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biRocheEmisDtry bRloUcMk 2 Tulane School of Headaches Part 2
Biochemistry Block 2
119
Biochemistry
Post-Graduate
09/18/2012

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Term
Mitochondria and Hsc70
Definition
Heat Shock Proteins keep cytosolic mitochondrial proteins unfolded until they arrive at the kingdom of mitochondria / Once in the walls, it helps fold the protein
Term
TOM Import Receptor
Definition
Binds to the Matrix Targeting Sequence on the N' end of matrix bound proteins / TOM = Translocase of the Outer Mitochondrial membrane... brings proteins to Gereral Import Pore, which gets it through the outer membrane
Term
TIM proteins
Definition
Translocase of the Inner Mitochondrial membrane / TIM44 and Hsc70 pull the proteins into the matrix
Term
"Path A" Mitochondrial Inner Membrane Targeting
Definition
Protein contains Matrix-Targeting sequence and hydrophobic Stop Transfer Sequence / Zips through Tom40 and then the Stop Sequence stops transfer through the inner membrane and the Matrix signal is snipped.
Term
"Path B" Mitochondrial Inner Membrane Targeting
Definition
Protein contains Matrix-Targeting sequence and an Oxal-Targeting sequence / The protein goes through both membranes before the Oxa1 protein in the inner membrane grabs it and sticks it back twice into the inner leaflet
Term
"Path C" Mitochondrial Inner Membrane Targeting
Definition
Protein contains Matrix-Targeting sequence and multiple internal targeting sequences / Tim9/10 then prevents folding in intermembrane space and aid in multiple passes
Term
Outer Mitochondrial Membrane Targeting
Definition
Proteins possess Outer Membrane Targeting and Stop Transfer Sequence, which interacts with the Tom40 GIP / Not fully understood
Term
What kind of proteins would have a SKL tag?
Definition
Proteins to be sacrificed to the insatiable Peroxisome / PTS1 and PTS2 Peroxisome Targeting Sequence / It is NOT cleaved in the peroxisome
Term
Where are you going to find the SKL tag?
Definition
The C' end
Term
What is going on in that Peroxisome?
Definition
Oxidizes the nasties and the fatties, making H202 / Catalase then takes care of the H2O2 / Peroxisomes can divide and form de novo
Term
Pex5
Definition
Binds to PTS1 on peroxisome protein, with is ALREADY FOLDED / Pex5 brings complex to Pex14 on the peroxisome
Term
Pex2/10/12
Definition
Co-transports the ENTIRE Pex5/protein complex into the peroxisome and spits Pex5 back into the cytosol telling it to get back to fucking work
Term
Pex3 and Pex16
Definition
Peroxisome de Novo Synthesis: Insert into ER membrane / Mediate Pex19 into ER membrane / w Pex19 promotes insertion of PMP70 (making a Peroxisomal ghost!!!!), Pex2/10/12, and Pex14 --> Can accept new proteins
Term
Pex19
Definition
Peroxisome de Novo Synthesis: Once in ER membrane promotes budding / w Pex3 and 16 promotes insertion of PMP70 (making a Peroxisomal ghost!!!!), Pex2/10/12, and Pex14 --> Can accept new proteins
Term
Pex11
Definition
Facilitates Peroxisomal division
Term
What proteins would have a Nuclear Localization Sequence (NLS)?
Definition
Ones going TO the nucleussssssss.
Term
What proteins would have Nuclear Export Sequence (NES)?
Definition
Ones LEAVING the nucleusssssss.
Term
Riddle me this? What is the NPC?
Definition
The nuclear pore complex / Made up of nucleoporins / Intermediate filaments extend into cytoplasm / Nuclear basket in nucleoplasm / Ions and small (20-40 kDa) molecules can get through
Term
Goddess, sing to me of the NLS?
