MCB 2 FINAL

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*--- Lecture 7: Membrane Transport 3 ---*

*LO1: Define depolarization and hyperpolarization of the plasma membrane.* *LO2: Distinguish ion channels by gating mechanism, ion permeability, and postsynaptic response (EPSP vs IPSP).* *LO3: Describe an action potential's origination and movement down the acon, including participating ion channels.* *LO4: Explain the role of myelin in action potential conductance.* *LO5: Describe the actions of channels in the neuromuscular junction.* *LO6: Summarize the roles of AMPA and NMDA receptors in Long Term Potentiation.* *LO7: Identify diagnoses attributed to too much or too little synaptic pruning.*

*--- Lecture 6: Membrane Transport ---*

*LO1: Differentiate channel proteins and transporters in terms of structure, kinetics, and function.* *LO2: Describe various mechanisms of channel selectivity (aquaporin, K+, Cl- channels).* *LO3: List and describe mechanisms of channel gating, including example channels for each mechanism.* *LO4: Identify and describe the channel and gating mechanisms for: voltage-gated Na+ channels, acetylcholine receptors, mechanoreceptors, MscS channels.* *LO5: Define equilibrium potential of an ion.* *LO6: Calculate the equilibrium potential of an ion at given conditions using the Nernst Equation.* *LO7: Predict ion movement using the equilibrium potential of an ion at given conditions.*

How does a bacterial MscS channel work?

- "MechanoSensitive Conductance Small" - the channel opens when H2O swells the bacterium and pressure is put onto its membrane ... this allows H2O to flow out of the cell in compensation

What does SEM stand for and how does it work?

- "Scanning Electron Microscopy" - electrons that bounce off the specimen are detected, giving an image to the outside of the specimen (think surface!!!)

What is SRP?

- "Signal Recognition Particle" - receptor that recognizes the ER signal sequence - binds to signal peptide of protein as it emerges from the ribosome and to the ribosome itself - binds to an SRP receptor on the ER membrane

What is STED?

- "Simulated Emission Depeltion" - elimination of fluorescence in the doughnut around the refracted light, leaving only a point ... leads to better resolution - uses 2 lasers

What does TEM stand for and how does it work?

- "Transmission Electron Microscopy" - an electron beam is aimed at a specimen and electron dense areas scatter more electrons, so fewer are passed through the specimen ... these areas appear darker in pictures - dark and light regions can be seen within the cell

How much greater in length and volume are eukaryotic cells when compared to bacterial cells?

- 10-30x bigger in length - 1,000-10,000x bigger in volume

Collagen

- 25% of protein mass in mammals, major component of skin and bone - triple-stranded helix ---> each subunit = chain of repeating 3 AAs ... every 3rd is a glycine bc they can pack very tightly into the interior of the helix - most common types = fibrillar - secreted by fibroblasts

connexin

- 4-pass transmembrane protein - 6 make up a connexon - 2 different kinds

What is bacteriorhodopsin and how does it function?

- 7-pass transmembrane protein (7 helices form a ring structure) - transforms light energy into ATP by pumping H+ through itself ---> pumps H+ from the inside to the outside of the cell, setting up a H+ gradient that drives the production of ATP

What are the 4 types of membrane proteins?

- ? - ? - ? - ?

SCF proteolysis control

- E3-ubiquitin ligase - adds ubiquitin to G1/S cyclins and CKIs that limit entry into the S phase ---> important for the G1-->S transition - F-box protein on active SCF complex recognizes the phosphorylated CKI, causes ubiquitin to be added to CKI

when do things happen during plant cell mitosis lol

- G2 = band of MT and actin filaments that sort of lines up like it would have in the contractile ring - telophase = golgi-derived vesicles coming in - cytokinesis = golgi-derived vesicles start to link up and form the cell plate - G1 = golgi-derived vesicles fuse into the new cell wall; membrane on the outside of the vesicle will fuse and become continuous with the PM on each side

What does a GPI anchor do as a PTM?

- GPI anchor attached to proteins as the SS is clipped off

What are the 3 classes of ATP-powered transport proteins?

- P-type pump - ABC transporter - V-type proton pump and F-type ATP synthase

tell me about the dynein that is found in a mitotic spindle pls

- anchored at plasma membrane - moves towards the minus end - interacts with astral microtubule - pulls a spindle away from another

What is an optical trap assay and how does it work?

- bead is captured where the laser focuses ... the assay measures how/where the bead moves ("it moves a little bit, one way or the other") - beads = attached to actin

tell me about cofilin pls

- binds ADP-actin (old) filaments, accelerates disassembly

What is compression resistance?

- due to hydrated glycosaminoglycans (GAGs) and proteoglycans (proteins with sugars) ... form a gel (hydrated ... has water in it and can resist compression)

What are proteins that bind to the plus end of a microtubule called?

- end-binding proteins - plus end tracking proteins

What do the organizational proteins do?

- filament bundling - cross-linking - attachment to membranes

What is LDL?

- low density lipoprotein - fatty acid bound/esterified to cholesterol

What are the structural components of cholesterol?

- polar head group - rigid steroid ring structure - nonpolar hydrocarbon tail

tell me about tropomodulin pls

- prevents assembly and disassembly at the minus end - binding and capping at the minus end

tell me about capping protein pls

- prevents assembly and disassembly at the plus end - capping proteins for the plus end

How does transmembrane transport work?

- protein translocators in the ER membrane - proteins must usually unfold to fit through

What are the ways that cells can adjust their sensitivity to a signal?

- receptor sequestration - receptor down-regulation - receptor inactivation - inactivation of signaling protein - production of inhibitory protein

How does receptor down-regulation work?

- receptor ubiquitination causes destruction of the receptor - activation of the receptor leads to eventual destruction of the receptor in the endosome/lysosome

tell me about catastrophe factor (kinesin-13) pls

- similar to motor proteins, but instead of moving on the microtubule, it's utilizing ATP hydrolysis to drive prying apart of the microtubule - since it can pry apart the microtubule and reveal the part of it that doesn't have a GTP cap, it makes these really unstable and there could be a catastrophe

What are the 3 categories of transmembrane protein?

- single alpha-helix - multiple alpha-helix - beta-barrel

hyaluronan

- single long unsulfated chain with no protein component - not produced in ER/golgi bc no protein required

What structure do microtubules have?

