Chromatin Meeting
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The document discusses the evolution of chromatin proteins and prediction of novel factors in chromatin dynamics. It summarizes that chromatin proteins show increasing complexity with organismal complexity. Analysis of protein domain architectures can reveal lineage-specific connections and predict novel functions. For example, it predicts that a family of proteins called DBC1 may integrate regulatory inputs from NAD metabolites. The document also predicts that some two-headed enzymes may exist that can modify both lysines and glutamates on histone proteins.
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Gutell 096.jmb.2006.358.0193
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Gutell 096.jmb.2006.358.0193
Mears J.A., Sharma M.R., Gutell R.R., McCook A.S., Richardson P.E., Caulfield T.R., Agrawal R.K., and Harvey S.C. (2006).
A Structural Model for the Large Subunit of the Mammalian Mitochondrial Ribosome.
Journal of Molecular Biology, 358(1):193-212.
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2) Key differences in prokaryotic and eukaryotic gene expression include larger eukaryotic genomes, different cell types requiring gene regulation, lack of operons, chromatin structure, and uncoupling of transcription and translation.
3) The lac operon in E. coli is regulated through negative control in the absence of lactose, double negative control in the presence of only lactose, and absence of positive control in the presence of both glucose and lactose.
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The document discusses gene expression and regulation in eukaryotes. It covers several key points in 3 sentences:
Eukaryotic genes require complex regulatory systems involving chromatin remodeling and transcription factors to initiate expression, unlike bacterial genes which can be transcribed without regulatory proteins. Development in multicellular organisms is controlled by signaling between cells using hormones and diffusible receptors which act as transcriptional regulators. Gene expression patterns in fruit flies establish polarity, segment the body, and determine segment identities through maternal, segmentation, and homeotic genes, providing insights into human developmental gene regulation.
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This document discusses gene regulation in prokaryotes. It begins by introducing the concept of gene regulation and how only a fraction of genes are expressed at any given time. It then discusses several key examples of gene regulation in prokaryotes, including the lac, trp, and arabinose operons. The lac operon regulates lactose metabolism in E. coli in response to glucose and lactose availability. The trp operon regulates tryptophan synthesis using both repression and attenuation. The arabinose operon regulates arabinose metabolism using both positive and negative regulation by the AraC protein. The document also briefly discusses the SOS response, stringent response, and gene regulation in bacteriophage lambda.
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The document summarizes regulation of gene expression in prokaryotes and eukaryotes. In prokaryotes, genes are organized into operons containing a promoter, operator, and multiple coding sequences. The lac operon in E.coli contains genes regulated by the repressor protein LacI and induced by lactose. In eukaryotes, gene expression is regulated at multiple levels including transcription, RNA processing, transport, translation and degradation. Mechanisms include histone modification, DNA methylation, hormone signaling, polyadenylation, splicing, transport and protein degradation.
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This document discusses G protein-coupled receptors (GPCRs), which are the largest family of membrane receptors in the human genome. GPCRs have seven transmembrane domains and signal by interacting with G proteins. They regulate many important physiological processes and are involved in many diseases. The document outlines the structure and function of GPCRs and G proteins, including how GPCRs activate G proteins, the different classes of GPCRs, mechanisms of GPCR regulation like phosphorylation and desensitization, and the roles of GTPases in general.
Post-Translational Modification
Post-translational modifications are important biochemical mechanisms that regulate protein function. Common types of post-translational modifications include phosphorylation, hydroxylation, glycosylation, and methylation. These modifications occur on amino acid side chains or termini and are catalyzed by specific enzymes. For example, phosphorylation regulates enzyme activity, while hydroxylation and glycosylation of amino acids are required for collagen assembly and function. Overall, post-translational modifications expand the functional diversity of the proteome.
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The gal operon is a prokaryotic operon, which encodes enzymes necessary for galactose metabolism. The operon contains two operators, OE and OI. The former is just before the promoter, and the latter is just after the galE gene.This slide share includes some of the reasearch done on the galactose operons explained with review articles
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The document discusses gene expression and regulation in eukaryotes. It covers several key points in 3 sentences:
Eukaryotic genes require complex regulatory systems involving chromatin remodeling and transcription factors to initiate expression, unlike bacterial genes which can be transcribed without regulatory proteins. Development in multicellular organisms is controlled by signaling between cells using hormones and diffusible receptors which act as transcriptional regulators. Gene expression patterns in fruit flies establish polarity, segment the body, and determine segment identities through maternal, segmentation, and homeotic genes, providing insights into human developmental gene regulation.
