Biol 3320 - Cell Biology Exam 01 Notes PDF

9/19/2024 2024/09/19 Thursday Biol 3320 Cell Biology CRN 13746 Gene Expression and Its Control (III) Exam_01 will be available for viewing by next Tuesday...

9/19/2024 2024/09/19 Thursday Biol 3320 Cell Biology CRN 13746 Gene Expression and Its Control (III) Exam_01 will be available for viewing by next Tuesday 1 1 Proteins are made on polyribosomes A polyribosome A series of ribosomes can simultaneously translate the same eukaryotic mRNA molecule 39 Fig 6 - 77 2 1  9/19/2024 Nonsense-mediated mRNA decay Quality-control mechanisms prevent translation of damaged mRNAs Fig 6 - 80 Upf: upframeshift 3 Steps in the creation of a functional protein The completed polypeptide A growing polypeptide chain must fold correctly into acquires its secondary its 3D conformation, bind and tertiary structure as any cofactors required, and it emerges from a assemble with its partner ribosome protein chains, if any Protein glycosylation and protein phosphorylation are the most frequent modifications 4 Fig 6 - 82 4 2  9/19/2024 Different chaperones cooperate to ensure correct protein folding hsp: heat shock proteins Fig 6 - 85 5 V. Multi-level Control of Eukaryotic Gene Expression 6 6 3  9/19/2024 Multiple steps at which eukaryotic gene expression can be controlled Fig 7 – 6 7 Transcription is controlled by gene control regions Promoter: the DNA sequence where the general TFs & the polymerase assemble cis-regulatory sequences: Many transcription binding sites for transcription regulators act regulators which affects the through mediator, rate of transcription initiation while some interact with the general TF and & polymerase directly Fig 7 – 20 8 4  9/19/2024 Eukaryotic transcription regulators assemble into complexes on DNA Some assembled complexes activate gene transcription, while another represses transcription Proteins that do not themselves bind DNA but assemble on other DNA-bound transcription regulators are termed co-activators or co-repressors Fig 7 – 21 9 Eukaryotic transcription activator proteins direct local alterations in chromatin structure Fig 7 - 22 10 5  9/19/2024 Six of ways in which eukaryotic repressor proteins can operate e.g. H3K9me3; H3K27me3 Fig 7 - 27 11 The importance of combinatorial gene control for development Combinations of a few transcription regulators can generate many cell types during development In this example, 5 different transcription regulators have created 8 final cell types (G-N). Fig 7 - 36 12 6  9/19/2024 A small set of transcription regulators can convert one differentiated cell type into another Liver cells grown in culture were converted into neuronal cells via the artificial expression of three nerve-specific transcription regulators, which involves the activation of many nerve-specific genes as well as the repression of many liver-specific genes Fig 7 - 37 13 Expression of the Drosophila Eyeless gene in precursor cells of the leg triggers the development of an eye on the leg A fruit fly larva contains either the normally expressed Eyeless gene (left) or an Eyeless gene that is additionally expressed artificially in cells that normally give rise to leg tissue (right) Fig 7 - 38 14 7  9/19/2024 A positive feedback loop can create cell memory Protein A is a master transcription regulator that activates the transcription of its own gene, as well as Fig 7 - 42 other cell-type-specific genes (not shown) 15 Formation of 5-methyl cytosine occurs by methylation of a cytosine base in the DNA double helix In vertebrates, this event is largely confined to selected cytosine (C) nucleotides located in the sequence CG Fig 7 - 46 16 8  9/19/2024 How DNA methylation patterns are faithfully inherited Because of the existence of a methyl-directed methylating enzyme (the maintenance methyl transferase), once a pattern of DNA methylation is established, that pattern of methylation is inherited in the progeny Does this really matter? Fig 7 - 47 17 Multiple mechanisms can produce especially stable gene repression DNA- & histone- modifying enzymes may interact and collaborate in chromatin modification Fig 7 - 48 18 9  9/19/2024 Genomic imprinting can cause non-Mendelian pattern of inheritance An epigenetic phenomenon that causes genes to be expressed or not, depending on their parental origin. Imprinting can cause a non-Mendelian pattern of inheritance Fig 7 - 51 19 Five patterns of alternative RNA splicing A single type of RNA transcript is spliced in several alternative ways to produce distinct mRNAs Fig 7 - 59 20 10  9/19/2024 The compact genome of HIV, the human AIDS virus Five patterns of alternative RNA splicing in HIV The Rev protein binds to RRE & interacts with Crm1 which is a nuclear receptor that directs the movement of viral RNAs through the nuclear pores into the cytosol Fig 7 - 66 21 Regulation of nuclear export by the HIV Rev protein Early in HIV infection, only the fully spliced RNAs (which contain the coding sequences for Rev, Tat, and Nef) are exported from the nucleus and translated Fig 7 - 67 22 11  9/19/2024 Some mRNAs are localized to specific regions of the cytosol Mechanisms for the localization of mRNAs The mRNA to be localized At their destination, the leaves the nucleus through mRNAs are held in place by nuclear pores anchor proteins Each mechanism requires specific signals on the mRNA, which are typically located in the 3′ UTR. Additional components can block the Fig 7 – 68 translation of the mRNA until it is properly localized 23 Two post-transcriptional controls mediated by iron Fig 7 - 74 24 12  9/19/2024 RNA Silencing (a.k.a. RNA Interference, RNAi) in Eukaryotes Make transgenic petunia in an attempt to enhance flower color The Pigment gene (CHS) was used Frequently, BOTH transgene and endogenous CHS were inactivated - termed cosuppression CHS genes were transcribed just fine but the mRNA gets turned over very quickly Transgene CHS Endogenous CHS DNA mRNA DNA RNA PROTEIN Termed as: Post-transcriptional Gene Silencing (PTGS) or RNA Silencing Napoli et al. (1990) Plant Cell 2: 279-289 25 E8 - 1 van der Krol et al. (1990) Plant Cell 2: 291-299 25 RNA Silencing (a.k.a. RNA Interference, RNAi) in Eukaryotes 1990 Cosuppression ( Post-Transcriptional Gene Silencing, PTGS) in plants 1993 First microRNA gene lin-4 identified, known as small temporal (st) RNAs 1998 RNA interference (RNAi) in C. elegans dsRNA induces silencing in plants Gene “knock-down” through RNA interference (RNAi) in worms Fire et al. (1998) Nature 391, 806-11 26 Fig 8 – 60 Waterhouse et al (1998) PNAS 95,13959-64 26 13