- α-β dimers that have GTP binding proteins (α-tubulin and β-tubulin) ---> called a heterodimer because the 2 subunits are different

Name 5 second messengers. For each, what can cause an increase in cytosolic concentration?

1. Ca2+ ... increase by: ligand gated Ca2+ channels on ER (activated by IP3), voltage-gated Ca2+ channels, or Ca2+-induced Ca2+ release, etc. 2. cAMP ... increase by: adenylyl cyclase forming more 3. cGMP ... increase by: guanylyl cyclase forming more 4. IP3 ... increase by: PLC-β 5. DAG (not really cytosolic) ... increase by: PLC-β forming more

caspase pathway --> DNA fragmentation

1. executioner caspase cleaves iCAD off of inactive CAD-iCAD 2. active CAD cleaves spaces between nucleosomes (this is what creates the distinctive DNA laddering seen on a gel during apopotsis)

how do mitogens activate Myc?

1. mitogen binds to mitogen receptor 2. mitogen receptor activates Ras 3. Ras activates MAP kinase 4. activation of gene regulatory protein 5. Myc made ----- 6. Myc leads to expression of G1-cyclin 7. G1-cyclin activated G1-Cdk 8. Rb is phosphorylated and inactivated 9. increased E2F activity --> makes G1/S-cyclins and S-cyclins 10. entry into S phase

What are the steps that an image goes through in order to become 3D in confocal microscopy?

1. pictures taken in different focal planes 2. create a z-stack 3. pictures are reconstructed into a 3D image

How many ribulose 1,5-bisphosphate molecules actually form in Calvin cycle?

3 1,5-bisphosphates (15 total carbons)

How many CO2 molecules enter the Calvin cycle in each round?

3 CO2 molecules

How many pores are in the nuclear membrane?

3,000-4,000 pores

How wide are the SER tubules (for the lumenal space)?

30-60 nm wide

If a cell is 10 microns in diameter, how long does it take a lipid to diffuse across the membrane?

5 seconds

How many gamma-TuScs associate to make a gamma-TuSc spiral?

7 gamma-TuScs associate ... 14 gamma-tubulins total (2 gamma-tubulins per gamma-TuSc)

What is the normal pH of a cell?

7.2

Photosystem I absorbs light at what wavelength?

700 nm

ok fair warning i am not making too many notecards for this lecture because i still kind of remember this stuff from phys so i'm sorry

What do the light reactions of photosynthesis convert light energy into?

ATP (chemical energy) and NADPH (energy of redox potential/electron donors)

At the G2-M checkpoint, DNA must be successfully replicated. What mechanism pauses the cell cycle if it is not? A. Activation of p53 B. Inactivation of Cdc25

At the G2-M checkpoint, DNA must be successfully replicated. What mechanism pauses the cell cycle if it is not? A. Activation of p53 *B. Inactivation of Cdc25*

Autophagy of mitochondria (mitophagy) is stimulated by ... A. phosphoinositides B. Rabs C. SNAREs D. a clathrin coat E. ubiquitination of mitochondrial outer membrane proteins

Autophagy of mitochondria (mitophagy) is stimulated by ... A. phosphoinositides B. Rabs C. SNAREs D. a clathrin coat *E. ubiquitination of mitochondrial outer membrane proteins*

Collagens are extremely rich in... A. tyrosine and phenylalanine. B. serine and threonine. C. glycine and proline. D. alanine and valine. E. lysine and arginine.

Collagens are extremely rich in... A. tyrosine and phenylalanine. B. serine and threonine. *C. glycine and proline.* D. alanine and valine. E. lysine and arginine. ----- Both glycine (small size) and proline (unique backbone angles) are important in the formation of the triple-stranded helix in collagen.

What is a good mnemonic for remembering the AAs commonly found in membranes?

FAMILY VW

For a nuclearly-encoded mitochondrial protein of the inner mitochondrial membrane to be inserted by the cytochrome oxidase activity (OXA) complex, it must ... A. have a mitochondrial targeting sequence B. be imported into the matrix C. have a second signal sequence that targets it to OXA from the matrix D. all of the above

G proteins Rac and Rho stimulate formation of different organization of actin filaments based on A. involvement of Arp2/3 by one and formin by another B. involvement of myosins by one and decreased involvement of myosin by another C. both

what happens when G1 cyclins are transcribed?

G1-Cdk is activated ... S-phase cyclin transcription

G1-S transition is regulated by APC, CKI, and controlled cyclin transcription. How does APC affect cyclin? A. Binds and sequesters S and M cyclin. B. Prevents E2F from actin as a cyclin transcription factor. *C. Polyubiquitylates S and M cyclin.* D. Activates G1-cyclin via phosphorylation of T-loop. ----- A. CKI family does this B. related to controlling cyclin transcription ... role of Rb D. necessary for G1 cyclins to be activated and everything else to happen, but doesn't involve APC

Is chondroitin sulfate a GAG or a fibrous protein?

GAG

Is hyaluronan a GAG or a fibrous protein?

GAG

What stimulates deactivation of a Rho?

GAP

What activates Gs-α?

GPCR

What turns a monomeric G protein "on"?

GTP binding (stimulated by a GEF)

Where does the oxygen consumed by mitochondria end up?

H2O

Where does photosystem II get the electron that it donates to the electron transport chain?

H2O -------------- um ok so i think this is wrong?? this came from the trivia but like i'm pretty sure the electron that gets used is the one that comes from chlorophyll and the one from water just replaces it?? yikes

If the electron that replaces the electron that had been separated from chlorophyll doesn't come from water, what does it come from? When is this done?

H2S or nitrite ... these compounds could have served as reducing agents in ancestral photosynthetic organisms

In regard to the MAP-kinase pathway, ~what phosphorylates a MAPKK~?

MAPKKK

What does calmodulin (+ Ca2+) activate?