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Posttranslational modification (PTM) is a key step in protein biosynthesis. After proteins are synthesized by ribosomes translating mRNA into polypeptide chains, the chains undergo PTM such as folding, cutting, and other processes to become mature proteins. PTMs extend the range of protein functions by attaching biochemical groups like phosphates or making structural changes like formation of disulfide bridges.
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Sugars are molecules of fundamental importance for life on earth. Sugars act as primary carriers of captured energy from the sun. Sugars not only fuel cellular carbon and energy metabolism but also pay pivotal role as signaling molecules and sugar status modulates & coordinates internal regulators that govern growth and development. The genes involved in production of carbon from photosynthesis with its utilization, mobilization and allocation in various tissues at different developmental stages are highly regulated by sugars. In most plants, sucrose (Suc) is the end product of photosynthesis for translocation from the source to heterotrophic sinks through the sieve element/companion cell complex of the phloem.
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The document summarizes regulation of gene expression in prokaryotes and eukaryotes. In prokaryotes, genes are organized into operons containing a promoter, operator, and multiple coding sequences. The lac operon in E.coli contains genes regulated by the repressor protein LacI and induced by lactose. In eukaryotes, gene expression is regulated at multiple levels including transcription, RNA processing, transport, translation and degradation. Mechanisms include histone modification, DNA methylation, hormone signaling, polyadenylation, splicing, transport and protein degradation.
signal transduction
Signal transduction pathways allow plants to respond to environmental stimuli. Receptors on the plasma membrane or inside the cell detect stimuli and activate secondary messengers like calcium or G-proteins. These messengers activate effector molecules like protein kinases that modulate gene expression and trigger responses like tolerance to abiotic stresses. Manipulating these pathways could help protect plants from stresses under climate change.
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Here, I am discussing the several signaling pathways.....It is highly dependent on the 3rd lecture; Receptors.
Enjoy :)
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The document discusses the genetic basis for protein synthesis. It begins by explaining how genes encode proteins through transcription of DNA into mRNA and translation of mRNA codons into amino acid sequences. Early scientists like Garrod and Beadle and Tatum established through experiments that genes encode enzymes through a one gene-one polypeptide hypothesis. The genetic code is then explained, where mRNA codons specify 20 amino acids. Translation follows the codon sequences to produce a polypeptide with directionality from N-terminal to C-terminal end.
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Hormones act as chemical messengers that bind to receptors and elicit responses in target cells. There are three main types of chemical messengers based on their method of travel: endocrine (travel via bloodstream), paracrine (travel between nearby cells), and autocrine (act on the producing cell). Hormone receptors contain sites for ligand binding and signal transmission. When a hormone binds its receptor, it triggers intracellular responses such as changes in gene expression that produce physiological effects. Termination of signaling is important to regulate responses and prevent improper cell growth.
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E. coli RNA polymerase is an enzyme that catalyzes the formation of phosphodiester bonds between nucleotides during transcription. It is composed of five subunits - two α subunits, one β subunit, one β' subunit, and one ω subunit. Together with a sigma factor, these subunits form the holoenzyme which is required for transcription initiation by binding to promoter sequences on DNA. The sigma factor recognizes specific promoter sequences and directs the holoenzyme to begin RNA synthesis. E. coli has multiple sigma factors that direct transcription of different genes depending on environmental conditions.
Mapk modified
The MAPK pathway is a signal transduction pathway that responds to extracellular stimuli and regulates various cellular processes. It involves a phosphorylation cascade from MAPKKK to MAPKK to MAPK that ultimately regulates transcription factors and gene expression. Second messengers like cAMP, IP3, and calcium amplify extracellular signals and allow cross-talk between different pathways. The MAPK pathway controls processes like cell growth, division, survival, and metabolism.
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Organization and Regulation of Mitochondrial Protein Synthesis
Mitochondria contain their own genome (mtDNA) which encodes some essential subunits of the oxidative phosphorylation complexes, as well as tRNAs and rRNAs required for mitochondrial protein synthesis. Mitochondrial translation requires nuclear-encoded factors and has adapted mechanisms to function within mitochondria. The mitochondrial ribosome (mitoribosome) is specialized for translation within this organelle, having evolved from bacterial ancestors. Translation in mitochondria involves initiation through IF2 and IF3 binding, elongation of the polypeptide chain, and termination. Adaptations allow for membrane insertion of proteins and regulation of mitochondrial protein synthesis.
GENE REGULATION.pptx
The document summarizes gene regulation in prokaryotes and eukaryotes.
