Gene Expression Regulation + Epigenetics PDF

🧬 Topic 5 - Gene Expression Regulation + Epigenetics Gene Expression Regulation in Eukaryotic Cells What is the purpose of gene regulation cells need to conserve energy + resources...

🧬 Topic 5 - Gene Expression Regulation + Epigenetics Gene Expression Regulation in Eukaryotic Cells What is the purpose of gene regulation cells need to conserve energy + resources break down proteins when necessary what are the 3 eukaryotic expression elements Promoter region - contains regulatory elements Enhancer/suppressor elements - found upstream/downstream that can regulate transcription by enhancing/supressing expression TATA Box - influences binding of TATA binding protein + RNA polymerase + formation of eukaryotic transition complex (prokaryotes lack an extensive regulatory system for transcription) Explain how the Eukaryotic Transcription Complex works Topic 5 - Gene Expression Regulation + Epigenetics 1  TATA binding protein (TBP) recognizes TATA box and binds to DNA (sometimes with TFII D.) TFII A and TFII B bind to TBP. RNA polymerase binds to the complex. Basal Trasncription factors subsequently bind (TFIIE, TFIIH, and TFIIF) Once all components are bound, the transcription initiation complex is complete. co-activators may join to help regulate transcription. Explain how the Metabolic pathway regulation works Regulation of biochemical pathways can occur in two ways: 1. Regulation of enzyme activity. 2. Regulation of enzyme production. enzyme inhibition —> Abundant tryptophan binds to the first enzyme in the pathway, inhibiting subsequent steps in the pathway. negative feedback —> Abundant tryptophan can provide negative feedback to the genes responsible for encoding enzymes in the pathway. It does this by inhibiting transcription of these genes, so enzymes aren't produced. Topic 5 - Gene Expression Regulation + Epigenetics 2  What are operons? An operon = operator, the promoter, and the genes it controls — all in one stretch of DNA. The "switch" in DNA is called an operator, and it's often found within the promoter. What are repressible operons + give an example A repressible operon is a switch that is usually on 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 trp operon is an example repressible operon explain how trp operons functions in E. coli as an example tryptophan present, repressor active, operon off, no RNA Made Tryptophan absent, repressor inactive, operon on, RNA Made Topic 5 - Gene Expression Regulation + Epigenetics 3  What are inducible operons An inducible operon is typically turned off, and can be activated by a small molecule An inducer molecule can deactivate the repressor, switching on gene transcription. e.g. lac operon → inducible operon and contains genes that code for enzymes used in the hydrolysis and metabolism of lactose Lactose absent, repressor active, operon off. Topic 5 - Gene Expression Regulation + Epigenetics 4  Lactose present, repressor inactive, operon on. Define negative gene regulation Negative regulation: operons are switched off due to active repressor Explain how Positive Gene Regulation occurs Positive regulation: stimulatory protein, such as cyclic AMP receptor protein (CRP), an activator of transcription cAMP binds to CRP → activates CRP → enhances mRNA synthesis → increases likelihood of RNA Polymerase binding to promoter (inactive lac repressor present) cAMP absent + lac present → transcription occurs → little mRNA synthesised → RNA Polymerase less likely to bind to the promoter. (Inactive repressor present) Topic 5 - Gene Expression Regulation + Epigenetics 5  Differential gene expression Cells within an organism share the same genome., Different cell types arise from using different genes within the genome. Genes respond to signals from their surroundings and internal conditions.. Irregular gene expression can cause diseases, like cancer. How do enhancers work Enhancers are areas before the promoter where activator molecules can attach. DNA-bending proteins bend and loop the DNA to bring the enhancer closer to the promoter. helps stabilize the transcription complex and initiate transcription. Topic 5 - Gene Expression Regulation + Epigenetics 6  Explain how nuclear hormone receptors initiate transcription Example: Glucocorticoid receptor (GR). GR is inactive + bound by heat-shock protein (HSP) in the cytoplasm. When cortisol is present, it binds to GR, displacing HSP due to stronger binding. GR becomes active, changes shape, and carries a specific sequence to the nucleus. In the nucleus, GR finds DNA sequences and activates the basal transcription complex to start transcription. In the absence of cortisol, GR stays