MLCK ... which phosphorylates myosin light chains

Which one removes a sugar group from a N-linked CHO? A. glycosidase B. glycosyltransferase C. kinase D. phosphatase

Which one removes a sugar group from a N-linked CHO? *A. glycosidase* B. glycosyltransferase C. kinase D. phosphatase

Which one transfers sugar from a sugar-nucleotide to a N-linked CHO? A. glycosidase B. glycosyltransferase C. kinase D. phosphatase

Which one transfers sugar from a sugar-nucleotide to a N-linked CHO? A. glycosidase *B. glycosyltransferase* C. kinase D. phosphatase

Which plays a role in vesicle targeting by binding specific tethering proteins on the target membrane that are themselves localized by the same class of protein? A. Rab B. Arf C. Sar1 D. Ran E. Ras

Which plays a role in vesicle targeting by binding specific tethering proteins on the target membrane that are themselves localized by the same class of protein? *A. Rab* B. Arf C. Sar1 D. Ran E. Ras

Which promotes membrane curvature? A. COPII coat assembly B. COPI coat assembly C. presence of BAR domain proteins at the membrane D. clathrin coat assembly E. all of the above

Which promotes membrane curvature? A. COPII coat assembly B. COPI coat assembly C. presence of BAR domain proteins at the membrane D. clathrin coat assembly *E. all of the above*

Which promotes polymerization? A. profilin B. thymosin C. both D. neither

Which promotes polymerization? *A. profilin* B. thymosin C. both D. neither

Which protein acts as a scaffolding protein that determines the length of the actin filament? A. CapZ B. tropomodulin C. titin D. nebulin

Which protein acts as a scaffolding protein that determines the length of the actin filament? A. CapZ B. tropomodulin C. titin *D. nebulin*

Which recruits AP2 to the donor membrane and also causes a conformational change in AP2 that allows it to bind cargo receptors? A. a specific phosphoinositide B. cargo C. cargo receptors D. clathrin triskelions

Which recruits AP2 to the donor membrane and also causes a conformational change in AP2 that allows it to bind cargo receptors? *A. a specific phosphoinositide* B. cargo C. cargo receptors D. clathrin triskelions

Which space has a greater positive charge? A. matrix B. intermembrane space C. both the same

Which space has a greater positive charge? A. matrix *B. intermembrane space* C. both the same

Which spring-like protein anchors the thick filament? A. CapZ B. tropomodulin C. titin D. nebulin

Which spring-like protein anchors the thick filament? A. CapZ B. tropomodulin *C. titin* D. nebulin

Which step of spindle assembly DOES NOT depend on motor protein forces acting on the MTs? A. Pushing minus MT ends away from the chromosomes B. Gathering minus ends C. MT nucleation near chromosomes D. Assembly of antiparallel MT bundles

Which step of spindle assembly DOES NOT depend on motor protein forces acting on the MTs? A. Pushing minus MT ends away from the chromosomes B. Gathering minus ends *C. MT nucleation near chromosomes* D. Assembly of antiparallel MT bundles

What is ARF GAP?

a G-protein that causes assembly of the coat ... when it is inactive, the coat dissociates very rapidly

What does a GPCR act similar to (for heterotrimeric proteins)?

a GEF

In polymerization of microtubules, the alpha-beta end comes in bound to _____.

a GTP (at the beta subunit) ... it gets hydrolyzed over time

What is fluorescence?

absorbing light at one wavelength and emitting light at another higher wavelength (direction = purple --> red)

What does photosystem I do/how does it work?

accepts energy and donates an electron to NADP+ to make NADPH

How does a lamellipodium get formed?

actin skeleton can polymerize at one edge of the cell and if that edge has some anchoring it can protrude the edge of the cell (this forms the lamellipodium)

What does it mean when a subunit is in D form?

actin-ADP

What does it mean when a subunit is in T form?

actin-ATP

What is something that can alter filament dynamics?

actin-filament-binding cap proteins

What is the result of having a stronger membrane depolarization?

action potentials are generated more rapidly

What does ~the β/γ complex associated with Gi~ do?

activates K+ channels (leads to hyperpolarization as K+ leaves the cell)

What does G β/γ-i do?

activates K+ channels which causes K+ to leave and causes hyperpolarization

What does EGF do?

activates RTK, which activates Ras ........

What does G12 do?

activates a Tho GEF, leading to actin skeleton reorganization

What does ~Gs~ do?

activates adenylyl cyclase (... produces cAMP ... activates PKA)

What does ~Gt~ do?

activates cGMP phosphodiesterase

What does G α-t (transducin) do?

activates cGMP phosphodiesterase in vertebrate rod photoreceptors

What causes ER Ca2+ release?

activation of a GPCR

immune therapy

antibodies block the receptors for proteins that hold the cell to the T cell (this holding prevents apoptosis when the antibodies aren't there) ... this causes apoptosis of the cancer cell

Where is kynesin found in a mitotic spindle?

between two interpolar microtubules

Where are sister chromatids found a mitotic spindle?

between two kinetochore microtubules

What is a lamellipodium?

big, flat protrusion at the front end of the cell

How does FRAP work?

bleach a protein that is tagged with a fluorophore in a certain area and watch its recovery over time as those diffuse out of the patch and active fluorescence diffuses into the patch ex: the golgi is full of a protein that is tagged with GFP that we suspect cycles between the golgi and the ER ... 1. shine a bright light onto the GFP and bleach it 2. all the protein in the golgi at this time point disappears 3. over time, fluorescence starts to build up again in the golgi because of new molecules of a protein coming into the same location

How are mitochondria and chloroplasts similar?

both rely on chemiosmosis

What does a amphipathic alpha-helix associate with?

both the hydrophobic lipid bilayer and the cytosol (has polar and nonpolar parts)

How do intermediate filaments organize?

bundle up into rope-like structures

How does myosin generate force?

by coupling ATP hydrolysis to conformational changes

how are multipass transmembrane tight-junction proteins linked to cytoskeletal actin filaments?

by intracellular C and N terminals

What second messenger does the effector protein of Gs-α produce?

cAMP

What regulates kinesin/dynein action in melanophore cells?

cAMP concentration

What is another name for protein kinase A (PKA)?

cAMP-dependent protein kinase

What does gelsolin do to actin filaments?

directly severs them, creating more minus ends (speeds depolymerization because minus ends are more likely to depolymerize than to polymerize)

if p53 doesn't detect double stranded DNA break and play its role what happens?

double strand break, cell divides and fragment gets left behind and during DNA replication they accidentally get attached to other chromosomes (you are breaking genes/putting other genes together!!)