In prokaryotes:
- Genes are organized into operons that are regulated by repressor proteins binding to operator sequences. This allows for coordinated expression of genes in response to environmental conditions, as seen in the lac and tryptophan operons.
In eukaryotes:
- Gene expression is influenced by chromatin structure and modifications to histone proteins like acetylation and methylation that make DNA more or less accessible. DNA methylation can also silence genes. Post-transcriptional mechanisms further regulate gene expression.
Presentation chromatin remodelling
Chromatin remodeling is the process by which nucleosome positioning along DNA is altered to regulate gene expression. There are two main classes of chromatin remodeling enzymes: Class I enzymes like histone acetylases modify histones without changing nucleosome position, while Class II enzymes use ATP to actively reposition nucleosomes, exposing regulatory DNA sequences. Chromatin remodeling plays a key role in processes like transcription and is disrupted in cancers when proteins involved in remodeling are mutated, leading to uncontrolled cell growth and differentiation.
An overview of mitochondrial biology
Mitochondria generate most of a cell's ATP through oxidative phosphorylation. They contain their own genome separate from the nuclear genome. Mitochondria have a double membrane structure with the inner membrane forming folds called cristae. The mitochondrial genome is a circular DNA present in multiple copies that encodes proteins, rRNAs and tRNAs. Mitochondrial DNA is replicated, transcribed and the RNAs processed independently of the nuclear genome. Key processes involve the RNA polymerase, transcription factors and the DNA polymerase for replication. Mutations in mitochondrial DNA can cause human diseases.
Genetic regulation 06 08-13
The document discusses gene regulation in cells. It explains that not all genes are expressed at all times, and that gene expression is regulated at multiple levels, including transcription, post-transcription, translation, and post-translation. It provides examples of constitutive genes that are continually expressed and inducible genes that are only expressed when needed. Key concepts like operons, promoters, repressors, and chromatin remodeling are introduced to illustrate gene regulation mechanisms in prokaryotes and eukaryotes.
Lecture_Chromatin remodelling_slideshare.pdf
1. Chromatin remodeling complexes use ATP hydrolysis to modify nucleosome structure and expose DNA for gene expression. The main classes are ATP-independent complexes and ATP-dependent complexes like ISWI and SWI/SNF.
2. Post-translational modifications of histone tails like acetylation, methylation, and phosphorylation can affect chromatin structure and transcription by altering DNA-histone interactions.
3. Chromatin remodeling is important for differential gene expression in specialized cell types and controlling DNA accessibility for transcription.
Translation
This presentation explains the fundamentals of Genetic Code, Protein synthesis mechanism and Antibiotics that inhibits at various stages of Translation.
transciption powerpoint
This document summarizes transcriptional gene regulation in eukaryotes. It discusses the basic mechanisms of transcription including initiation, elongation, and termination. It describes the role of general transcription factors, promoter elements like TATA boxes, and RNA polymerase in basal transcription. It also explains how distal enhancer elements and transcription factors regulate gene expression by interacting with the promoter and basal transcription machinery. Chromatin structure is also noted to influence transcription. The modular and combinatorial nature of transcriptional control is emphasized.
bacterial genetics
This document provides an overview of bacterial genetics. It discusses the structure and function of bacterial genetic material, including DNA and RNA. It describes protein synthesis through transcription and translation. It also covers extrachromosomal genetic elements in bacteria, bacterial variation, mutation, and gene transfer. The key topics covered include the lac operon and its role in regulating lactose metabolism, different types of mutations and their effects, and the mechanisms of genetic variation and antibiotic resistance in bacteria.
Postranslational Modification
This document discusses post-translational modifications (PTMs) of proteins. It provides examples of common PTMs like phosphorylation, acetylation, glycosylation, and discusses how they impact protein targeting, stability, function and activity regulation. The document also discusses how PTMs are studied, noting the Human Proteome Initiative aims to map all human protein modifications. Histone modifications and their impact on chromatin structure and gene expression are discussed in detail. Mitochondrial protein phosphorylation and its role in organelle regulation is also mentioned.
Synthesis of proteins__regulation_11
Posttranslational modifications and regulation of gene expression are discussed. Protein synthesis involves transcription of DNA to mRNA in the nucleus, then transport of mRNA to the cytoplasm where translation occurs on ribosomes. The genetic code is explained where codons consisting of three nucleotides specify each of the 20 amino acids. Mutations can occur that result in changes to the amino acid sequence of proteins.
