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Intracellular compartments

and vesicular trafficing

Chapters 12 and 13

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2/58Figure 15-2 Essential Cell Biology ( Garland Science 2010)

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3/58Table 15-1 Essential Cell Biology ( Garland Science 2010)

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MEMBRANE-ENCLOSED ORGANELLES

Eucaryotic Cells Contain a Basic Set of Membrane-enclosed

OrganellesMembrane-enclosed Organelles Evolved in Different Ways

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5/58Table 15-1 Essential Cell Biology ( Garland Science 2010)

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6/58Table 15-2 Essential Cell Biology ( Garland Science 2010)

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MEMBRANE-ENCLOSED ORGANELLES

Eucaryotic Cells Contain a Basic Set of Membrane-enclosed

OrganellesMembrane-enclosed Organelles Evolved in Different Ways

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8/58Figure 15-3 Essential Cell Biology ( Garland Science 2010)

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9/58Figure 15-4 Essential Cell Biology ( Garland Science 2010)

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PROTEIN SORTING

Proteins Are Imported into Organelles by Three MechanismsSignal Sequences Direct Proteins to the Correct CompartmentProteins Enter the Nucleus Through Nuclear PoresProteins Unfold to Enter Mitochondria and ChloroplastsProteins Enter the Endoplasmic Reticulum While BeingSynthesizedSoluble Proteins Are Released into the ER LumenStart and Stop Signals Determine the Arrangement of aTransmembrane Protein in the Lipid Bilayer

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11/58Figure 15-5 Essential Cell Biology ( Garland Science 2010)

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PROTEIN SORTING

Proteins Are Imported into Organelles by Three MechanismsSignal Sequences Direct Proteins to the Correct CompartmentProteins Enter the Nucleus Through Nuclear PoresProteins Unfold to Enter Mitochondria and ChloroplastsProteins Enter the Endoplasmic Reticulum While BeingSynthesizedSoluble Proteins Are Released into the ER LumenStart and Stop Signals Determine the Arrangement of aTransmembrane Protein in the Lipid Bilayer

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13/58Table 15-3 Essential Cell Biology ( Garland Science 2010)

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14/58Figure 15-6 Essential Cell Biology ( Garland Science 2010)

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PROTEIN SORTING

Proteins Are Imported into Organelles by Three MechanismsSignal Sequences Direct Proteins to the Correct CompartmentProteins Enter the Nucleus Through Nuclear PoresProteins Unfold to Enter Mitochondria and ChloroplastsProteins Enter the Endoplasmic Reticulum While BeingSynthesizedSoluble Proteins Are Released into the ER LumenStart and Stop Signals Determine the Arrangement of aTransmembrane Protein in the Lipid Bilayer

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16/58Figure 15-8 Essential Cell Biology ( Garland Science 2010)

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17/58Figure 15-9 Essential Cell Biology ( Garland Science 2010)

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18/58Figure 15-10 Essential Cell Biology ( Garland Science 2010)

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PROTEIN SORTING

Proteins Are Imported into Organelles by Three Mechanisms

Signal Sequences Direct Proteins to the Correct CompartmentProteins Enter the Nucleus Through Nuclear PoresProteins Unfold to Enter Mitochondria and ChloroplastsProteins Enter the Endoplasmic Reticulum While BeingSynthesizedSoluble Proteins Are Released into the ER LumenStart and Stop Signals Determine the Arrangement of aTransmembrane Protein in the Lipid Bilayer

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Figure 15-11 Essential Cell Biology ( Garland Science 2010)

TOM

complex

TIM complex

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PROTEIN SORTING

Proteins Are Imported into Organelles by Three Mechanisms

Signal Sequences Direct Proteins to the Correct CompartmentProteins Enter the Nucleus Through Nuclear PoresProteins Unfold to Enter Mitochondria and ChloroplastsProteins Enter the Endoplasmic Reticulum While BeingSynthesizedSoluble Proteins Are Released into the ER LumenStart and Stop Signals Determine the Arrangement of aTransmembrane Protein in the Lipid Bilayer

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Figure 15-13 Essential Cell Biology ( Garland Science 2010)

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PROTEIN SORTING

Proteins Are Imported into Organelles by Three Mechanisms

Signal Sequences Direct Proteins to the Correct CompartmentProteins Enter the Nucleus Through Nuclear PoresProteins Unfold to Enter Mitochondria and ChloroplastsProteins Enter the Endoplasmic Reticulum While BeingSynthesizedSoluble Proteins Are Released into the ER LumenStart and Stop Signals Determine the Arrangement of aTransmembrane Protein in the Lipid Bilayer