What is the "pinchase" for clathrin-coated vesicles?

dynamin

What allows the vesicle to leave the membrane?

dynamin pinches it off!

what happens to centrioles during S?

each mother centriole will start to spawn off a daughter structure

cell plate

early structure in plants that becomes the cell wall

What is used to solubilize integral membrane proteins?

either ionic or nonionic detergents ... they are "cone-shape" and form micelles in water

Is NADPH an electron donor or an electron acceptor?

electron donor

What is a "3 parent baby"?

embryo has mitochondria from one donor and nuclear DNA from two other donors

The pancreas secretes insulin which travels through the bloodstream to a distant target cell. What kind of signaling is this?

endocrine

~A tissue secretes a signaling molecule that travels through the bloodstream and acts on a distant target cell.~ What kind of signaling is this?

endocrine signaling

What is endocytosis?

engulfing cargo

What is the effector protein for tranducin?

cGMP phosphodiesterase

What facilitates the attachment of "cadherin like-expressing" cells?

cadherin interaction being homophilic

How does ~cytochlasin B~ work?

caps filament plus ends ... only leaves minus end free ... more likely to depolymerize at minus end

If you diet and exercise and lose 10 pounds of fat, where did the atoms of the fatty acids end up (where did the fat go)?

carbons end up in CO2 ... hydrogens and oxygens end up in H2O

What binds lumen proteins with exit signals?

cargo receptors

At the end of the whole cycle, after separation of chromosomes what happens?

contractile ring formation

Cohesins and condensins are in the _____ family.

Smc (structural maintenance of chromosomes)

The face of the membrane of an intralumenal vesicle (formed by endocytosis into the endosome) that faces the endosomal lumen is similar to the ________ face of the endosome. A. cytosolic B. lumenal

The face of the membrane of an intralumenal vesicle (formed by endocytosis into the endosome) that faces the endosomal lumen is similar to the ________ face of the endosome. A. cytosolic *B. lumenal*

Where does phospholipids synthesis takes place on the ER membrane? Which ER?

cytosolic side of SER

What can be bused to tag the plus ends? A. +TIP ends B. gamma tubulin C. tau

What can be bused to tag the plus ends? *A. +TIP ends* B. gamma tubulin C. tau ----- - gamma tubulin at the minus end - tau = bundling protein ... you would see it all along the bundles! (so not this one)

What cause GTP binding by Rab? A. Rab GEF B. Rab GAP C. Rab GDI

What cause GTP binding by Rab? *A. Rab GEF* B. Rab GAP C. Rab GDI

What does G-actin bind? A. ATP B. ADP C. GTP D. GDP

What does G-actin bind? *A. ATP* B. ADP C. GTP D. GDP

What is the function of SCF? A. An E3-ubiquitin ligase B. A kinase C. A phosphatase D. A protease

What is the function of SCF? *A. An E3-ubiquitin ligase* B. A kinase C. A phosphatase D. A protease

When a cell secretes an extracellular signaling molecule that enters the bloodstream and travels to a distant target cell, that is ... A. autocrine signaling B. paracrine signaling C. endocrine signaling D. synaptic signaling

Which are least dynamic? A. actin filaments B. microtubules C. intermediate filaments (although they can dissociate or associate under certain conditions)

Which are least dynamic? A. actin filaments B. microtubules *C. intermediate filaments (although they can dissociate or associate under certain conditions)*

Which best describes effects of protein phosphorylation? A. it activates a protein B. it inhibits a protein C. it could change the protein's conformation or function, which might include both A or B, depending on the protein

Which best describes effects of protein phosphorylation? A. it activates a protein B. it inhibits a protein *C. it could change the protein's conformation or function, which might include both A or B, depending on the protein*

Which can walk toward the plus ends of two interpolar microtubules, pushing mitotic spindles away from each other? A. kinesin 13 B. kinesin 14 C. myosin II D. kinesin 5

Which can walk toward the plus ends of two interpolar microtubules, pushing mitotic spindles away from each other? A. kinesin 13 B. kinesin 14 C. myosin II *D. kinesin 5*

Which caps actin filaments at the minus end? A. CapZ B. tropomodulin C. titin D. nebulin

Which caps actin filaments at the minus end? A. CapZ *B. tropomodulin* C. titin D. nebulin

Which caps actin filaments at the plus end? A. CapZ B. tropomodulin C. titin D. nebulin

Which caps actin filaments at the plus end? *A. CapZ* B. tropomodulin C. titin D. nebulin

Which caps the minus end of actin in a sarcomere? A. tropomodulin B. titin C. myosin D. nebulin E. CapZ

Which caps the minus end of actin in a sarcomere? *A. tropomodulin* B. titin C. myosin D. nebulin E. CapZ

Which caps the plus end of actin in a sarcomere? A. tropomodulin B. titin C. myosin D. nebulin E. CapZ

Which caps the plus end of actin in a sarcomere? A. tropomodulin B. titin C. myosin D. nebulin *E. CapZ*

Which cyclin/Cdk complex rises in concentration slowly during G2 and is degraded rapidly at the onset of anaphase? A. G1-S Cdk B. S Cdk C. M Cdk

Which cyclin/Cdk complex rises in concentration slowly during G2 and is degraded rapidly at the onset of anaphase? A. G1-S Cdk B. S Cdk *C. M Cdk*

Which determines the length of the actin filament in a sarcomere? A. tropomodulin B. titin C. myosin D. nebulin E. CapZ

Which determines the length of the actin filament in a sarcomere? A. tropomodulin B. titin C. myosin *D. nebulin* E. CapZ

Which end is more likely to have actin bound to ADP? A. plus B. minus

Which end is more likely to have actin bound to ADP? A. plus *B. minus*

Which is NOT a proteoglycan? A. Hyaluronan B. Aggrecan C. Heparan Sulfate

Which is NOT a proteoglycan? *A. Hyaluronan* B. Aggrecan C. Heparan Sulfate

Which is similar to a GEF? A. a G protein coupled receptor (GPCR) B. a G-α subunit C. a G-β/γ complex

Which is similar to a GEF? *A. a G protein coupled receptor (GPCR)* B. a G-α subunit C. a G-β/γ complex

Which might play a role in recruiting proteins involved in signaling or in forming signaling complexes? A. generation of phosphoinositides B. phosphorylations that create binding sites for other proteins C. both

