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Transcript
Systems biology The goal is to understand how the organization of the cell arises by complex interactions between its various components and parts 1 All modern cells come from preexisting cells by division All cells posses a genome Living cells require pre-existing molecules Cells require pre-existing organization 2 Cell’s genetic information produces proteome Information in most genes is used to make mRNA molecules that encode amino acid sequences of proteins Study of individual proteins does not provide a broad integrated look at the dynamic nature of the cell 3 Genomes, proteomes and cell structure function and organization The proteome is largely responsible for the structure and function of living cells Gene and protein regulation causes the proteome to be dynamic Proteins have sorting signals 4 Molecular machines A machine is an object that has moving parts and does useful work These machines provide structure and organization to cells and enable them to carry out complicated processes ATP synthase is a molecular machine that makes ATP Molecular recognition allows for complex assembly Subunits recognize each other and bind in a specific way 5 http://vcell.ndsu.nodak.edu/animations/atpgradient/movie.htm 6 Other molecular machines 7 Cytoskeleton Key role in cell organization and many processes that maintain the cell Provides mechanical strength, cell shape, organization and direction to intracellular and cellular movements 8 9 10 Molecular recycling Large molecules, except DNA, have finite lifetimes Half-life varies from 5 minutes for mRNA in prokaryotes to 30 minutes to several days for mRNA in eukaryotes Continual degradation of faulty or nonfunctional proteins and synthesis of new ones 11 Proteasome Molecular machine for protein degradation Ubiquitin directs unwanted proteins to proteasomes in eukaryotes Proteases degrade the unwanted protein into peptides and amino acids 12 13 Four systems work together 1. 2. 3. 4. Interior of the nucleus Cytosol Endomembrane system Semiautonomous organelles Play a role in their own structure and in the structure and organization of the entire cell 14 15 Nucleus Genome produces the proteome that is responsible for the structure and function of the entire cell Gene regulation important in creating specific cell types and enabling response to environmental change Nucleus organizes itself with the nuclear matrix Collection of filamentous proteins 16 Endomembrane system Secretory pathway to move substances in and out of the cell Secretory and endocytic pathways Membranes are dynamic and change over time Nuclear membrane during cell division Lipids and proteins made and sorted Storage and recycling Vacuoles and lysosomes 17 Endomembrane system (Nucleus, endoplasmic reticulum), Golgi apparatus, lysosomes, vacuoles, secretory vesicles, and plasma membrane Reside in cytosol Much of its activity related to transport between compartments Critical for lipid synthesis, protein synthesis and sorting, and the attachment of carbohydrates to lipids and proteins 18 Semiautonomous organelles Tend to be independent Mitochondria make ATP Crucial for cell organization Chloroplasts capture light to store energy for later use 19 Lipid synthesis Cytosol and endomembrane system work together to synthesize most lipids Building blocks of phospholipids made by enzymes in the cytosol or from the diet Phospholipids initially made in cytosolic leaflet but flipases in ER membrane transfer some to the other leaflet 20 21 Lipid transfer Lipids found in the ER membrane can be transferred to other membranes by… Lateral diffusion Vesicle transport Lipid exchange proteins 22 23 24 Protein localization Sorting signals or traffic signals are short amino acid sequences that direct protein to correct cellular location Most eukaryotic proteins begin synthesis (translation) on ribosomes in the cytosol 25 Protein localization Proteins that stay in the cytosol lack sorting signals so they stay in the cytosol Proteins for the nucleus, mitochondria, chloroplasts, and peroxisomes occur after the protein is made Post-translational sorting Synthesis of other proteins destined for ER, Golgi, lysosome, vacuole, plasma membrane, or secretion halts until the ribosome is bound to the ER Cotranslational sorting 26 27 Protein localization Proteins that stay in the ER have ER retention signals Other proteins must be sorted Transported by vesicles Vesicles incorporate coat proteins Also incorporates v-snare indicative of cargo T-snare on target recognizes v-snare and vesicle fuses with target membrane 28 29 Glycosylation Attachment of a carbohydrate to a protein Glycoprotein May aid in protein folding, extracellular protection, and protein sorting 30 2 forms of glycosylation N-linked Carbohydrate attaches to nitrogen atom of asparagine in polypeptide chain in ER lumen Occurs in cell membrane surface proteins Role in cell-to-cell signaling O-linked String of sugars attaches to oxygen of serine or threonine in polypeptide Occurs only in the Golgi apparatus Important in extracellular matrix proteins 31 32 Semiautonomous organelles Semiautonomous because they divide by fission to produce more of themselves Somewhat independent Genetic material, synthesize some proteins, divide independently of cell Do depend on the cell for raw materials and most of their proteins 33 Mitochondria and chloroplasts 1. 2 traits similar to bacteria Contain DNA separate from the nuclear genome 2. Mitochondrial and chloroplast genome Single small circular double stranded chromosome Similar to bacterial chromosomes Reproduce via binary fission Like bacteria 34 35 Mitochondria and chloroplasts are derived from ancient symbiotic relationships Endosymbiosis- a smaller species lives symbiotically inside a larger species Beneficial for both species Genes of mitochondria and chloroplasts are very similar to bacterial genes Endosymbiosis theory Modern mitochondria and chloroplasts have lost most of their genes through transfer to nucleus Origins of peroxisomes unclear but may be same path