BSCI222 Exam 3 Study Guide- Dr. O’BrochtaChapter 17- Control of Gene Expression in EukaryotesI. 17.1 Eukaryotic Cells and Bacteria Have Many Features of Gene Regulation in Common,but They Differ in Several Important Ways- Similarity: DNA-binding proteins influence the ability of RNA polymerase to initiate transcription- Difference: a.Most eukaryotic genes are not organized into operons and are not transcribed together into a single mRNA moleculeo Each structural gene of eukaryotes typically has its own promoter and is transcribed separatelyb. Chromatin structure affects gene expression in eukaryotes; DNA must unwind from histone proteins before transcription can take placec.The presence of the nuclear membrane in eukaryotic cells separates transcription and translation in time and spaced. Larger genomes in eukaryotes; greater sequence complexityII. 17.2 Changes in Chromatin Structure Affect the Expression of Genes-Gene control in eukaryotic cells is accomplished through modification of chromatin structure-In nucleus, histone proteins associate to form octamers, around which helical DNA coils to create chromatin (represses gene expression)-DNA needs to become more accessible in order for transcription and translation to occura.DNase I Hypersensitivityo As genes become transcriptionally active, regions around genes become sensitive to action of DNase I (DNase I Hypersensitive sites);develop ~100 nucleotides upstream of the start site, suggesting chromatin has an open configuration during transcriptiono Correspond to binding sites for regulatory proteins-3 processes affect gene regulation by altering chromatin structure:1. Modification of histone proteins-Histones in the octamer core of nucleosome have two domains: (1) a globulardomain that associates with other histones and DNA and (2) a positively charged tail domain that interacts with negatively charged DNA (phosphate backbone)-Tails of histone proteins are often modified (histone code= encode information that affects how genes are expressed)a. Methylation of histones-addition of methyl group to the tails of histone proteins, bringing about either the activation or repression of transcriptionb. Acetylation of histones-addition of acetyl group (CH3CO) to histone proteins, stimulating transcription by destabilizing chromatin structure-acetyl groups added by acetyltransferase enzymes; removed by deacetylase enzymes, which represses transcription2. Chromatin remodeling -chromatin-remodeling complexes: alter chromatin structure without altering the chemical structure directly; they bind directly to DNA and reposition the nucleosomes, allowing transcription to occur(1) cause the nucleosome to slide along DNA so it is in between nucleosomes and more easily accessible for gene expression(2) cause conformational changes in DNA, nucleosomes, or both so DNA is exposed-C-R complexes are targeted to specific DNA sequences by transcriptional activators or repressors3. DNA methylation-addition of methyl group to cytosine bases, yielding 5-methylcystosine-heavy methylated DNA is associated with repression of transcription (transcriptionally activate DNA=unmethyated); abnormal methylation associated with cancer-DNA methylation is common on cytosines adjacent to guanine nucleotides (CpG)-DNA regions with many CpG sequences are called CpG islands, found near start sites-CpG methyl group removed before initiation of transcription**DNA methylation and deacetylation of histones repress transcriptionIII. 17.3 Epigenetic Effects Often Result from Alterations in Chromatin Structure- Epigenetics: alterations to DNA and chromatin structure that affect traits and are passed on to other cells or future generations but are not caused by changes in DNA base sequences (everything talked about above)o Effects:a. Epigenetics changes induced by maternal behavior (more groming= different methylation, alters expression of certain genes)b. Epigenetic effects caused by prenatal exposurec. Epigenetic effects in monozygotic (identical) twins- Paramutation: one allele of a genotype alters expression of another alleleo Violates Mendel’s law of segregation= when gametes are formed, each allele separates and is transmitted independently to the next generation- Molecular mechanisms of epigenetic changes: the fact that epigenetic marks are passed on to other cells and possibly future generations means that changes in chromatin structure associated with epigenetic phenotypes must be faithfully maintained when chromosomes replicateo After replication, special methyltransferase enzymes recognize the hemimethylated state of CpG dinucleotides and add methyl groups to the unmethylated C bases, creating two new DNA molecules that are fully methylatedo Epigenome: the overall pattern of chromatin modifications possessed by each individual organism; helps explain stable patterns of gene expression (i.e. distinguish between nerve cell and liver cell)a. Embryonic stem cells are undifferentiated cells that are capable of forming every type of cell, a property referred to as pluripotencyIV. 17.4 The Initiation of Transcription Is Regulated by Transcription Factors and Transcriptional Regulator Proteins- Control through the binding of proteins to DNA sequences that affect transcriptiono General transcription factors and RNA polymerase assemble into a basal transcription apparatus, which binds to a core promoter located upstream of a gene.o The basal transcription apparatus is capable of minimal levels of transcription;transcriptional regulator proteins are required for normal transcription and they bind to a regulatory promoter upstream from core promoter, as well as to enhancers- Transcriptional activator proteins stimulate and stabilize the basal transcription apparatus at the core promoter (directly or indirectly via protein coactivators)- Some activators and coactivators have acetyltransferase activity to stimulate transcription by altering chromatin structure- Activators have two distinct functions:o Binding DNA at a specific base sequence (consensus sequence in regulatory promoter or enhancer); transcriptional activator proteins contain one or more DNA-binding motifs Affect assembly or stability of basal transcription apparatus at core promoter One of the components of the basal transcription apparatus is the mediator, which makes contact with the activator proteins and affect rate of transcription initiationo Interact with other components of transcriptional apparatus