Which minus-end-directed kinesin pulls spindles toward each other? A. kinesin 13 B. kinesin 14 C. myosin II D. kinesin 5

Which minus-end-directed kinesin pulls spindles toward each other? A. kinesin 13 *B. kinesin 14* C. myosin II D. kinesin 5

Which of the following does a 14-3-3 domain bind? A. motifs containing phosphotyrosine B. proline-rich motifs C. a specific phosphoinositide D. motifs containing phosphoserine or phosphothreonine

Which of the following does a 14-3-3 domain bind? A. motifs containing phosphotyrosine B. proline-rich motifs C. a specific phosphoinositide *D. motifs containing phosphoserine or phosphothreonine*

Which of the following does a Src homology 3 (SH3) domain bind? A. motifs containing phosphotyrosine B. proline-rich motifs C. a specific phosphoinositide D. motifs containing phosphoserine or phosphothreonine

Which of the following does a Src homology 3 (SH3) domain bind? A. motifs containing phosphotyrosine *B. proline-rich motifs* C. a specific phosphoinositide D. motifs containing phosphoserine or phosphothreonine

Which of the following interact with integrins? A. selectins B. lectins C. NCAMs D. ICAMs E. Ig Superfamily proteins

Which of the following interact with integrins? A. selectins B. lectins C. NCAMs *D. ICAMs* E. Ig Superfamily proteins

Which of the following is NOT transported through nucleoporin complexes? A. Ions B. Small proteins C. mRNAs D. Ribosomal subunits E. Complete ribosomal complexes

Which of the following is NOT transported through nucleoporin complexes? A. Ions B. Small proteins C. mRNAs D. Ribosomal subunits *E. Complete ribosomal complexes* ----- A. yes, can diffuse bc pore/H2O filled channel B. yes C. yes D. yes E. no! too big

Which of these kinesins generally carries vesicular cargo toward microtubule plus ends? A. kinesin-1 B. kinesin-5 C. kinesin-13 D. kinesin-14

Which of these kinesins generally carries vesicular cargo toward microtubule plus ends? *A. kinesin-1* B. kinesin-5 C. kinesin-13 D. kinesin-14

What is special about contractile bundles?

they are parallel, and far enough apart that myosin can fit in the middle ... motor protein that can work on the actin

Why do carbohydrate groups attract water?

they are polar, especially if sulfated (negative charge added)

How are proteins without exit signals brought into the ER?

they are randomly engulfed by vesicles

What happens to electrons accepted by NADH?

they are used to fuel the creation of a H+ gradient (pumping H+ against their gradient)

What happens to saturated fatty acids at a lower temperature?

they freeze

What purpose do fats and carbohydrates serve in respiration?

they function as electron donors (form of PE) ... they can donate electrons to a higher affinity acceptor

What is important to note about the structure of Arp 2/3?

they have a similar structure to actin

How do soluble proteins get to the ER?

they need import signal sequences

What happens to unsaturated fatty acids at lower temperatures?

they stay fluid/flow

What do kinases do?

transfer a phosphate group from a donor to a target (usually from ATP to -OH group) (puts Ps on)

What does a glycosyltransferase do?

transfers sugar from nucleotide phosphate to a target

How does the Cl-/HCO3- antiporter work? How does it impact pH?

uses Cl- to drive removal of HCO3- Cl- IN HCO3- OUT ***decreases pH/makes cell more acidic

How does the Na+ HCO3-/Cl- antiporter work? How does it impact pH?

uses Na+ to drive Cl- out and bring HCO3- in to soak up p+ Na+ and HCO3- IN Cl- OUT ***increases pH/makes cell more basic

Does the Calvin cycle use or produce ATP?

uses it!

Does the Calvin cycle use or produce NADPH?

uses it!

What does a glucosyltransferase do?

uses nucleotide-linked sugars (transfers sugar from a sugar-nucleotide to a N-linked carbohydrate)

How does the Na+/H+ antiporter work? How does it impact pH?

uses the Na+ gradient to drive extra p+ out of the cell Na+ IN H+ OUT ***increases pH/makes cell more basic

What is the function of the SNARES?

v-SNARE interacts with t-SNARE to form the trans-SNARE complex, and draw the vesicle in closer to the target membrane

What SNAREs are on vesicles?

v-SNAREs (vesicular SNAREs)

What protein acidifies the lysosome? Draw it and the direction of H+ movement it mediates.

v-type ATPase or proton pump pumping protons from cytosol into the lumen and requires the energy of ATP to do that ----- i def clicked on the wrong picture for this so just ignore it sorry

Where are GLUTs located in a unstimulated cell?

very few at the plasma membrane because there is little insulin around ... they are located in an intracellular pool in specialized recycling endosomes

How do large uncharged polar molecules (glucose, sucrose, etc.) get across the lipid bilayer?

very few get through, they need transporters to get across!

What mediates partial trans-SNARE complex assembly?

vesicle and plasma membrane SNARE/SNARE-like proteins

What is an exosome?

vesicle that is in the extracellular fluid

How does a protein of the ER membrane reach the peroxisome?

vesicular trafficking (vesicle fuses with peroxisome)

How does cholesterol travel in the bloodstream?

via apolipoprotein B

When are 2 objects considered resolved?

when their point spreads overlap at less than 50% intensity

when do cells undergo replicative senescence?

when their telomeres become too short

When is mTOR inactive?

when there is a low level of nutrient availability ... it activates autophagy

how do Ras and Myc cause cancer?

when they are mutated, they are continuously active - Myc always on ... lots of G1-cyclin ... G1-Cdk activation ... Rb phosphorylation and inactivation ... increased E2F activity ... G1/S-cyclin and S-cyclin produced ... entry into S phase

how do scientists figure out what kind of tissue cancer came from?

intermediate filament proteins - desmin = started in muscle cells - keratin = started in skin cells

Nonclassical cadherins connect _____ to desmosomes.

intermediate filaments

What has a role in nuclear lamina?

intermediate filaments

What is the nuclear lamina made up of?

intermediate filaments

What is ~synaptic~ signaling?

involves nearby cells, but really it's a specialized type of signaling that involves a neuron and release of a neurotransmitter

How is NF-AT inactivated and inactivated?

