Final Flashcards
What are the steps of creating lysosomes (5)?
Enzymes go through sec path (targeted bc n term hypho leader seq)
Thru ER via cotranslation (translocon)
In cis golgi, man 6 phosphate attached
M6P attaches to receptor in cis golgi, buds off in clathrin coated vesicle
fuses w/s endosome, change in pH releases M6P
What direction do COP1’s travel?
Retrograde
What direction do COP2’s travel?
Anterograde
Through what does COP1 move materials?
Trans -> medial -> cis golgi
What path do COP2 vesicles travel through?
RER -> cis golgi
Where are clathrin coated vesicles found?
TGN
When are clathrin coats used?
Recep mediated endocytosis
What 2 shapes compose clathrin?
Pent, hexagons
What two proteins are used to make clathrin?
Heavy/light chain
What does the clathrin light chain do?
Holds heavy chains in place
What does the clathrin heavy chain have?
Feet at end terminus
What is the role of the clathrin triskels in vesicles?
Imparts curvature of membrane
What’s another name for adaptor proteins and how many types are there?
Assembly particle, 4
What is required to initiate vesicle formation?
ARF
What does ARF stand for
ADP Ribosylation Factor
How many ARFs are there?
6
What are the 2 roles of ARFs?
GTP binding protein and GTPase
What happens to ARF on binding GTP?
Shape change
What tickles ARFs to switch GDP w/ GTP
GEF
What proteins do SAR1 resemble?
ARF
What do adaptor proteins recognize?
ARF on membrane, cargo
Define heterotetramer
4 distinct protein complex
What kind of polymer is AP2?
Heterotetramer
What does GGA stand for (adaptor)
Golgi localized Gamma ear ARF (adaptor)
What is the address on a lysosomal hydrolase?
Mannose 6 Phosphate
What is released when ARF GPD is tickled and given GTP?
Lipid tail to insert into membrane
How does GGA know that M6P recep is the right recep
Address (YXX/O/)
What is AP2 used in?
Recep Med Endo
What subunit of AP2 does the C face of a membrane recep bind to?
Mu
What is inositol?
A glycolipid
What gives specificity to membranes
Different phosphorylations of inositol
What starts recep mediated endo?
Inositol 4,5 bisphosphate
How does RMEndo start?
AP2 changes shape after recognizing I(4,5)P2, binding a membrane receptor to mu subunit
Where are AP1,3,4 found?
Endosome or TGN
What does Dynamin use as energy to pinch off vesicles?
GTP
What protein starts COP2 ves form?
SAR1-GTP
In COP2 what inserts into the membrane to give curvature?
SAR1-GTP
What binds to SAR1-GTP in COP2
Sec 23/24
What binds to Sec 23/24 in COP2?
Sec 13/31
What do the receps in COP1 vesicles recognize?
KDEL amino sequence
What does RAB stand for
RAS-like protein isolated from rabbits (RAS are the family of ARF/SAR)
Where are RABs found?
On vesicles
What are attached to vesicular RABs?
VSNARE proteins (SNAP Receptors) (Snares)
What does the a helix in the VSNARE have (define heptag repeat)
(A)BC(D)EFG where A, D are hypho
What occurs when a vesicle bumps into target?
Tethering
Where are RABs found in membrane fusion
Vesicle and Target (both w/ GTP)
Where are RABs found w/o GTP?
Cytosol
What gives membrane fusion specificity?
Like RABs on Ves and Target
How does SNAP 25 insert itself in target membrane
Lipid tail
What’s the neuroterm for VSNARE
synaptobrevin
What’s the neuroterm for TSNARE
syntaxin
How are vesicles pinched off in membrane fusion?
VSNARE + TSNARE&SNAP25 zip together
What is and what does NSF do?
N-ethylmaleiamide sensitive factor, unzips SNARES/SNAPS
What does SNAP stand for?
Soluble NSF attach protein
What does NSF do?
ATP to unwind SNARES/SNAPS
Where is plasmalogen created, found?
Peroxisomes, myelin sheaths
What is plasmalogen and what is weird about it?
Phospholipid, attached to gycerol using ether
How is membrane potential usually distributed?
+ on outside
What does Botulism do?
Cleaves V/TSNARES
What depolarizes a membrane
Na+ entering cells
What depolarizes a membrane
K+ out
What happens when an action potential reaches synaptic cleft?
Ca+ enters cell, reacts w/ synaptogabin, cause vesicles to bind to membrane, empty into cleft
What do peroxisomes do?
Break down >22 carbon fatty acids, no ATP generation
What enzymes do peroxidases use to make hydrogen peroxide?
Oxidases
What molecule do peroxisomes detoxify?
Ethanol
What do peroxisomes use to convert H2O2 to water?
Catalase
What is the address on peroxisomal enzymes and where is it found?
SKL, C terminus
PTS1 (peroxisomal targeting sequence 1)
What is the name for peroxisomal enzymes?