Definition
Nuclear Localization Sequence: Rich in basic amino acids (PKKKRKV) / REQUIRES Ran (GTP binding) and Importin to work
Term
Ran
Definition
Nuclear localization protein: GTP binding protein (monomeric G protein) / Active with GTP bound / GEF mediates the exchange of GDP and GTP (activating Ran) / GAP hydrolysis GTP to GDP (inactivates Ran)
Term
Nuclear Import Mechanism (Getting Cargo into Nucleus)
Definition
Cargo protein with NLS binds to Importin / Nucleoporins aid in PASSIVE diffusion into nucleus w/ Ran-GDP co-transport
Term
Nuclear Import Mechanism (Getting Import Proteins back into Cytoplasm)
Definition
Ran-GDP interacts with GEF and GDP is replace with GTP (active Ran) / Ran-GTP has high affinity for Importin, ergo disassociation of cargo from Importin / The Ran-GTP-Importin difuses thru NPC into cytosol
Term
Nuclear Import (The Return of the Ran-GDP)
Definition
Ran-GTP-Importin interacts with GAP, which hydrolyses the GTP to GDP / Low affinity for Ran-GDP and importin (ergo dissociation)... back to the beginning or end or middle... there are no beginnings or end in circles
Term
What kind of transport is Nuclear Import?
Definition
It is passive--> We are always following concentration gradients. The hydrolysis of GTP causes conformational changes and affinities for Cargo and Importin... this is PASSIVE, PASSIVE, PASSIVE.
Term
Nuclear Import: Concentration gradients of Ran-GTP/GAP, via GEF and GAP
Definition
Inside of the nucleus Concentrations of Ran-GDP-Cargo is low due to GEF, thus in cytoplasm, it wants in / GAP activity in cytosol is high, thus very little Ran-GTP-Importin in cytosol is very low. It moves quickly out of the nucleus
Term
What kind of proteins will have a NES?
Definition
Only the lucky ones... I always wanted an NES. Nuclear Export Signal: The ones going bye bye out of nucleus / It is leucine rich
Term
Ran Dependent Nuclear Export (Getting Cargo out of the nucleus)
Definition
GEF changes Ran-GDP to Ran-GTP / Ran-GTP has a high affinity for Exportin-Cargo(con NES) complexes / This Ran-GTP-Exportin-Cargo complex diffuses out of nucleus
Term
Ran Dependent Nuclear Export (Getting the export machinery back into the nucleus)
Definition
GAP changes Ran-GTP to Ran-GDP, which has a low affinity to exportin / They dissociate / Ran-GDP and Exportin passively diffuse back into the nucleus
Term
Ran-Independent mRNA Export
Definition
Exporters Nxt1 and TAP associate with mRNP and the NPC and aid in diffusion
Term
Dbp5
Definition
A helicase that unwinds mRNA's secondary structure and removes exporting proteins
Term
How do TAP, Nxt1, and Dbp5 get back into the nucleus
Definition
Importin-Ran mechanism
Term
PDH deficiency
Definition
Causes Lactic acidosis / Problem with E1 subunit (which ends up in the mitochondria) located on chromosome Xp22.1 / Arginine to Proline mutation screws up the matrix targeting sequence) Prevents conversion of pyruvate to Acetyl-CoA / Causes CSF problems
Term
Methylmalonic acidemia
Definition
Mutation in the mitochondrial sequence of methymalonyl-CoA mutaase prevents translocation into mitochondria
Term
Hyperoxaluria type 1
Definition
Cryptic mitochondrial targeting sequence --> peroxisomal enzyme, alanine:glyoxylate aminotransferase, into mitochondria whatever the fuck that means!
Term
What are microtubules good for?
Definition
1. Separate sister chromatids during mitosis 2. Arrange cellular organelles during interphase 3. Tracts for movement 4. Flagella and cilia
Term
Composition of microtubules:
Definition
Linear repeats of alpha and beta heterodimers
Term
What nucelotide triphosphate is on microtubule monomers? And what does it do?
Definition
GTP. On the alpha monomer, it remains GTP. On the beta it is hydrolysed.
Term
Taxol
Definition
Stabilizes microtubules. Abrogates mitosis. Cancer killer.
Term
What is a protofilament?