Protein sorting & targeting.pptx by SOMESH Govt. Nehru PG College
.pptx by SOMESH Govt. Nehru PG College Guided By Mr. AVINASH SINGH/Mr.PRABHAT BAIS
BiologyExchange.co.uk Shared Resource
The document provides an overview of biology concepts related to cellular control, biotechnology, environments, and responding to the environment. It covers topics such as how DNA codes for proteins through gene expression and protein synthesis, cellular control mechanisms like the lac operon, genetic inheritance and mutations, developmental biology processes like apoptosis and meiosis, and more. The document is organized into 8 sections that describe these concepts through explanatory text, diagrams, and lists.
Proteomics ppt
Proteomics is the study of the structure and function of proteins. It involves identifying and quantifying the proteins expressed by a genome or cell type. Key aspects of proteomics include protein separation techniques like gel electrophoresis, mass spectrometry to identify proteins, and analyzing protein interactions and post-translational modifications. While genomes provide the blueprint, proteomics helps understand the diversity of proteins expressed and how they function together to direct cellular activities. It is a promising tool for disease diagnosis by identifying protein biomarkers.
Structure and function of the ribosome
This document provides scientific background on the 2009 Nobel Prize in Chemistry, which was awarded for studies of the structure and function of the ribosome. It summarizes the key contributions of Venkatraman Ramakrishnan, Thomas Steitz, and Ada Yonath, including obtaining the first high resolution crystal structures of the ribosomal subunits, solving the long-standing mysteries of the ribosome's catalytic mechanisms and role in protein synthesis, and advancing understanding of its accuracy and interactions with antibiotic drugs. Their work over decades was instrumental in revealing the ribosome's structure and function at the atomic level.
Control of gene expression in plants
Gene expression is regulated through a variety of mechanisms that control which genes are expressed in a cell. These mechanisms include regulation of transcription, post-transcriptional modification, RNA transport and translation. Regulation allows cells to increase or decrease expression of genes as needed and is essential for cellular differentiation in multicellular organisms. Gene expression can be regulated at many stages including chromatin structure, transcription, RNA processing and protein modification.
The 5' terminal uracil of let-7a is critical for the recruitment of mRNA to A...
This document investigates the interaction between let-7a microRNA, Argonaute2 protein, and mRNA targets. It finds that recombinant Argonaute2 is sufficient to direct let-7a-guided cleavage of a fully complementary mRNA target in vitro. Additionally, it determines that the 5' terminal uracil of let-7a is critical for recruitment of the mRNA target to the let-7a-Argonaute2 complex. Mutation of this 5' uracil inhibits formation of the ternary let-7a-Argonaute2-mRNA complex, but does not affect formation of the binary let-7a-Argonaute2 complex. This suggests the 5' urac
Cromatin Remodeling
1. Chromatin remodeling is the process by which chromatin structure is dynamically modified to allow access of DNA for processes like transcription.
2. There are two main types of chromatin remodeling - covalent histone modification and ATP-dependent chromatin remodeling complexes.
3. ATP-dependent complexes use energy from ATP hydrolysis to move, eject, or restructure nucleosomes, allowing access to DNA.
4. Examples of chromatin remodeling complexes include SWI/SNF, ISWI, CHD, and INO80 families, which have different activities like nucleosome sliding or histone variant exchange.
Transcriptional and Post-transcriptional Regulation of Gene Expression.pptx
Mr. Prabhat Kumar Singh presented on transcriptional and post-transcriptional regulation of gene expression. There are two main steps in gene expression - transcription and translation. Transcription involves creating mRNA with RNA polymerase enzymes. Translation involves using mRNA to direct protein synthesis. Regulation can occur at multiple levels including replication, transcription, post-transcription, and translation. Transcriptional regulation differs between prokaryotes and eukaryotes due to eukaryotes having nuclei. Prokaryotes use operon systems like the lac and trp operons to regulate transcription. Eukaryotes use promoter elements like TATA boxes. Post-transcriptional regulation in eukaryotes includes RNA splicing and modifications. Pro
Protein protein interactions
The document discusses protein-protein interactions (PPIs) and methods used to study them. It defines PPIs as physical contacts between two or more proteins through biochemical or electrostatic forces. It describes different types of PPIs including homo-oligomers, hetero-oligomers, covalent and non-covalent interactions. Common methods to study PPIs are also summarized, such as yeast two-hybrid systems, co-immunoprecipitation, and protein interaction databases. The applications and importance of PPI research are mentioned including roles in various cellular processes and diseases.
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Organization and Regulation of Mitochondrial Protein Synthesis
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The 5' terminal uracil of let-7a is critical for the recruitment of mRNA to A...