Peroxins
In what shape are peroxins carried in?
linearly
How many bilayers does the nucleus have?
2
What occurs in the nucleolus
rRNA produced, Ribosomes assembled
Outermembrane of nucleus contiguous with
RER, SER
What is the space between the nuclear bilayers
Perinuclear space
What attachement sites are found on the inside of the inner nuclear membrane
Lamina, mesh, attaches to chromatin
What are the attachment sites on the outside of the outer nuclear membrane and what do they bind to?
Nesprin 1/2 bind actin
Nesprin 3 binds int fils
What are nuclear lamins composed of and what are those pieces called?
Intermediate filaments, called lamina
What are the three compnent pieces of nuclear lamins and how are they hooked up?
A, B, C
A bound to C, both bound to B which is bound to the membrane
What destroys lamins before mitosis?
Phosphorylation by MPF which is a cyclin dependent kinase
What does a defect in nuclear lamins cause
Progeria
What proteins are allowed to enter the nucleus?
Have NLS (Nuclear localization signal)
What is the NLS (Nuclear localization signal?
PKKKRKV
What is on the C face of the nuclear pore?
Annulus, octoganal repeating protein complex
What is a nuclear pore protein called?
Nucleoporin
How many proteins compose the (8)n repeating annulus complex?
30
What radiates from the C face of nuclear pores?
Cytoplasmic filaments
What does the N face of the nuclear pore look like?
Basket
What is the main feature of the nucleoporins in the nuclear pore?
Fg repeats (phenylalanine glycine)
Where is importin alpha originally and what does it look for to bind to?
In cytosol, looking for PKKKRKV (NLS) on proteins
What finds and binds importin alpha?
Importin beta
What happens to importin beta once it binds alpha bound to protein cargo
Cytoplasmic filaments grab it and carry it through the membrane
What is an important feature of importin beta?
Fg repeats
What occurs once the importin complex enters the nucleus
RAN-GTP binds Imp beta, releasing Imp alpha and protein
Once RAN-GTP binds Imp beta what happens
Moves back into the cytoplasm
What happens once RAN-GTP+Imp B enters cytosol
RAN-GAP converts GTP=>GDP, releasing Imp B
RAN-GDP reenters nucleus where it is tickled by RAN-GEF
What family of proteins does RAN belong to and what are 3 examples?
RAS
SAR1, ARF, RAB
How is Imp A removed from nucleus
Exportin finds Nuclear Export Signal on it, binds and carries out
What are histones, what is their charge and what are the variaties
H1, H2A, H2B, H3, H4
Describe hyperacetylation
Histone acetylase attaches acetyl groups to histones, tightening and repressing transcription
How is DNA coiled?
Negatively supercoiled
Where are coding genes located
tips of cohesin loops
@ n terminus of histones, what affects gene expression
Acetylation on lysine
Methylation of argenine/lysine
What kind of chromatin is always ready for transcription
Euchromatin
What is the telomerase gene sequence
TTAGGG
What is the Hayflick limit
Max times a cell can divide
What is a feature of mitochondrial outer membrane porins?
B pleated sheets
What are 4 features of the mitochondrial inner membrane
Cardiolipin, ATP synthase, cristae, ETS
Where is cardiolipin found and what does it do?
Mitochondrial inner membrane
Impermeabilizes membrane to p+, holds protein pumps
What is the equation to make NADH
(NAD+) reduced with (p+) and 2(e-)
What are the products of glycolysis
2 pyruvate
2 ATP
2 NADH
What happens to pyruvate at the start of KREBs
pyruvic dehydrogenase removes carboxyl => CO2
What does pyruvate become post pyruvic dehydrogenase
Acetyl
ACoA + oxaloacetate produces what?
citric acid + 2CO2
What do uncouplers do
Allow free flow of protons through membrane
What changes the shape of B subunit of ATP synthase
rotation of gamma shaft by PMF
How often does the shape of B subunit of ATP synthase change?
Every 120 deg
How are protiens carried into the mitochondria
Unfolding by HSPs through Transport Outer Membrane Proteins (TOMs)
Where do mictrotubs begin?
MTOC, radiate outward
What is the role of MicTubs
maintain cell shape, also movement and chromo movement
What are MicTubs composed of?
Alpha Beta dimers creating a protofilament strand
Which protofil dimer constituent hydrolyses its GTP?
Beta
Which is the busy end of the MicTub
Beta terminus (+)
How many protofils to a MicTub
13
What are 2 MTOCs
Centrsome and Basal Body of flagella/cilia
What is the centriole in the centrosome composed of
9 triplets of MicTubs
What does colechicine and colecemin do?
Depolymerizes Mic Tubs
What does gamma tubulin have to do with MicTub growth?