Definition
A line of microtubule heterodimers
Term
How many protofiliments does it take to make a microtubule?
Definition
13
Term
What will find a the negative end of a microtubule?
Definition
The alpha monomers
Term
What will find a the positive end of a microtubule?
Definition
The beta monomers
Term
Singlet Microtubule
Definition
13 protofiliments / Used in interphase and mitosis
Term
Doublet Microtubule
Definition
13 and 10 protofiliments / Cilia and flagella
Term
Triplet Microtubule
Definition
13, 10, and 9 protofiliments / Basal bodies and centrioles
Term
Critical concentration of microtubule dimers
Definition
The concentration of heterodimers needed for them to spontaneously polymerize / The concentration of heterodimers will not exceed the Cc
Term
Microtubule assembly kinetics and polarity
Definition
(+) side has low Cc / (-) side has high Cc / Assembly occurs more quickly at (+) / (+) side usually the "assembly end" while the (-) end is usually the depolymerization end
Term
Microtubule Treadmilling
Definition
Most beta tubulin is GTP bound on the (+) side and all beta tubulin that is added must be GTP bound / It begins to get push backwards (treadmilling) and eventually hydrolyses the GTP to GDP, which makes the tubulin less stable at the (-) side.
Term
The GTP-bound dimer pool is high. What is going to happen?
Definition
polymerization at (+) end / Forms a GTP cap (very stable with GTP bound B tubulin concentrations are above Cc, and very unstable when below Cc)
Term
Catastrophe
Definition
GTP cap is in a solution under the Cc for GTP bound B tubulin / Rapid depolymerization
Term
Three Microtubule Associated Proteins (MAPs) and what they do and how they do it
Definition
Tau, MAP2, MAP4 / Stabilize / They contain lots of + charged AA, which bind to - charged AA on tubulin, neutralizing the charge repulsion between tubulin subunits
Term
MAP projection domains
Definition
Negatively charged acidic projection on MAPs that maintain a certain distance between microtubules / Often in neurons
Term
What happens if you phosphorylate a MAP?
Definition
You would knock out the positive charge and emasculate the MAP. It would then cause depolymerization
Term
Kinesin-13
Definition
Bind to the (+) side of microtubule, bends protofiliments, promoting catastrophe / ATP hydrolysis is needed to remove dimers
Term
Stathmin
Definition
Also known as OP18 / Bind to the (+) side of microtubule, bends protofiliments, promoting catastrophe / Also enhances GTp hydrolysis / Can be inactivated by phosphorylation
Term
Katanin
Definition
Can sever or induce breaks in the microtubules, which exposes GDP bound B tubulin monomers... AH! CATASTROPHE! HEAD FOR THE HILLS!!
Term
Colchicine
Definition
Drug / Binds tubulin dimers and sequesters them / Lowers dimer concentration (thus more dimers are needed to reach Cc) / Used to reduce WBC migration and inflammation in Gout
Term
Vinblastine
Definition
Drug / Binds tubulin dimers and sequesters them / Lowers dimer concentration (thus more dimers are needed to reach Cc) / Used to treat Nonhogkins lymphoma, lung, breast, testicular cancers
Term
Podophyllotoxin
Definition
Drug / Binds tubulin dimers and sequesters them / Lowers dimer concentration (thus more dimers are needed to reach Cc) / Used treat lymphomas, lung and genital cancers, and HPV genital warts
Term
Nocodazole
Definition
Synthetic drug that prevents spinal assembly during mitosis / Arrest in G2 cell cycle phase / Used to synchronize cells in culture
Term
Alzheimer's and microtubules
Definition
Improper phosphorylation of Tau proteins / Destabilizes microtubules
Term
Pin1
Definition
Proline isomerase converts spontaneously formed proline cis isomers back to trans. This drives dephosphorylation of APP and Tau and the microtubules remain sound. Defective Pin1 will causes more cis proline isomers on Tau and APP, which will then be phosphoylated, which will then causes depolymerization of microtubules in brain, which will cause amyloid plaques and neurofibrillary tangles, which will cause Alzheimer's Disease.
