Gene Regulation

Genes can be ______ from cells or they can be ______, ______, or ________.

deleted, amplified, rearranged, modified (e.g. methylated)

Operons (more detailed summary)

- A set of genes that are adjacent to one another in the genome and are coordinately controlled; that is, the genes are either all turned on or all turned off - The structural genes of an operon code for a series of different proteins - A single polycistronic mRNA is transcribed from an operon. This single mRNA codes for all the proteins of the operon. - A series of start and stop codons on the polycistronic mRNA allows a number of different proteins to be produced at the translational level from the single mRNA

What condenses and what loosens chromatin?

- Addition of methyl groups can condense chromatin - Addition of phosphate groups next to the methylated amino acid can loosen chromatin

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

Epigenetic Inheritance of Chromatin Modifications

- Although chromatin modifications 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

Repressible enzymes usually function in ____________ pathways.

- Anabolic - Their synthesis is repressed by high levels of the end product

Control Elements

- Associated with most E 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

Inducible enzymes usually function in _______________ pathways.

- Catabolic - Their synthesis is induced by chemical signal

Induction (in E Coli)

- E. Coli uses glucose preferentially whenever it is available - The enzymes in the pathways for glucose utilization are made constitutively (constantly being produced) - If glucose is not present in the medium but another sugar is available, E. Coli produces the enzymes and other proteins that allows the cell to drive energy from that sugar **This process of regulation is call INDUCTION

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

Distal Control Elements

- Groups of which are called enhancers - May be far away from a gene or even located in the intron

Lactose (Lac) Operon

- Inducible - A metabolite of lactose, allolactose, is the inducer - Proteins produced by the genes of the lac operon allow the cell to oxidize lactose as a source of energy - Gene Z produces a alpha-galactosidase; gene Y, a lactose permease; and Gene A, a transacetylase - The lac operon is induced ONLY in the absence of glucose

Regulation of trp and lac operons

- Involves negative control of genes because operons are switched off by the active form of the repressor

Proximal Control Elements

- Located close to the promoter

Genomic Imprinting

- Methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development

Two strategies for regulation of metabolic pathways in prokaryotes

- Natural selection has favored bacteria that produce only the products needed by that cell - A cell can regulate a metabolic pathway by regulation of the ENZYME ACTIVITY (e.g. feedback inhibition) or the production of enzymes by regulation of GENE EXPRESSION - Gene expression in bacteria is controlled by the operon model

siRNAs

- Products of double stranded RNAs - Can have viral origin or be products of repeats transcription, etc. - They bind to mRNA in the case of complete complimentarity

Tryptophan (trp) Operon

- Repressible - Tryptophan is the corepressor - The proteins encoded by the trp operon are involved in the synthesis of tryptophan - The trp operon is repressed in the presence of tryptophan, since cells do not need to make the amino acid if it is present in the growth medium

DNA methylation

- The addition of methyl groups to certain bases in DNA - Associated with reduced transcription in some species - Can cause long term inactivation of genes in cellular differentiation

Regulation of transcription initiation

- The frequency with which RNA Polymerase binds to the promoter and initiates RNA synthesis determines the amount of transcription from most genes

Gene Regulation at the protein synthesis level

- 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 - ex. Translation initiation factors are simultaneously activated in an egg following fertilization

miRNA

- The products of many genes scattered throughout the chromosome, some even located in the introns of the genes they regulate - micro RNAs - Products of dsRNAs encoded in the genes of our genome - They do not require full complementarity to bind with target mRNA, e.g. one type of miRNA may regulate many genes, as well as one gene can be regulated by several miRNAs

Transcription Factors

- To initiate transcription, E RNA polymerase requires the assistance of proteins called transcription factors (tf) - General tfs are essential for the transcription of all protein-coding genes - In E, high levels of transcription of particular genes depend on control elements interacting with specific transcription factors

Promoter region and the "operator"

- Transcription begins near the promoter region, located upstream from the group of structural genes - Associated with the promoter is a short sequence, the OPERATOR, which determines whether the genes are expressed or not - Binding of a repressor protein to the operator region prevents the binding of RNA polymerase to the promoter and inhibits transcription of the structural genes of the operon - Repressor proteins are encoded by regulatory genes which may be located anywhere in the genome

