1 chapter 6 systems biology of cell organization prepared by brenda leady, university of toledo
TRANSCRIPT
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CHAPTER 6
SYSTEMSBIOLOGYOF CELLORGANIZATION
Prepared by
Brenda Leady, University of Toledo
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Systems biology
Researchers study living organisms in terms of their underlying network structure rather than their individual molecular components
The goal is to understand how the organization of the cell arises by complex interactions between its various components and parts
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All modern cells come from preexisting cell by division All cells posses a genome Living cells require pre-existing molecules Cells require pre-existing organization
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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
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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
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Proteins often undergo protein-protein interactions
Cells must continually synthesize new molecules and break down unwanted components
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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 ATPMolecular recognition allows for complex assembly
Subunits recognize each other and bind in a specific way
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Other molecular machines
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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
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Molecular recycling
Large molecules, except DNA, have finite lifetimesHalf-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
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Proteasome
Molecular machine for protein degradation 4 stacked rings with caps in eukaryotes Ubiquitin directs unwanted proteins to
proteasomes in eukaryotes Proteases degrade the unwanted protein
into peptides and amino acids
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Four systems work together
1. Interior of the nucleus2. Cytosol3. Endomembrane system4. Semiautonomous organelles Play a role in their own structure and in
the structure and organization of the entire cell
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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
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Cytosol
Important coordination center Compartment for metabolism- synthesis
and breakdown Cytoskeleton found here
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Endomembrane system Secretory pathway to move substances in and
out of the cellSecretory and endocytic pathways
Membranes are dynamic and change over timeNuclear membrane during cell division
Lipids and proteins made and sorted Storage and recycling
Vacuoles and lysosomes
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Semiautonomous organelles
Tend to be independent Mitochondria make ATP
Crucial for cell organization Chloroplasts capture light to store energy
for later use
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Endomembrane system
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
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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
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Lipid transfer
Lipids made in the ER membrane can be transferred to other membranes by…Lateral diffusionVesicle transportLipid exchange proteins
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Palade demonstrated that secreted proteins move sequentially through organelles of the endomembrane system
Thousands of different proteins must be sorted to the correct locations
George Palade’s team used pulse-chase experiments to determine where radioactive proteins were produced and the pathways they took
Studied pancreatic cells secreting proteins Followed radioactive proteins from synthesis in the
rough ER and movements through cellular compartments
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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
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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
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Proteins that stay in the ER have ER retention signals
Other proteins must be sortedTransported by vesiclesVesicles incorporate coat proteinsAlso incorporates v-snare indicative of cargoT-snare on target recognizes v-snare and
vesicle fuses with target membrane
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Glycosylation
Attachment of a carbohydrate to a proteinGlycoprotein
May aid in protein folding, extracellular protection, and protein sorting
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2 forms of glycosylation
N-linkedCarbohydrate attaches to nitrogen atom of
asparagine in polypeptide chain in ER lumenOccurs in cell membrane surface proteinsRole in cell-to-cell signaling
O-linkedString of sugars attaches to oxygen of serine or
threonine in polypeptideOccurs only in the Golgi apparatus Important in extracellular matrix proteins
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Semiautonomous organelles
Semiautonomous because they divide by fission to produce more of themselves
Somewhat independentGenetic material, synthesize some proteins,
divide independently of cell Do depend on the cell for raw materials
and most of their proteins
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Mitochondria and chloroplasts 2 traits similar to bacteria
1. Contain DNA separate from the nuclear genome
Mitochondrial and chloroplast genome Single small circular double stranded chromosome Similar to bacterial chromosomes
2. Reproduce via binary fission Like bacteria
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Mitochondria and chloroplasts are derived from ancient symbiotic relationships
Endosymbiosis- a smaller species lives symbiotically inside a larger speciesBeneficial for both species
Genes of mitochondria and chloroplasts 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
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Post-translational sorting
Most proteins for mitochondria, chloroplasts, and all proteins for peroxisomes sorted post-translation
Must have sorting signal Example- protein destined for
mitochondrial matrix
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