Intracellular Compartments

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Author:
mnvang321
ID:
302011
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Intracellular Compartments
Updated:
2015-05-04 17:46:17
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cellbio
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cell bio
Description:
chapter 12
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  1. -lipid metabolism
    -oxidative phosphorylation
    -photosynthesis
    -allows specialized compartments
    Internal Membranes
  2. -beginning of protein synthesis/degradation
    -intermediary metabolism
    Cytosol
  3. -soluble/insoluble membrane protein synthesis
    -rough=attached ribosomes 
    -lipid production
    -Ca+2 storage (muscle cell)
    Endoplasmic reticulum
  4. -receives lipids and proteins from ER 
    -modifies and dispatches
    Golgi Apparatus
  5. -oxidative phosphorylation
    Mitochondria
  6. -photosynthesis
    Chloroplasts
  7. -digestion of defunct (no longer in effect/use) organelles/ingested particles 
    -endomsome and peroxisomes deliver to lysosomes
    Lysosomes
  8. -histone protein
    -polymerase
    -gene regulatory proteins
    -RNA processing proteins
    -ribosomal proteins
    Import into nucleus
  9. -rRNAs 
    -mRNAs 
    -ribosomes
    Export from nucleus
  10. -responsible for transport nucleus <--> cytosol

    -125 million Da (1 million AAs)

    -30 diff NPC proteins (nucleoporins)

    -transports ca. 500 molecules / second
           ~slow transportation of larger molecules (requires energy)

    - small molecule (<5 kDa "5000 Daltons") diffuse freely (80-90AA)

    -large molecules (>60 kDa "60000 Daltons") are mostly excluded (cannot attach; gets repelled)
    Nuclear Pore complex
  11. -nuclear import involves nuclear import receptor proteins 

    -these bind to NPC (nucleoporins)
           ~FG repeats (phenylalanine,glycine) (in loops)

    -movement involve sequential binding to dif FG-repeats 

    -export governed by related export receptor proteins (phylogenically similar)
    Import Receptor proteins
  12. -A molecular switch that can exist in 2 conformational states, depending on if its bound to GTP or GDP.

    -2 ran-specific regulatory proteins trigger conversion btwn 2 states
           ~a cytosolic GTPase-activating protein (GAP) triggers GTP hydrolysis and converts Ran-GTP to Ran-GDP and thus converts Ran-GDP to Ran-GTP. 

    -Ran-GAP (Ran-GTPase activating factor) is located in cytosol so it contains mainly Ran-GD

    -Ran-GEF (Ran guanine exchange factor) is located in nucleus so it contains more Ran-GTP.
    Ran GTPase
  13. - 2-D network of proteins 

    -Made of nuclear lamins 

    -anchored to nuclear core complexes (NPCs)

    -interacts with membranes proteins and chromatin

    -depolymerizes during mitosis 
          ~phosphorylation by cyclin dependent kinase Cdk
    Nuclear Lamina
  14. -made in cytosol 

    -imported w/in minutes 

    -one or more signal peptides 

    -matrix proteins 
          ~N-terminal peptides 
          ~removed by signal peptides 

    -outer/inner/inter-membrane proteins 
          ~intergral signal peptides 
          ~not removed 

    **signals are necessary and sufficient 
    Mitochondrial Precursor Proteins
  15. -signal=helix 
            ~one side (+) charged, other is hydrophobic residues cluster on opposite side 
            ~amphiphilic alpha helix 

    Protein translocators 
    TOM(translocase out men) complex: transfers proteins across outer membrane
    TIM23 & TIM22 (translocase inner mem): transfer proteins across inner membrane 

    Protein import into mitochondrial matrix
    -proteins unfolded UNTIL import
    -transport occurs at same time thru both membranes
    Import of proteins into mitochondrial matrix
  16. -occurs post-translationally 

    -requires signal sequences (amphiphilic)

    -signals removed after use 

    -requires energy use 
           ~Use GTP and ATP for inner and outer membrane
           ~H+ for thylakoid membrane


    THYLAKOID membrane (insertion of proteins into thy.mem.)

