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martins lectures
martins
| Question | Answer |
|---|---|
| what is phenotype | morphology, function and behaviour) of the cell |
| Gene expression | is required to convert the information that resides within our DNA into gene products |
| explain how on common genome can create many different cell types | Using the same common set of genes (i.e. the genome), cells differentially express these genes by turning on, or off, specific subsets of genes at different times and places to achieve a huge diversity of cell types or cellular activation states |
| why are liver cells liver cells and neurons neurons | due to on and of switching of different subsets of genes |
| what is critical to achieving different outputs/phenotypes from the same genome. | The ability to regulate gene expression and environmental and developmental cues cueing on and off switch. |
| what are the flanking regions? | 5' UTR: Contains regulatory sequences that influence translation initiation and mRNA stability.Promoter Region: Directly upstream of the gene, where transcription is initiated. introns:.3' UTR:Polyadenylation Signal |
| where can mutation occur | Mutations can be in either the protein-coding part or regulatory part of the gene. |
| what is the molecular definition of the gene | A transcriptional unit encoding an RNA or protein, where the gene product has some biochemical or cellular function |
| coding sequence | the sequence that is actually transcribed into RNA |
| Changes to the gene regulatory sequence | can affect when and where and how much of a gene is expressed and this, in turn, will have an impact on the phenotype |
| is all RNAs encoded into genes ? | many genes encode RNAs that do not become translated into protein |
| what are the regulatory rNAS? | regulatory RNAs such as snRNA (small nuclear RNA), microRNA (miRNA) and long non-coding RNA (lncRNA) that influence the expression and translation of the protein-coding genes into proteins |
| what is the highest percentage of RNAs | ribosomal and transfer RNAs comprise approximately 80-90% of the total RNA within cells, with mRNA comprising only 2-3% |
| prokaryotic genomes are | relatively compact and gene dense |
| what fraction is actually transcribed | 2% |
| what does the non coding sequence do ? | The rest of the genome consists of non-coding sequence that regulates the expression of the coding fraction of the genome. |
| fruit fly vs mammal | fruit flys about 14,000 genes and mammals only 25,000 or so but how we regulate the expression of these genes is under more sophisticated control |
| how was dolly produced | Ian Wilmut at the Roslin Institute in Scotland,transfer of a nucleus from afully differentiated somaticcell udder ) into a sheep egg that had been denucleated (had its nucleus removed), could produce a fully of clone the donor sheep. implatation. |
| why are all genes not expressed in all cells | Thus, within a given organism, all cells have the same genes but not all genes are “expressed” in every cell. |
| how if differential gene expression controlled | Differential gene expression is controlled through activating signaling pathways that activate the correct transcription factors (TFs), leading to further cascades of gene expression as many TFs also induce the expression of other TFs |
| what controls the correct switching of transcription factors? | Switching on the correct transcription factors is typically achieved through external signals (either from the environment or other cells), |
| nurse cells and spatial signals | During early development of a fly embryo, spatial signals are provided to the developing embryo by cells of the mother that effectively instruct cells within the embryo to express genes involved in making the different parts of the fly. |
| who is spatial signals achieved | nurse cells transferring mRNAs largely encoding 2 proteins, Bicoid and Nanos, |
| what do Bicoids do? | cause a this transcription factor gradient then induces the expression of a variety of other transcription factors (Hunchback, kruppel, Knirps, Giant) |
| Hox genes | that in turn switch on the correct genes to make a leg, a wing, an antenna, a sex bristle, etc |
| pathogen-associated molecular patterns (PAMPs) | PAMP receptors enable cells of the immune system to detect the presence of pathogens in the body(toll like receptionors ) |
| toll like receptors do what? | Toll-like receptors capable of detecting these foreign substances, the receptor becomes activated and this results in activation of a transcription factor called NFkappaB |
| NFkappaB | switches on a diverse array of genes (numbering in the hundreds) that are involved in coordinating the process of inflammation |
| what are housekeeping genes | a subset of gene expressed in almost every cell for common (cytoskeleton, plasma membrane, microtubule organizing center etc.) nucleus, mitochondrial, golgi, endoplasmic reticulum, lysosomes |
| Tissue-specific genes: | Expressed in specific cell types (e.g., haemoglobin, insulin, liver enzymes, neurotransmitter receptors, etc.) |
| In mammalian cells only or so of the DNA is copied into functional RNA. | 2% |
| what effects patters' of gene expression | 1. Transcriptional (i.e. factors that affect RNA transcription) 2. Post-transcriptional (factors that affect stability or composition of RNAs) 3. Translational translation of mRNAs into protein)4. Post-translational (factors that affect protein |
| At its most basic, gene expression is regulated through | binding of an RNA polymerase to the regulatory elements (called a promoter region) upstream of a gene |
| Most bacterial promoters have the same basic organization | -10 bp (the TATA box, also called the Pribnow box) and -35bp (TTGACAT) upstream of the transcription start site of the gene. |
| σ (sigma) subunit, | which positions the polymerase at the correct position to initiate transcription and also separates (melts) the strands of the double helix apart to enable transcription to begin. |