Term
Microfilaments
Definition
Made from actin, which is made by the intertwining of two thin filaments / Can polymerize and depolymerize / Muscle contraction, cell adhesion, motility, and stabilization of microvilli / The smallest
Term
Intermediate filaments
Definition
Mechanical integrity of the cell, motility, and serves as scaffolds for signaling molecules / No polymerization and depolymerization / stiff
Term
Duchenne Muscular Dystrophy and actin
Definition
Dystrophin links the actin cytoskeleton to the extracellular matrix / Dystrophin binds the protein alpha/beta Dystroglycan in the plasma membrane / On the other side of the membrane, there are extra cellular matrix proteins like laminin, agrin, and perlecan that bind to carbohydrates on the alpha/Beta Dystroglycan / Muscle contraction needs dystrophin to stabilize the interaction between the cytoskeleton and the extracellular matrix / Without dystrophin, the extracellular proteins will tear the plasma membrane, causing destruction of muscle cells / Fibroblast cells migrate to site and create nonfunctional scar tissue
Term
Actin monomer
Definition
G-actin
Term
Polymerized actin
Definition
F-actin
Term
Spectrin
Definition
With Actin, gives red blood cell there biconcave shape
Term
What is required for actin polymerization?
Definition
ATP and Mg2+
Term
What is the (-) end of G-actin?
Definition
Where the ATP-binding cleft is exposed to the surface
Term
What is the (+) end of G-actin?
Definition
Opposite where the ATP-binding cleft is exposed to the surface
Term
Explain actin polymerization
Definition
A (+) and (-) G-actin end bind together to make F-actin
Term
Cofilin
Definition
Binds to F-actin with ADP containing subunits and breaks them, speeding up depolymerization
Term
Profilin
Definition
Enhances the exchange of ADP to ATP on G-actin / This is needed if the G-actin will be used again
Term
Thymosin Beta 4
Definition
Binds to to ATP-G-actin and sequesters it or releases it to keep a constant concentration: This helps keep a constant pool of ATP-G-actin
Term
CapZ
Definition
Binds to (+) end of F-actin and prevents addition of new ATP-G-actin monomers
Term
Tropomodulin
Definition
Binds to (-) end of F-actin and stabilizes it
Term
Formin
Definition
Stimulate the assembly of of long unbranched F-actin. These fibers are found in stress fibers and contractile rings.
Term
Arp2/3
Definition
Stimulates the formation of branched filaments, which are found in the leading edge of migrating cell / Controlled by signal transduction
Term
Chemotactic attractant
Definition
Cause cell migration / Very often growth factors that bind receptors on migrating cells, setting up a signalling cascade
Term
Steps of mammalian cell migration
Definition
Step 1: The extension of the plasma membrane to form lamellipodium via increasing the length of actin filaments / Step 2: Adhesion of lamelliodium / Step 3: Translocation - bulk of cell moves toward adhesion point / Step 4: Adhesion point in back is broken, via pulling by F-actin. Membrane proteins are recycled
Term
Fimbrin
Definition
cross linked parallel F-actin in intestinal microvilli / Fibrin stabilizes these structures
Term
Alpha actinin
Definition
Organizes F-actin of the stree fibers during migration / Also muscle contraction
Term
Spectrin
Definition
Cross links and organizes F actin into a meshwork network just under the plasma membrane / It is a long fibrous molecule that forms the cross linking with F actin / Supports plasma membrane
Term
Integrins
Definition
Cross link the cytoskeletal proteins to extracellular matrix / Transmembrane proteins / This fixes cells to their tissues
Term
Hereditary Spherocytosis
Definition
Has weak RBCs due to a defect spectrin, protein 4.1, or ankyrin / Patients usually have anemia and/or large spleens or gallstones with excess amounts of heme.