it is inactive when it's phosphorylated ... so when there is high Ca2+ in the T cell, calcineurin attaches to NF-AT and causes those Ps to leave the protein (dephosphorylate) and the protein to get activated - it's activated in the cytosol (with high [Ca2+] causing attachment of calcineurin and dephosphorylation) and inactivated in the nucleus (with low [Ca2+] causing detachment of calcineurin and phosphorylation)

What is catastrophe?

loss of microtubule GTP cap ... really rapid depolymerization occurs (because when GDP is bound there, the protofilaments are less stable)

What would be more fluid: a membrane consisting of unsaturated hydrocarbon chains with cis-double bonds or a membrane consisting of saturated hydrocarbon chains?

membrane consisting of unsaturated hydrocarbon chains with cis-double bonds

What do the fibrils of a nuclear pore do?

messy on cytoplasmic side on inside of nucleus ... make a basket structure that is important for transport

What do detergents in water exist as at high concentrations?

micelles

What pushes the MTOC toward the cell center?

microtubule growth from nucleating complexes

What is the MTOC?

microtubule organizing center ... where the centrioles are located (inside of it)

What are kinesins?

microtubule-associated nucleotide switch proteins with differential actions based on their structures

What forms the network along which vesicular trafficking occurs by movement of motor proteins?

microtubules

What is the refractory period?

minimum time between APs ... VG Na+ channels are inactivated

What end of actin does ATP/ADP bind to?

minus end

What end of actin has actin-ADP?

minus end

What is mitophagy?

mitochondrion being delivered to the lysosome

What does MAP-K stand for?

mitogen activated protein kinase

what happens in M phase?

mitosis and cytokinesis

What subunits are actin polymers composed of?

mixture of subunits in T form and D form

How can nuclear import of proteins bc controlled?

modifications like phosphorylation/dephosphorylation

How does passive transport by a carrier protein work?

molecules bind to the carrier on the side of the membrane with the highest concentration, carrier protein changes conformation, molecules are released on the other side of the membrane

What happens when you have increased myosin activity and formins causing actin bundle growth?

more stress fibers being formed ... integrins clustering and focal adhesion formation

What happens if there happens to be an actin filament right next to a myosin head?

myosin can either create movement of the myosin filament or it can create tension

Where did the names "barbed end" and "pointed end" come from?

myosin heads bound to the minus end looked pointed and myosin heads bound to the plus end looked barbed on the original microscope images

What is the sliding filament assay used to assess?

myosin's motor function

Is ~receptor down-regulation~ an example of positive or negative feedback?

negative feedback ... leads to suppression of the very same signal that started the signaling cascade

Is ~receptor inactivation~ an example of positive or negative feedback?

negative feedback ... leads to suppression of the very same signal that started the signaling cascade

Can a ~TGF-β receptor~ create binding sites for proteins with SH2 or PTB domains?

Can ~Akt, PKA, and PKC~ create binding sites for proteins with SH2 or PTB domains?

Do dyneins rely on nucleotide switch proteins to function?

Is hyaluronan a proteoglycan?

does hyaluronan have a core protein?

no (just a sugar chain by itself)

What would happen if there was no cGMP in the G α-q pathway?

no smooth muscle relaxation would occur

Can chaperones enter transport vesicles?

no! because they indicate unfolded/misfolded proteins

In the JAK-STAT signaling pathway, is the receptor an enzyme?

no! but it is associated with one that is

Do only proteins go through nuclear pores?

no! different kinds of RNAs do as well

Is H+ pumping by a v-type ATPase involved in ATP production in mitochondria and chloroplasts?

no! that would only be in lysosome/endosome/golgi (maybe)

Is there synthesis of proteins directly in the peroxisomal lumen?

no! they don't have their own DNA so like unlike mitochondria and chloroplasts, this does not happen there

do most human cells have telomerase?

no! they just undergo replicative senescence

Is mitochondria stagnant (does it stay in one place)?

no! they move around motor proteins on microtubules ... they fuse, divide, and move around

Do hydropathy plots work on beta barrel proteins?

no, because they tend to hang around 0

Do channel proteins have binding sites for the solute?

no, but they have some interaction ... "selectivity filter"

extracellular face of desmosome

nonclassical cadherin proteins reach across and form a connection

What kinds of AAs typically make up transmembrane alpha-helical regions?

nonpolar AAs and also some polar uncharged ones as well

Is a lysosomal hydrolase that is randomly secreted gone for good? Why not?

nope -- retrieved by M6P receptor

Are the phosphoinositide species on different membranes throughout the cell the same?

nope!

Is vesicular transport a one-way process?

nope!

T-cadherin

not a transmembrane protein but it has a sugar linkage

Why are beta-sheets more rigid than alpha-helices?

not every AA in the chain ... R groups alternate which side they face (hydrophobic side vs hydrophilic side) ... they hang out around 0 on a hydropathy plot

Are mitochondria stable, or do they dynamically divide (fission) and fuse?

not stable! they are moving, dividing, and fusing

What does formin do?

nucleates actin filaments (makes straight filaments)

What is the rate-limiting step in the formation of actin filaments?

nucleation

What is the spontaneous association and disassociation of G-actin (bound to ATP) until there is enough of an aggregation called?

nucleation

In V-type and F-type pumps, what is moving?

only protons are being pumped!!! p+ is always crossing the membrane and no other solutes

How do ligand-gated channels work?

open following noncovalent binding of an intracellular ligand (ex: cAMP) or extracellular ligand (neurotransmitters) ex: Ach receptor

Do dyneins and kinesins move in the same or in the opposite direction?

opposite direction (generally) - most kinesins are plus end directed, while dyneins are minus end directed

Are profilin and thymosin opposites or similar?

opposites

Are Arp 2/3 and thymosin similar or opposites?

opposites! they are nucleating actin

What can be used to determine how far the myosin head is moving the actin?

optical trap assay

what does a single centrosome do in each half of the spindle?

organizes three distinct sets of MTs whose minus ends all point towards the centrosome

When the inositol ring is phosphorylated, what is the molecule known as?

phosphoinositide

Dynamin is a _____.

pinchase (b/c it pinches off the vesicle that was forming at the donor membrane lmao)

What does a mannose 6-phosphate tag do?

plays a key role in the trafficking of proteins to the lysosome

What end does formin act on?