| Upon initiation of transcription, the σ (sigma) subunit | dissociates from the promoter and the RNA polymerase proceeds along the DNA molecule, unwinding the strands apart and copying the DNA into RNA (called the elongation phase). |
| rho | Alternatively, a protein called Rho, can recognize certain sequence elements that are also termination signals and upon binding to these elements, can then bind to RNA polmerase causing it to fall off the DNA and release the RNA |
| hairpins | These sequences typically cause hairpins to form in the growing RNA molecule that causes it to fall off the DNA template |
| operons are arranged into | functionally related groups |
| why are operons arranged like this ? | This is because bacteria live in harsh and ever changing environments where food sources may vary rapidly, requiring the bacterium to be able to rapidly express new sets of genes that are required to deal with varying food sources. |
| what is the enzyme produced when bacteria is grown on lactose | They discovered that the enzyme β-galactosidase, They found that growth on lactose depends on three enzymes: β-galactosidase (lacZ) Permease (lacA) Thiogalactoside transacetylase (lacY) |
| no lactose | lacI encodes a repressor (LacI) that switches off the whole operon in the absence of lactose (by binding to the Operator for the Lac Operon) |
| what needs to be added to mRNA for stability and transport | addition of sequences to the 5' end of the RNA (the 5'cap) as well as the 3' end (the polyA tail) |
| what causes the slicing | splicing by small nuclear RNAs (snRNAs) |
| what are promoters continually off | (a) The requirement for specific and general transcription factors that regulate the binding of the RNA Pol complex to the promoter, and (b) Due to the physical inaccessibility of gene promoters due to the presence of histones |
| RNA Pol I creates what | rRNA precursor molecules, |
| RNA Pol II | generates mRNA |
| RNA Pol III generates | small RNAs such as tRNAs and 5S rRNA. |
| why is pol II similar to procaryotes | A common feature of these promoters (located -30 to the transcription start site) is an A-T rich region called the TATA box. |
| uncommon upstream elements of | Pol II promoters are the GGCCCAATCT element or CCAAT box (cat box),which typically lies at -75 |
| what is needed for the rna polymerases to recognise the promotor region in eukaryoutes? | transcription factors (TFs) |
| what are the two types of transcription factors? | general and gene specific. |
| name the general transcription factors | RNA Pol II are TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH and TFIIJ. |
| what is the most important binding protein? | TATA box-binding protein (TBP). As its name suggests, TBP binds to the TATA box bringing the rest of TFIID along with it. |
| what does the tata box binding protein cause | Binding of the TBP to the TATA box induces a dramatic distortion |
| what is binding distortion | Binding of the TBP to the TATA box induces a dramatic distortion in this region of the DNA.Allowing access of the RNA polymerase to the template |
| what is the orber of binding of the transcrition factors | D, A, B, F + Pol II, E, H and J. david after being fresh pulls avas head joyfully. |
| what happens after igintation | Upon assembly of the RNA Pol II preinitiation complex, the C-terminal domain of the largest subunit of RNA polymerase II becomes heavily phosphorylated by HFIID |
| What are the other tfs that interact by the major grove of dna by noncovalent interactions | The zinc finger motif 2. The helix-loop-helix (HLH) motif 3. The leucine zipper (LZ) motif 4. The high mobility group-box (HMG) motif |
| enhancer sequences how can they be enhanced from thousands of base pairs away | This is because chromatin looping,by specific TF and associated proteins called mediators |
| how can histones be opened and closed? | acetylation, methylation, phosphorylation or modifications In general, modifications that neutralize the positive charges on histones reduce their affinity for DNA. |
| Polycomb proteins | They introduce specific histone modifications (like H3K27me3) that signal the chromatin to remain in a closed or condensed state |
| epigenetic control | One of the key features of Polycomb proteins is their ability to establish epigenetic memory. Once they silence a gene, they can maintain that silenced state through cell divisions. |
| SWI/SNF | complexes are crucial for transcriptional activation because they help move nucleosomes off promoter regions,and seems to act as an ATP-driven ‘nucleosome plough’ to facilitate transcription |
| nucleotides ate sometimes metalated at cytosine regions | Thus methylation is likely involved in silencing gene expression. Almost all of the methylated cytosines are found in CG dinucleotides,GC-rich regions (called CpG islands) |
| Then, around the time of implantation of the embryo in the uterus, | a wave of de novo methylation is seen which establishes a new pattern of methylation throughout the DNA |
| maintenance methylation | passed on to daughter |
| Methylation is though to inhibit transcription in two ways: | (1) By interfering with the recognition of DNA-binding sites by TFs and (2) By attracting transcriptional repressors to certain sites |
| exons | expressed regions |
| introns | intervening regions |
| doe bacteria have introns? | Studies in bacteria indicated that genes were comprised of uninterrupted stretches of coding sequence. |
| splice sites are usually | similar sequences found at boundaries |
| 5’ splice site (or donor site) and 3’ splice site (or acceptor site) | boundaries |
| one error in slicing causes | shift in reading frame in the resulting mRNA. |
| alternative slicing controlled by | regulated by molecules that sit on the pre-mRNA |
| Alternitive slicing example | The DSCAM gene in Drosophila is involved in specifying neural circuitry has over 38,000 possible protein isoforms due to alternative splicing |
| trna is shaped as what | tRNAs are cloverleaf shaped polynucleotide sequences |
| Shine Dalgarno sequence | recogniser in AGGAGG for mrna to bind to ribosmes |
| what does the start codon always code for AUG | methionine |
Created by:
janeandchemistry