter-proximal elements and enhancers. Basal transcription factors are required for transcription to occur they are not cell specific and do not provide much in the way of regulation. The basal transcription bind with the promoter to form a basal transcription complex

TATA-binding protein (TBP)

binds to a specific sequence, known as the TATA box, within the promoter. The TATA-binding protein allows RNA polymerase to contact DNA. The basal transcription complex then recruits RNA polymerase, and transcription begins.

trp Operon

by default the trp operon is on the genes for tryptophan synthesis are transcribed. When tryptophan is present, it bind 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.

Regulation of the trp and lac operons involves what?

involves negative control of genes because operons are switched off by the active form of the repressor.

Corepressor

is a molecule that cooperates with a repressor protein to switch an operon off. EX: E. coli can synthesize the amino acid tryptophan when it has insufficient tryptophan.

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. Repressible enzymes usually function in anabolic pathways; their synthesis is repressed by high levels of the end product.

Inducible Operon

is the one that is usually off; a molecule called an inducer inactivates the repressor and turns on transcription. The (lac) 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. Inducible enzyems usually function in catabolic pathways; their synthesis is induced by a chemical signal.

Repressors

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

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.

Regulation of chromatin structure

the structural organization of chromatin helps regulate gene expression in several ways. Genes within highly packed heterochromatin are usually not expressed. Chemical modifications to histones and DNA of chromatin influence both chromatin structure and gene expression