plus end

What end of actin has actin-ATP?

plus end

What drives the creation of a proton gradient?

potential energy in redox potential of electron donors

What kind of energy is ATP?

potential energy in the form of chemical energy

In the example of the solubilization of the Na+/K+ pump, what are experiments optimized for?

really tiny liposomes that hold only 1 protein each and use sorting to find which ones face inward/outward

What function does a phosphoinositide embedded in the membrane (on cytosolic side) have?

recruits proteins that have specific binding domains that can bind the phosphoinositide that initiates binding of ESCRT complexes

What is rescue?

regaining of the microtubule GTP cap

connective tissue

region rich in ECM and occasional cells

what do Bcl2 family proteins do?

regulate the release of cytochrome C from mitochondria required to initiate caspase activation

What does a glycosidase do?

removes a sugar

What does glucosidase do?

removes glucose from precursor oligosaccharide chain

What does activation of small, monomeric G protein cause?

reorganization of the cytoskeleton

What gives muscle its striped appearance?

repeated assembly of sarcomeres

What does it mean when a secretory pathway is regulated?

secretory vesicle carrying its contents only fuses with the plasma membrane when there's a certain condition in the cell (for example: a signal that causes secretion)

What are vesicles on the trans golgi called?

secretory vesicles

What causes the bending force in cilia/flagella to become sliding force?

severing of tethering/linking proteins

What does katonin do?

severs up microtubules into smaller fragments that probably lack a GTP cap, so they're probably all undergoing a catastrophe

What are membranes more fluid: whey they consist of short or long chains?

short chains

What does an uncoupler do to any proton gradient?

shuts it down (no ATP made)

How can proteins be directed towards a certain place?

signal patch/signal sequence

Why do proteins produced in the presence of microsomes appear smaller?

signal sequences cleaved

What is ~endocrine~ signaling?

signaling that involves movement of the signaling molecule in the bloodstream

Different phosphoinositide species recruit only proteins with ...

specific phosphoinositide binding domains

What does taxol (paclitaxel) do to microtubules?

stabilizes them

centriole replication, what phase?

starts in S phase but is completed in G2

How do things between 17,000-60,000 daltons get into the nucleus?

take 2 minutes to equilibrate across the membrane via nuclear pore (??)

What is the central location of the MTOC a function of?

the mechanical function of all the microtubules pressing at the periphery

What is equilibrium potential?

the membrane voltage at which an ion stops moving across the membrane

What happens to a microtubule when the cap is lost?

the microtubule is depolymerizing ... this is called catastrophe!

What end do actin filaments depolymerize/are less stable at?

the minus end

What happens as more of the lipid bilayer and other proteins are trafficked back to the trans golgi network?

the more that's trafficked back, the more concentrated the secretory contents of the vesicle are

What does transfer from a low affinity donor to a high affinity acceptor allow for?

the movement of protons against a gradient (it releases E that can be harnessed to do this)

What happens with Gt in the light?

there is a low [cGMP] ... rhodopsin is active and activates transducin (Gt) ... cation channels remain closed ... cell is hyperpolarized ... low rate of NT release

*--- Lecture 1: Types of Cells ---*

*N/A*

How long is the distance between turns of an alpha-helix?

- 3.6 amino acids - .54 nm

What are some examples of P-type pumps?

- Na+/K+ pump - Ca2+ ATPase - fungal H+ pump

what are the 3 types of cancer?

- carcinoma - sarcoma - leukemia

What are some characteristics of differential-interference-contrast (DIC/Nomarski) microscopy?

- increased resolution ... can visually see structures more clearly - looks 3D (boosted curvature)

connexon

- made up of 6 connexins - can be homomeric or heteromeric

What are the processes that deliver cargo to lysosomes? Draw them.

- phagocytosis - endocytosis - autophagy - macropinocytosis

tell me about melanophores pls

- pigment cells - can move melanosomes

What is passive transport?

- polar and charged molecules/ions moving down their concentration gradients across membranes using a transporter - added molecule involved

What is fimbrin?

- small actin binding protein with 2 actin binding domains ... short, so actin fibers are bundled close together in parallel - tight packing prevents myosin II from entering bundle

Proteins translated without microsomes are ______. Proteins translated with microsomes are ______.

- soluble - pellet

What are the 2 classes of proteins that are imported into the RER?

- soluble proteins - transmembrane proteins

tell me about tropomyosin pls

- stabilizes filament - side-binding actin binding protein

If cargo needs to be taken to the minus end of actin, which myosin takes it there? What about to the plus end?

- to minus end = myosin 6 - to plus end = myosin 5

how can senescence be avoided?

- you can force expression of telomerase! - some cancer cells do this!

To what functional group is an O-linked oligosaccharide attached?

-OH (hydroxyl group)

About how many mitochondrial proteins are encoded by the human nuclear genome?

1,000+ proteins ("a snotload")

What are the steps of the MAP kinase pathway?

1. RTK activates Ras (turns it into Ras-GTP) 2. active Ras protein activates MAP-KKK 3. MAP-KKK phosphorylates and activates MAP-KK 4. MAP-KK phosphorylates and activates MAP-K 5. changes in protein activity and gene expression

how many copies of mutation does a tumor-suppressor need?

2 copies

How many carbons are in ribulose 1,5-bisphosphate?

5 carbons

What has a domain that will bind to a specific phosphoinositide?

AP2 (an adaptin protein)

An example ER retention signal for soluble ER lumen proteins is ... A. KKXX B. KDEL receptor C. KDEL D. mannose 6-phosphate (M6P)

An example ER retention signal for soluble ER lumen proteins is ... A. KKXX B. KDEL receptor *C. KDEL* D. mannose 6-phosphate (M6P)

Is this Anaphase A or Anaphase B?: Kinetochore MTs depolymerize at the plus end

Anaphase A

Is this Anaphase A or Anaphase B? Interpolar MT kinesins push the poles apart

Anaphase B

Is this Anaphase A or Anaphase B?: Astral MTs are acted upon by dyneins.

Anaphase B

What starts the membrane curvature?

BAR domain (clathrin then helps later on)

drug designed to address the oncogene produced by the Philadelphia chromosome

Bcr blocks ATP binding pocket of Bcr-ABI (the Frankenstein fusion protein)

What is the source of carbon that's fixed in photosynthesis?