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Figure 15-15 Essential Cell Biology ( Garland Science 2010)

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PROTEIN SORTING

Proteins Are Imported into Organelles by Three Mechanisms

Signal Sequences Direct Proteins to the Correct CompartmentProteins Enter the Nucleus Through Nuclear PoresProteins Unfold to Enter Mitochondria and ChloroplastsProteins Enter the Endoplasmic Reticulum While BeingSynthesizedSoluble Proteins Are Released into the ER LumenStart and Stop Signals Determine the Arrangement of aTransmembrane Protein in the Lipid Bilayer

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Figure 15-16 Essential Cell Biology ( Garland Science 2010)

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Figure 15-17 Essential Cell Biology ( Garland Science 2010)

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VESICULAR TRANSPORT

Transport Vesicles Carry Soluble Proteins and Membrane

Between CompartmentsVesicle Budding Is Driven by the Assembly of a Protein CoatVesicle Docking Depends on Tethers and SNAREs

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Figure 15-18 Essential Cell Biology ( Garland Science 2010)

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VESICULAR TRANSPORT

Transport Vesicles Carry Soluble Proteins and Membrane

Between CompartmentsVesicle Budding Is Driven by the Assembly of a Protein CoatVesicle Docking Depends on Tethers and SNAREs

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Figure 15-19a Essential Cell Biology ( Garland Science 2010)

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Figure 15-20 Essential Cell Biology ( Garland Science 2010)

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Table 15-4 Essential Cell Biology ( Garland Science 2010)

COP Ibud from golgi compartments

COP IIbud from ER

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VESICULAR TRANSPORT

Transport Vesicles Carry Soluble Proteins and Membrane

Between CompartmentsVesicle Budding Is Driven by the Assembly of a Protein CoatVesicle Docking Depends on Tethers and SNAREs

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Figure 15-21 Essential Cell Biology ( Garland Science 2010)

Rab1ER and golgi

Rab2cis Golgi

Rab3Asynaptic vesicles

Rab4/rab11 recycling endosomes

Rab5Aplasma membrane, clathrin

coated vesicles, early endosomesRab5Cearly endosomes

Rab6medial and trans Golgi cisternae

Rab7late endosomes

Rab8early endosomes

Rab9late endosomes, trans Golgi

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Figure 15-22 Essential Cell Biology ( Garland Science 2010)

Botulinum toxin

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SECRETORY PATHWAYS

Most Proteins Are Covalently Modified in the ER

Exit from the ER Is Controlled to Ensure Protein QualityThe Size of the ER Is Controlled by the Amount of Protein thatFlows Through ItProteins Are Further Modified and Sorted in the Golgi ApparatusSecretory Proteins Are Released from the Cell by Exocytosis

Gl l i

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Figure 15-23 Essential Cell Biology ( Garland Science 2010)

Started in ER,

finished in

Golgi

Glycosylation

on asparagine

residues

Dolichol holds

oligo in ER

lumen

Oligosacchary

l transferase

Glycosylation

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SECRETORY PATHWAYS

Most Proteins Are Covalently Modified in the ER

Exit from the ER Is Controlled to Ensure Protein QualityThe Size of the ER Is Controlled by the Amount of Protein thatFlows Through ItProteins Are Further Modified and Sorted in the Golgi ApparatusSecretory Proteins Are Released from the Cell by Exocytosis

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SECRETORY PATHWAYS

Most Proteins Are Covalently Modified in the ER

Exit from the ER Is Controlled to Ensure Protein QualityThe Size of the ER Is Controlled by the Amount of Protein thatFlows Through ItProteins Are Further Modified and Sorted in the Golgi ApparatusSecretory Proteins Are Released from the Cell by Exocytosis

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Figure 15-25 Essential Cell Biology ( Garland Science 2010)

Unfolded protein

response:

upregulation of genesinvolved in protein

folding

ER chaperones,

proteins involved in

retrotranslocationand protein

degradation

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SECRETORY PATHWAYS

Most Proteins Are Covalently Modified in the ER

Exit from the ER Is Controlled to Ensure Protein QualityThe Size of the ER Is Controlled by the Amount of Protein thatFlows Through ItProteins Are Further Modified and Sorted in the Golgi ApparatusSecretory Proteins Are Released from the Cell by Exocytosis