Differences in eukaryotic and prokaryotic cells important for the regulation of gene expression (11)

1) Eukaryotic cells undergo differentiation, and the organisms go through various developmental stages 2) E contain nuclei. Therefore, transcription is separated from translation. In P, transcription and translation occur simultaneously 3) The DNA is complexed with histones in E, but not in P. Regulating the association of the DNA with histones can regulate gene expression in E 4) The mammalian genome contains about 1,000 times more DNA than E. Coli 5) Most mammalian cells are diploid 6) The major part of the genome of mammalian cells does not code for proteins 7) Some E genes, like most bacterial genes, are unique (i.e. they exist in one or small number of copies per genome) 8) Other E genes, unlike bacterial genes, have many copies in the genome (e.g. genes for tRNA, rRNA, histones) 9) Relatively short, repetitive DNA sequences are dispersed throughout the E genome. They do not code for proteins (e.g. Alu sequences) 10) E genes contain introns. Bacterial genes do not 11) Bacterial genes are organized in operons (sets that are under the control of a single promoter) Each E gene has its own promoter

The process of induction

1) The inducer binds to the repressor, inactivating it 2) The inactive repressor does not bind to the operator 3) RNA Polymerase can bind to the promoter and transcribe the operon 4) The structural proteins encoded by the operon are produced

Activator

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

Alternative polyadenylation sites

Can be used to generate different mRNAs

Gene silencing

Can occur through the use of small RNA products (miRNA, siRNA, etc.) which can either block the translation of a target mRNA or induce degradation of the target mRNA

Bound activators

Cause mediator proteins to interact with proteins at the promoter

Inducers (in gene regulation)

Cause proteins to bind to DNA sequences (response elements) and stimulate transcription of specific genes

Operons (short summary)

Contain promoter regions where proteins bind and facilitate or inhibit the binding of RNA polymerase

Regulatory elements in DNA sequences

Control the expression of genes that produce proteins. They include: - The basal promoter (TATA box and other sequences near the start site) - Enhancer sequences - Silencer sequences

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

RNA polymerase in gene regulation

RNA Polymerase transcribes the genes of an operon into a polycistronic mRNA - It codes for more than one protein

Gene regulation occurs during what process and involves what?

Regulation occurs during the processing of RNA to form mRNA and involves: - Use of alternative start sites for transcription - Alternative splice sites for removal of introns - Alternative poly-adenylation sites for addition of the poly(A) tail - RNA editing

Gene regulation in eukaryotes

Regulation of protein synthesis can occur at every level of the process: - Modification of DNA or the chromatin - Level of transcription within the nucleus - Processing of mRNA in the nucleus - Translation in the cytoplasm - Post-translational modification or degradation throughout the cell

Repression (more detailed summary)

The process whereby a corepressor (a small molecule) inhibits the transcription of an operon - The corepressor is usually an amino acid and the proteins produced from the repressible operon are involved in the synthesis of the amino acid

Induction

The process whereby an inducer (a small molecule) stimulates the transcription of an operon - The inducer is frequently a sugar (or a metabolite of sugar) and the proteins produced from the inducible operon allow the sugar to be metabolized

Degradation of mRNAs

mRNAs can be degraded by nucleases after their synthesis in the nucleus and before their translation in the cytoplasm

Histones _________ ____________ transcription of genes

non-specifically repress

Histone acetylation

- Acetyl groups are attached to positively charged lysines in histone tails - This process loosens chromatin structure promoting the initiation of transcription

Process of repression

1) The corepressor binds to the repressor, activating it 2) The active repressor binds to the operator 3) RNA Polymerase cannot bind to the promoter and that operon is not transcribed 4) The cell stops producing the structural proteins encoded by the operon

Repression (short summary)

As opposed to induction, if an amino acid is present in the medium, E. Coli does not need to synthesis that amino and conserves energy by ceasing to produce the enzymes required for its synthesis. ----> This is called repression

RNA editing

Involves the alteration (editing) of bases in mRNA after transcription

Regulation of Protein synthesis in prokaryotes

Mainly transcriptional and is coordinated in operons