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Transcriptional and Post-transcriptional Regulation of Gene Expression.pptx
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Overall life span (LS) was 1671.7±1721.6 days and cumulative 5YS reached 62.4%, 10 years – 50.4%, 20 years – 44.6%. 94 LCP lived more than 5 years without cancer (LS=2958.6±1723.6 days), 22 – more than 10 years (LS=5571±1841.8 days). 67 LCP died because of LC (LS=471.9±344 days). AT significantly improved 5YS (68% vs. 53.7%) (P=0.028 by log-rank test). Cox modeling displayed that 5YS of LCP significantly depended on: N0-N12, T3-4, blood cell circuit, cell ratio factors (ratio between cancer cells-CC and blood cells subpopulations), LC cell dynamics, recalcification time, heparin tolerance, prothrombin index, protein, AT, procedure type (P=0.000-0.031). Neural networks, genetic algorithm selection and bootstrap simulation revealed relationships between 5YS and N0-12 (rank=1), thrombocytes/CC (rank=2), segmented neutrophils/CC (3), eosinophils/CC (4), erythrocytes/CC (5), healthy cells/CC (6), lymphocytes/CC (7), stick neutrophils/CC (8), leucocytes/CC (9), monocytes/CC (10). Correct prediction of 5YS was 100% by neural networks computing (error=0.000; area under ROC curve=1.0).
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Chromatin Meeting
- 1. The Evolution of Chromatin Proteins and Prediction of Novel Factors in Chromatin Dynamics National Center for Biotechnology Information National Institutes of Health L. Aravind
- 2. Extraordinary diversity of eukaryotes “ crown group” Most studied “ microbial eukaryotes” Most diverse and prevalent animals fungi Slime molds plants Chlorophytes rhodophytes diatoms Heteroloboseans parbasalids Diplomonads Euglenozoa ciliates Apicomplexans
- 3. A lot of action around the conserved histones High conservation of core chromatin components: histones Non-linear expansion of transcription factors Increasing number and complexity of chromatin proteins
- 6. Overview The provenance of the MORC ATPases and prediction of a specific role in chromatin dynamics Architectural evolution of chromatin proteins in eukaryotes: Organismal complexity and chromatin protein complexity Unusual functional linkages in non-model systems Architectural analysis and prediction of novel functions The NAD metabolite network in eukaryotic chromatin A conserved enzyme predicted to catalyze two modifications of chromatin proteins
- 9. Overview The provenance of the MORC ATPases and prediction of a specific role in chromatin dynamics Architectural evolution of chromatin proteins in eukaryotes: Organismal complexity and chromatin protein complexity Unusual functional linkages in non-model systems Architectural analysis and prediction of novel functions The NAD metabolite network in eukaryotic chromatin A conserved enzyme predicted to catalyze two modifications of chromatin proteins
- 12. Analysis of architectures reveals novel lineage-specific connections Potential functional connections between methylation-based histone modification and ubiquitination is elaborated in the chromalveolate lineage Chromo Tudor Methylated histone- binding domains OTU-type DUB Ubiquitin C-terminal hydrolase JAB-type DUB RING finger Ubiquitin E3 ligase Ubiquitin-like domain Deubiquitinating enzymes BMB/PWWP Ciliates and oomycetes oomycetes Histone deubiquitination based on specific methylation marks? Ch Jab Otu UbCH Tu R Ubl Ch Ch Otu UbCH Ch Ubl Ch R Ch UbCH Tu Jab BM BM
- 13. Lineage-specific diversification of the NAD metabolite network in eukaryotes Macro PARP SIR2 SWI/SNF ATPase H Poly-ADP ribose polymerase SWI/SNF ATPase NAD-dependent Histone deacetylase ADP-ribose/derivatives Binding domain Histone domain NAD PARP SIR2 H Ac H N ADPr T Ac-ADPr T ADPr H Poly-ADPr NAD ? ? Potential MACRO domain target MACRO domain Active site H Macro PARP Macro SWI/SNF ATPase Macro SIR2 Macro macroH2A Some animals Filamentous fungi, Entamoeba , oomycetes Several eukaryotes Animals, ciliates, Naegleria Macro Plasmodium, ciliates
- 16. Concluding remarks Computational analysis suggests that are several interesting chromatin associated biochemistries still lying open for experimental investigation in model organisms … But Non-model eukaryotes, including some major pathogens, have several novel connections suggesting biochemistries beyond what we have learned from the models …
- 17. Acknowledgements Vivek Anantharaman S. Balaji Max Burroughs (RIKEN, Japan) Lakshminarayan Iyer M. Madan Babu (MRC-LMB, UK) Abhiman Saraswati Thiago Venancio Present group members at NCBI Former group members