Gene Control: Jacob-Monod: The Lac Operon

Gene Control Jacob-Monod: The Lac operon: The Jacob-Monod Lac operon was the first gene regulatory mechanism that was clearly understood (the idea that the control of enzyme levels is cells occurs at the level of transcription) Operon: a unit of genomic DNA containing a cluster of genes that are under control of a single regulatory signal (basically genes of an operon are expressed all together or not at all) If glucose is unavailable, then the cell has the option of using lactose as a backup energy source (the lac operon is activated by the removal of the repressor from the operator site) Inducer Molecule: is the molecule that induces the transcription of a particular set of genes (in this case it’s allolactose (an isomer of lactose) since it binds to the repressor) Inducer Exclusion: occurs when there is both glucose and lactose readily available (glucose transport generates a protein intermediate that binds to the lactose permease which inhibits it from bringing any lactose into the cell) DNA & Chromatin Regulation: The cell only wants to make proteins and stuff if it needs it (this leads to greater efficiency) Chromatin: is how DNA looks within a cell and is made up of DNA, histone proteins, and non-histone proteins Nucleosome: repeating organizational unit of chromatin (made up of 146 base pairs wrapped around a core of 8 histones - H2A, H2B, H3, and H4). An acetyl group is found at the amino terminal tails of these histone proteins (done by histone acetyltransferase) and the acetyl group is removed by histone deacetylase Acetylation of histones leads to an uncoiling of structure which allows it to be accessed by transcription mechanisms (RNA Pol, transcription factors, etc.) while deacetylation causes the coiling of the structure and blocks the genes from being transcribed Epigenetics: study of heritable changes in gene expression that do not involve changes to the actual DNA sequence (leads to a change in phenotype with no change in genotype) Heterochromatin: densely packed and transcriptionally silent DNA Euchromatin: less densely packed and transcriptionally active DNA Methylation: often paired with deacetylation occurs through a process known as gene silencing (a more permanent method of downregulating the transcription of genes) and involves the addition of a methyl group (-CH3) to the cytosine DNA nucleotides by the enzyme methyltransferase CpG Sites: sequences with a cytosine and a guanine right next to each other and this gene silencing occurs in areas high in cytosine concentration (like here) Regulation of Transcription: All cells have the exact same DNA General Transcription Factors: a general class of proteins that bind to specific sites on DNA to activate transcription Activator: further enhances the interaction between RNA polymerase and a promoter which further encourages the expression of that particular gene An example of this is the Catabolite Activator Protein (CAP) which activates transcription of the lac operon: cAMP that is produced during glucose starvation binds to CAP which conformationally changes the protein, allowing it to bind to a DNA site adjacent to the promoter. From here, it makes a direct protein-protein interaction with RNA pol in order to recruit it to the promoter Enhancer: sites on the DNA that are bound to by activators in order to loop the DNA in a certain way that brings a specific promoter to the initiation complex (makes sure that a certain portion of the gene will be transcribed Repressor: binds to the operator and impedes RNA polymerase from transcribing the DNA downstream of it (however, an inducer can interact with it and get rid of it) Silencer: regions of DNA that are bound by repressor proteins in order to silence gene expression (similar to enhancers where the DNA loops) Prokaryotes vs. Eukaryotes: Proks: regulation of transcription is needed in order for the cell to quickly adapt to the changing environment Euks: tends to involve regulation of a whole bunch of transcription factors, allowing for a more sophisticated response to multiple conditions in their environment Post-Transcriptional Regulation: This form of regulation (post-transcriptional regulation) only occurs in eukaryotic cells Introns are spliced out by spliceosomes (ligates exons together) Also, a 5’ cap (modified guanine is added and protects from degradation by exonucleases, regulates nuclear export, and helps bind to ribosomes) and a 3’ poly-AAA tail (a repeating sequence of adenine and does everything a 5’ cap does but also helps RNA pol know when to stop transcribing and is done by polyadenylate polymerase - built until its about 250 nucleotides long) RNA Editing: relatively rare and include insertion, deletion, and base substitution Non-coding RNAs: An ncRNA is a functional RNA that never gets converted into protein (most of which participate in transcription or translation in one way or another) Micro RNA (miRNA): function in transcriptional and post-transcriptional regulation of gene expression and they do this by base pairing with mRNA molecules and usually results in gene silencing Ribosomal RNA (rRNA): makes up a portion of a ribosome Transfer RNA (tRNA): adapter molecule that links the codons in an mRNA to the corresponding amino acid Small Nucleolar RNA (snoRNA): class of small RNA molecules that guide covalent modifications of rRNA, tRNA, and snoRNA through methylation or pseudouridylation (isomer of nucleoside uridine) Small Nuclear RNA (snRNA): gets their name because the average length of their molecules are about 150 nucleotides and their primary function includes processing of pre-mRNA (also aid in the regulation of transcription factors and maintains telomeres) Small Nuclear Ribonucleoproteins (snRNP): a combination of snRNA and protein (i.e. the spliceosome which is made up of snRNA and protein) Oncogenes: Oncogenes: genes that code for proteins that contribute to cell growth and differentiation (begin as proto-oncogenes) Mitogen: a chemical substance that encourages a cell to begin the cell division cycle, basically triggering mitosis 3 main ways that a protooncogene → oncogene: 1. Deletion/Point Mutation: produces a protein that is made in the same normal amount but is hyperactive for some reason or loss of regulation and the protein is simply overexpressed 2. Gene Amplification: increases mRNA stability and therefore leads to the overexpression of protein within the cell 3. Chromosomal Relocation: translocation of a gene to a nearby regulatory sequence that causes the normal protein to be overexpressed or fusion to an actively transcribed gene also leading to overexpression Basically either overexpression or normal expression but hyperactivity of the protein Src: first confirmed oncogene discovered in 1970 and codes for a non-receptor tyrosine kinase that phosphorylates specific tyrosine residues in other proteins Ras: codes for a small GTPase that hydrolyzes GTP → GDP + Pi and is activated by growth factor signaling Myc: codes for a transcription factor that induces self proliferation (common translocation event between chromosome 8 and chromosome 14 and is known as Burkitt’s Lymphoma) RTK: responsible for adding phosphates to other proteins to turn them on or off CTK: mediate responses to the activation of cell proliferation, migration, differentiation, and survival Tumor Suppressors: Tumor Suppressor Genes: proteins that have a halting effect on the regulation of the cell cycle or can also promote apoptosis DNA Repair Proteins: recognize DNA damage and repair it or initiate apoptosis if it can’t be repaired Cell Cycle Repressors: act as repressors of genes that are required for continuation of the cell cycle Two-Hit Hypothesis: states that both alleles must be mutated before an effect is manifested within the cell (the second copy is sort of a “backup” copy) p53 Protein: a tumor suppressor protein that and homozygous loss of this protein is found in about 65% of colon cancers, 50% of lung cancers, and also in breast cancers (activates DNA repair proteins when DNA is damaged and can also stop the cell cycle at the G1 → S portion of the cell cycle and gives the cell time to repair that DNA damage) Specifically, p53 binds DNA and activates including one that codes for a protein called p21 (which binds cyclin-CDK which is responsible for pushing the cell from the G1 phase to the S phase) It also functions in the initiation of apoptosis if the damage is irreparable A Dominant Negative is when the mutated p53 protein inhibits function of the wildtype p53 protein from the other allele