Starts MicTub growth @ MTOC binding alpha
What causes MicTubs to depoly naturally
Beta hydrolysing GTP
What are 3 MAPs (MicTub Assc. Proteins)
+TIP, MAP2, Tau
What is MAP2 involved in w/ Mic Tubs
Spacing
What is Tau implicated in in the brain
Alzheimers, amyloid tangles
What are the two MicTub motors and what are their endednesses
Kinesin (+), Dynein (-)
What are flagella/cilia internal structures called
Axonemes
What are axonemes composed of
9 doublets plus 2 MicTubs in center
What does the basal body look like
MTOC, 9 triplets of mictrotubles
What do the outer/inner dynein arms of axoneme require to move
Ca+ and ATP
What is the charge on the flagellar tip?
+
What are microfils composed of
Actin
What does g-actin need to become f-actin and what does f-actin resemble
Mg+ and ATP, double twisted strand of g-actin
What protein stims actin poly?
RACK
What protein stops actin poly
Rho
What binding site does the mysosin S1 head contain
ATP
What is unique about conventional myosin?
Bipolar filament
What is the subunit of the muscle fibre
myofibril
what is the subunit of the myofibril
the sarcomere
What does nebulin do
Acts as actin ruler in sarcomere
What does titin do
massive spring, myosin aligner and overstretch preventer
How is muscle contraction regulated
Tropomyosin lays on 7 actins
Troponin on Tropomyo
Ca+ causes troponin to change shape, moves tropomyo into groove on S1 head
Allows S1 to interact w/ actin
What are int fils good for?
Stable, good in nerve cells
How do int fils interact w/ other cysto skel elements
Plectin
Where do int fils polymerise
anywhere
What is the structureof int fils?
Dimer, tetramenr of those dimers, non polar
What does a tight junc look like and what is its purpose
honeycomb, prevents evaporation, movement of anytihng between cells
What are the 3 tight junction protiens
Occludin, Claudin and JAM
What is the purpose of desmosomes
Mechanical tolerance
What are the 2 cadherins in desmosomes
desmoglien and desmocollin
What is the role of Gap Juncs
Communcation
What is the gap junc protein
Connexin
What is the gao junc complex
A Connexon
How many connexins to a connexon
6
What is the nature of the gap junction channel
Hyphil
What causes connexons to close and how
Hi Ca+ presence rotates connexon, closing it
What is the role of Focal Adhesions
Attach cells to ECM
What are integrands found in
Focal adhesions and hemi desmosomes
What juncs use actin and what is the adherence between
Focal adhesions (cell-matrix)
What juncs use int fils and what is the adherence to
Hemi desmosomes (cell-matrix)
Desmosomes (cell-cell)
Both use keratin
How many times do G coupled protein receptors span the membrane
7
What is the G protein made of
G(alpha+beta+gamma) subunits
This receptor is also a GEF
G coupled protein receptor
What does GRK stand for
G coupled protein receptor kinase
What happens when Galpha-GTP binds the effector
ATP converted into cAMP
What prevents cAMP production due to Galpha-GTP at receptor
GRK
How does GRK operate
Phosphorylates GCPR, arrestin comes in
What can Arrestin trigger
calthrin coated vesicle formation to prevent further cAMP production
What are 5 2nd messengers and what do they activate
cAMP - ProkinA cGMP - Prokin G IP3 - Ca Calcium - Prokin C Diacylglycerol - Prokin C
How is the headgroup of PI cleaved?
Galpha-GTP stims phoslipC to cleave headgroup freeing IP3
What happens to the cleaved IP3 after released from PI
Recognized by smooth ER IP3 recep, releases Ca+ which stims prokinC
What happens when Ca+ is depleted from the cell
STIM in membrane aggragates, opening Orai1 Ca+ channels
What do Recp Tyrosine Kinase (RTK) recognize
Growth factors
What happens when RTK recognize a ligand
Dimerize, autotransphophorylate
What does Grb2 stand for
Growth factor receptor binding protein
What does Grb2 do?
Binds to kinase using SH2 domain
What binds to Grb2
Sos
What is Sos an example of
GEF
What does GAP stand for
GTPase Activating Protein
What starts the RAS cycle
Sos tickles to make RAS-GTP
What does RAS-GTP do?
Activates RAF via phosphorylation
What prevents RAS from cycling again?
GDP Dissociation Inhibitor
What does RAF(P) activate
MEK(P)
What does MEK(P) activate
ERK(P)
What does ERK(P) activate)
TF(P)
What phosphotase ends the MAP kinase pathway and how?
MKP1 cuts P from ERK(P)
What gives specificity to APC (anaphase promoting complex)
Acc. Proteins
What does APC-Cdc20 do
Destroys securin which was preventing separase from cleaving cohesin
What does APC-Cdh1 do
changes shape of mitotic cyclins
When is BRCA1/2 used
repairing DNA
What happens if BRCA1/2 fail
p53 leads cell to death
What are protooncogenes
Genes that could become cancer