Term
Keratins
Definition
Found in epithelial cells / Tissue strength and integrity
Term
desmin/vimentin
Definition
Found is muscle, glial, and mesenchymal cells / Sarcomere organization and integrity
Term
neurofilament
Definition
Found in neurons / Axon organization
Term
lamins
Definition
Found in nucleus / Nuclear structure and organization
Term
Epidermolysis bullosa simplex
Definition
Problem with keratin IFs / Blisters form very easily
Term
Type I OI (Osteogenesis Imperfecta)
Definition
Also called brittle bone disease - problems with collagen production - Could be a change for larger AA instead of the usual Gly
Term
Type II OI
Definition
Child dies at birth due to collapsed
Term
Bisphosphoonates
Definition
Used to treat Osteogenesis Imperfecta - it inactivate and destroy osteoclast - they also decrease the destruction of osteoblasts
Term
Collagen 4' Structure
Definition
Three collagen chains coiled into a left handed alpha triple helix
Term
Collagen consensus sequence
Definition
Gly-X-Y / X and Y are endo-proline and exo-hydroxyproline / right handed helix breakers
Term
Type I collagen
Definition
Tropocollagen - H-bonds between strands - Gly make steric hendernce not a problem
Term
Collagen Vs Elastin
Definition
Collagen (high tensile strength, low elongation, in tendons) / Elastin (low tensile strength, high elongation, in skin)
Term
Scurvy
Definition
Deficiency of vitamin C, which is an cofactor needed to turn proline to hydroxyproline / Thus, the collagen that is made falls apart very easily
Term
What enzyme is responsible for the hydroxylation of proline?
Definition
4-Prolyl-hydroxylase
Term
Mechanism of 4 Prolyl-hydroxylase
Definition
Uses molecular oxygen to hydroxylate proline and turns alphaketoglutarate to succinate / USED IRON AS COFFACTOR / Vit C is oxydized needed to keep iron reduced to ferrous iron
Term
Where in the cell does collagen biosynthesis take place?
Definition
Rough endoplasmic reticulum... it is then translocated into ER.
Term
Collagen biosynthesis traslocation into the ER...
Definition
Conversion of proline to hydroxyproline
Term
Collagen biosynthesis once in the ER...
Definition
Translocation signal is cleaved, creates PRO-COLLAGEN
Term
Creation of collagen triple helix...
Definition
Done by a creation of disulfide bonds between strands on C' ends and the triple helix / Procollagen is then secreted out to ECM where N' and C' ends are cleaved and mature collagen is formed
Term
ECM triple helix processing
Definition
Five collagen fibers cross linking to higher order
Term
How to higher order collagen fibers form in the ECM?
Definition
The enzyme Lysyl oxidase processes the cross linking / It uses Cu2+
Term
Menkes' Syndrome
Definition
Lysyl oxidase or Cu2+ / Kinky, steeled colored hair, growth problems
Term
Ehler-Danlos Syndrome
Definition
Deficincey in the ECM Procollagen peptidase / The C' and N' end are not cleaved, hence loose collagen
Term
Type I Collagen
Definition
Most abundant collagen - most connective tissue
Term
Type II Collagen
Definition
Cartilage and vitreous humor
Term
Type III Collagen
Definition
Extensible connective tissue (eg skin, lungs, blood vessels.
Term
Type V Collagen
Definition
Tissues containing type I
Term
Type XII Collagen
Definition
Fibril associated / Tissues containing type I collagen
Term
Type IV Collagen
Definition
Network forming / Basal lamina
Term
Type VII Collagen
Definition
Anchoring filament / Attachments of the basal laminae to underlying connective tissue
Term
Elastin
Definition
Hydrophobic / Rich in G,A,V,P,K / Few hydroxylated AA / deaminated lysines cause cross linking
Term
Marfan's Disease
Definition
Mutation in fibrillin gene / Impaired elastin function / Long slender limbs / Heart problems
Term
Elastase problems
Definition
Expressed in neutrophils and normally degraded in ECM / Alpha-1-antitrysin helps regulate this / Bad A1-AT builds up and causes damage to the liver / Too much elastase and not enough elasin to degrade causes lung degradation
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