inactive. Topic 5 - Gene Expression Regulation + Epigenetics 7  Alternative splicing different mRNA molecules are produced from the same primary transcript Production of different mRNA molecules depending on which regions are treated as exons and which are treated as introns Alternative splicing results in isoforms (mRNA with similar structure but result in different functions) - Provides an explanation for why there is a low number of genes in the genome that can result in a variation of proteins How is translation regulated (IRE-BP) Iron response element binding protein (IRE-BP) binds to mRNA, blocking translation. When iron is present, IRE-BP changes shape and releases mRNA, allowing translation. But downstream, IRE-BP binds again to prevent mRNA breakdown. Iron is no longer bound to mRNA, leading to IRE-BP degradation. How is translation regulated by micro RNA Micro RNAs, made by RNA polymerase II, are single-stranded molecules. They stick to mRNA with matching sequences, blocking ribosomes → stopping translation. Micro RNA can also lead to mRNA degradation Topic 5 - Gene Expression Regulation + Epigenetics 8  Where is the nucleotide sequence that influences the life span of mRNA found? Nucleotide sequences that influence the life span of mRNA in eukaryotes reside in the untranslated region (UTR) at the 3′ end of the molecule Chromatin and Epigenetic Regulation Chromatin structure Chromatin = DNA + protein Most chromatin is loosely packed in the nucleus during interphase chromatin condenses prior to mitosis Loosely packed chromatin is called euchromatin (nucleosomes aren’t close together) During interphase a few regions of chromatin (centromeres and telomeres) are highly condensed into heterochromatin Dense packing of the heterochromatin makes it difficult for the cell to express genetic information coded in these regions Topic 5 - Gene Expression Regulation + Epigenetics 9  chromatin fiber folded into loops → solenoid fibres 2 ways chromatin structure is regulated Chromatin remodelers (CRC, Chaperons, Chemical Modification) Histone modifiers State 3 Chromatin Remodelers Chromatin remodelling complex, chaperons, chemical modification Chromatin Remodelling complex A chromatin remodelling complex are enzymes (that uses energy from ATP) binds the nucleosome of DNA. ATP→ADP releases energy which pushes nucleosomes (DNA wrapped around histones) away from each other by sliding, exposing DNA regions important for transcription. Nucleosomes can be removed, which exposes DNA Topic 5 - Gene Expression Regulation + Epigenetics 10  Chaperons Chaperones = proteins that assist in forming, changing or rebuilding nucleosomes. Chaperons act as Remodelers with the remodelling complex to dissociate nucleosomes from DNA Chemical Modification Changing histone proteins tails, with chemical modifications like methylation, phosphorylation, or acetylation, sends signals for gene regulation. modifications are irreversible Histone Acetylation In histone acetylation, acetyl groups (-ve charge) are attached to an amino acid in a histone tail Adding acetyl groups to histone tails opens up the chromatin structure, making it more loosely packed Acetylation cancels out the positive charge on histone tails, preventing tight DNA wrapping, and encourages transcription. Methylation of DNA Methylation promotes DNA wrapping, reducing transcription, and can permanently silence genes during cellular development. In genomic imprinting, methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development. Methylation of Promoter elements Topic 5 - Gene Expression Regulation + Epigenetics 11  Methylation of promoter elements shuts down transcription by making it difficult for factors to bind or by attracting other proteins to bind instead. Define Allelic exclusion (Give 2 Examples) only one allele of a gene is expressed while the other allele is silenced Genomic Imprinting X-Chromosome Inactivation Genomic Imprinting Genomic imprinting = silencing of certain genes depending on which parent passes them on imprinting is the result of the methylation of cytosine nucleotides X Chromosome Inactivation In female mammals, one of their two X chromosomes is randomly turned off during embryonic development The turned-off X → condensed structure called a Barr body. This process involves DNA methylation and changes in chromatin structure. When a female is heterozygous of a gene on her X chromosomes, she can have a mix of traits related to that gene, creating a mosaic pattern Topic 5 - Gene Expression Regulation + Epigenetics 12  Define epigenetic inheritance The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence. Topic 5 - Gene Expression Regulation + Epigenetics 13