    4 ways 
    -SEC pathway (homologous to bacterial SEC protein) : uses components that are homologs of Sec proteins, which mediate protein translocation across bacterial plasma membrane.
    -SRP (Signal Recognition Protein Pathway): uses chloroplast homolog of signal recognition particle (SRP)
    -TAT(Twin Arginine tranlocation) pathway: 2 arg. are critical in signal seq that direct proteins in this pathway, which depends on H+ gradient across thylakoid membrane 
    -spontaneous insertion : doesn't require any protein translocator.
    Chloroplasts membrance insertion
  17. -single membrane
     
    -no genome
     
    -all proteins nuclear encoded
     
    -most proteins imported 4rm cytosol 

    -some proteins via traffic 4rm ER

    -often contain crystalloid core

    -contain oxidative enzyme 
            ~Peroxidase 
                      -produces peroxide by oxidation of org. substrates 
                      - RH2+O2--->R+H2O2

            ~Catalase 
                      -uses hydrogen peroxide (H2o2)
                      -can oxidize org. substrates 
                      -detoxifies formaldehyde, formic acid, phenols, and alcohols 
                      - 2 H2O2 -> 2 H2O + O2 
                      -H2O2 + H2R -> 2H2O + R 

    -B-oxidation
         ~ fatty acids -> acetyl-CoA 

    -urate oxidase 
         ~ uric acid -> 5-hydroxyisourate 
         ~ purine catabolism 

    -Plasmalogen synthesis
         ~ phospholipids in myelin 

    -In plants: photrespiration
         ~ conversion of seed lipid to carbohydrate
    Peroxisomes
  18. Import 
    -N and C terminal signal sequences 

    -receptor proteins in cytosol 

    -23 proteins involved aka peroxins 

    -ATP dependent 

    -proteins do NOT unfold; mechanism different 4rm mitochondria / chloroplasts 

    -Pex5 is a protein that accompanies cargo into perxisomes; cycled back 

    *can arise from ER or by fission
    Protein Imported into Peroxisomes
  19. - >50% of membranes 

    -continuous sheet enclosing single ER lumen space 

    -site of production of ALL trans-membered proteins for 
         ~ER
         ~Golgi
         ~Lysosomes
         ~Endosomes
         ~Secretory vesicles 
         ~Plasma membrane 
         
    -extends across entire cell, all parts of cell are close to some portion of ER
    Endoplasmic Reticulum (ER)
  20. -bound ribosomes 

    -proteins inserted as they are synthesized
    Rough ER
  21. -formation of transport vesicles (transitional ER)

    -lipid metabolism

    -steroid hormones synthesis 

    -hepatocytes
            ~lipoprotein synthesis
            ~cytochrome P450 - detox

    -sacroplasmic reticulum
            ~Ca+2 storage and release
    Smooth ER
  22. -required for ER insertion

    -6 protein subunits 

    -SRP RNA molecule 

    -Hydrophobic pocket lined with methionines 

    -recognizes 8 or more non-polar AAs 

    -binds to emerging protein / signal

    -blocks elongation factor binding site
           ~halts protein synthesis
           ~gives enough time to bind to ER
           ~ensures that proteins don't fold before being inserted 


    -can bind to internal signal seq

    -transfer seq can bind in both orientations, determining N and C terminal orientation in membrane 



    Signal-Recognition Particle (SRP)
  23. -core of the translocator 

    -forms aq. pore thru which PP passes 

    -found in prokaryotes and euks 

    -formed by alpha helices 

    -one helix forms 'plug
           ~ex: gate to prevent Ca2+ loss
    Sec61 Complex
  24. -start/stop of hydrophobic seq determined by location 

    -SRP scans polypeptide N->C terminus
    Multipass proteins
  25. -identifies 7 short hydrophobic regions in rhodopsin
    Hydrophobicity Plots
  26. -MOST proteins are glycosylated 

    -helps retention in ER til correctly folded 

    -few in cytosol are (glycosylation simpler too)

    -precursor oligosacharide 
           ~transferred in block
           ~dolichol:membrane lipid 
           ~transfer to asparagine side chain (N-linked)
           ~help protein folding
    Proteins in ER are glycosylated
  27. -attachment of protein on C-terminus 

    -forms in ER lumen 

    -proteins for plasma membrane 

    -proteins can be released by cleavage from anchor
    Glycosylphophaditidyl inositol (GPI) anchors
  28. -80% of protein transported in ER folded improperly

    -transported back to cytosol
         -retrotranslocation
         -dislocation

    requires
         -chaperone
         -energy (ATP)
         -transporter proteins (Sec61)

    -Gluconsase removes sugars in block
    Improper folding

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