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Figure 15-26 Essential Cell Biology ( Garland Science 2010)

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SECRETORY PATHWAYS

Most Proteins Are Covalently Modified in the ER

Exit from the ER Is Controlled to Ensure Protein QualityThe Size of the ER Is Controlled by the Amount of Protein thatFlows Through ItProteins Are Further Modified and Sorted in the Golgi ApparatusSecretory Proteins Are Released from the Cell by Exocytosis

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Figure 15-27 Essential Cell Biology ( Garland Science 2010)

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Figure 15-28 Essential Cell Biology ( Garland Science 2010)

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ENDOCYTIC PATHWAYS

Specialized Phagocytic Cells Ingest Large Particles

Fluid and Macromolecules Are Taken Up by PinocytosisReceptor-mediated Endocytosis Provides a Specific Route intoAnimal CellsEndocytosed Macromolecules Are Sorted in EndosomesLysosomes Are the Principal Sites of Intracellular Digestion

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Figure 15-32 Essential Cell Biology ( Garland Science 2010)

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ENDOCYTIC PATHWAYS

Specialized Phagocytic Cells Ingest Large Particles

Fluid and Macromolecules Are Taken Up by PinocytosisReceptor-mediated Endocytosis Provides a Specific Route intoAnimal CellsEndocytosed Macromolecules Are Sorted in EndosomesLysosomes Are the Principal Sites of Intracellular Digestion

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ENDOCYTIC PATHWAYS

Specialized Phagocytic Cells Ingest Large Particles

Fluid and Macromolecules Are Taken Up by PinocytosisReceptor-mediated Endocytosis Provides a Specific Route intoAnimal CellsEndocytosed Macromolecules Are Sorted in EndosomesLysosomes Are the Principal Sites of Intracellular Digestion

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Figure 15-33 Essential Cell Biology ( Garland Science 2010)

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ENDOCYTIC PATHWAYS

Specialized Phagocytic Cells Ingest Large Particles

Fluid and Macromolecules Are Taken Up by PinocytosisReceptor-mediated Endocytosis Provides a Specific Route intoAnimal CellsEndocytosed Macromolecules Are Sorted in EndosomesLysosomes Are the Principal Sites of Intracellular Digestion

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Figure 15-34 Essential Cell Biology ( Garland Science 2010)

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ENDOCYTIC PATHWAYS

Specialized Phagocytic Cells Ingest Large Particles

Fluid and Macromolecules Are Taken Up by PinocytosisReceptor-mediated Endocytosis Provides a Specific Route intoAnimal CellsEndocytosed Macromolecules Are Sorted in EndosomesLysosomes Are the Principal Sites of Intracellular Digestion

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Figure 15-35 Essential Cell Biology ( Garland Science 2010)

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Figure 15-36 Essential Cell Biology ( Garland Science 2010)

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Figure 15-27 Essential Cell Biology ( Garland Science 2010)

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9/24/12 CP: Chap 6- DNA to protein

s4- housekeeping genes (t-tubulin, actin) are always expressed. gene expression can be tested wit realtime PCR (done after transcription) and Western Blot (more per

s6- DNA-->RNA, start signals for gene expression is encoded in promotor( usually upstream(more 5') to a start codon of a gene, doesn't always have to be that way)

s8- CTD has a repeating tail 25-55 (tyr, ser, pro, thr, ser, pro, ser). once Pi it helps RNA P go down template

s9- supercoiling happens upstream ahead of RNA poly. if supercoiling isn't relieved then no DNA--> mRNA, cell will die: cancer cells with chemo.

s12- altern splicing of a gene ca result in diff mRNA sequences

s13- they are specific sequences that label introns and exons

s15- CBC- cab binding complex, rRNA comes from nucleolus, exosome starts at 3' end and start copping towards 5' (upstream), eILF- eukaryotic in linking factor

s16- start codon AUG (Meth), stop codon (UAA, UGG, UGA), assoc AA with letters and 3 letter

s19- clover leaf design. wobble is 3rd position (flexible) *1 and 2 tell what AA will be.

s22- 60s and 40s don't add up bc its a sedimentation factor. large and small unit made up of rRNA + protein.s23- synthesis and termination happens rapidly

s24- polyribosome. translating same protein just a different stages of translation

s25- common mech for antibiotics and. what drugs work on prokary, eukary or both?