CO2

What returns Ca2+ to the sarcoplasmic reticulum?

Ca2+ pumps

In what form is Cc lower?

Cc(T) is lower than Cc(D) (Cc is lower for the T form)

Cytokinesis involves A. microtubules B. actin filaments C. intermediate filaments D. all of the above

Cytokinesis involves A. microtubules *B. actin filaments* C. intermediate filaments D. all of the above

regulation of DNA replication - G2

DNA re-replication can't happen in G2 because Cdc6 is no present - ORC is still phosphorylated ... can't build preRC again - no Cdc6 around to accumulate those other factors

Do all GPCRs act by increasing cAMP? A. no way! B. way! (apologies to Wayne and Garth)

Do all GPCRs act by increasing cAMP? *A. no way!* B. way! (apologies to Wayne and Garth)

Dyneins are ... A. minus-end directed B. plus-end directed

Dyneins are ... *A. minus-end directed* B. plus-end directed

What allows for the cells in a dividing embryo to get packed tightly together as they divide?

E-cadherins

What do microtomes allow for?

ER-like processing of translated proteins

Endo H can cleave ... A. Complex oligosaccharides B. high-mannose oligosaccharides

Endo H can cleave ... A. Complex oligosaccharides *B. high-mannose oligosaccharides*

Gelsolin increases depolymerization rates by A. capping actin B. binding free G-actin C. severing actin filaments, creating more minus ends D. stimulating polymerization E. nucleation

Gelsolin increases depolymerization rates by A. capping actin B. binding free G-actin *C. severing actin filaments, creating more minus ends* D. stimulating polymerization E. nucleation

How many copies of the mitochondrial genome does a single cell have? A. none B. one C. two D. 100 E. many

How many copies of the mitochondrial genome does a single cell have? A. none B. one C. two D. 100 *E. many*

I thought GPCRs acted via cAMP, but here the darn thing generates lipid second messengers. How can this be? A. there are different types of G-α B. the cell does what it needs to do, which in this case, is to increase cytosolic [Ca2+] C. bc it wants to

I thought GPCRs acted via cAMP, but here the darn thing generates lipid second messengers. How can this be? *A. there are different types of G-α* B. the cell does what it needs to do, which in this case, is to increase cytosolic [Ca2+] C. bc it wants to

If a soluble protein from the lumen of a donor compartment is trafficked to a target compartment, it will be in ... A. The target compartment lumen B. The cytosol C. The target compartment membrane

If a soluble protein from the lumen of a donor compartment is trafficked to a target compartment, it will be in ... *A. The target compartment lumen* B. The cytosol C. The target compartment membrane

If the cytosolic pH is 7.2 and the lysosomal pH is 5.0, the v-type ATPase is moving H+ ... A. down a gradient B. against a gradient C. both

If the cytosolic pH is 7.2 and the lysosomal pH is 5.0, the v-type ATPase is moving H+ ... A. down a gradient B. against a gradient C. both ----- i'm a mess idk why this doesn't have an answer here but i don't even remember where i found it omg sorry!! i think it would be against a gradient tho?? because if the pH is lower inside the lysosome that would mean there are more H+s inside the lysosome and that's where the ATPase is pushing them into??

In a fluorescent microscope, the first barrier filter allows light of a _____ wavelength compared to the second barrier filter. A. similar B. stronger C. longer D. higher E. shorter

In a fluorescent microscope, the first barrier filter allows light of a _____ wavelength compared to the second barrier filter. A. similar B. stronger C. longer D. higher *E. shorter*

In light-harvesting antenna complexes, when light is absorbed by pigments such as chlorophyll, A. it frees an electron B. it produces O2 C. CO2 is fixed D. energy is transferred to neighboring pigments such as chlorophyl

In light-harvesting antenna complexes, when light is absorbed by pigments such as chlorophyll, A. it frees an electron B. it produces O2 C. CO2 is fixed *D. energy is transferred to neighboring pigments such as chlorophyl*

In modern plants, ________ is generally the electron donor that replaces an electron lost by chlorophyll ... A. water B. H+ C. chlorophyll D. CO2

In modern plants, ________ is generally the electron donor that replaces an electron lost by chlorophyll ... *A. water* B. H+ C. chlorophyll D. CO2

Initial recruitment of signaling proteins to an activated receptor tyrosine kinase is likely to be through ... A. PH domains B. SH3 domains C. SH2 or PTB domains D. 14-3-3 domains

Initial recruitment of signaling proteins to an activated receptor tyrosine kinase is likely to be through ... A. PH domains B. SH3 domains *C. SH2 or PTB domains* D. 14-3-3 domains

What is the transmembrane ER protein retrieval signal?

KKXX (lysine-lysine-any-any)

What is an ER retention sequence for a transmembrane protein?

KKXX (at C terminus of the protein)

Lamellipodia are formed by polymerization of branched actin networks. These are likely to be nucleated and organized by ... A. Arp2/3 B. formin C. fimbrin D. cofilin

Lamellipodia are formed by polymerization of branched actin networks. These are likely to be nucleated and organized by ... *A. Arp2/3* B. formin C. fimbrin D. cofilin

MAP2 is a fairly long microtubule cross-linking protein. Tau is much shorter than MAP2. Which spaces microtubules farther apart when it binds them? A. MAP2 B. Tau

MAP2 is a fairly long microtubule cross-linking protein. Tau is much shorter than MAP2. Which spaces microtubules farther apart when it binds them? *A. MAP2* B. Tau

Where do electrons that come from fats and carbohydrates go?

NADH

What are the products of photosynthesis?

O2 and carbohydrate molecules

What domain binds ~specific phosphoinositides~?

Phosphatidylserine flipping to the outer leaflet of the plasma membrane is a hallmark of: A. Necrosis B. Apoptosis C. De-differentiation D. Senesence

Phosphatidylserine flipping to the outer leaflet of the plasma membrane is a hallmark of: A. Necrosis *B. Apoptosis* C. De-differentiation D. Senesence

What type of protein ~stimulates G-α GTPase activity~?

RGS (regulator of G protein signaling)

Retrieval of cargo from the Golgi to the ER involves ... A. COPI coats B. clathrin coats C. COPII coats D. all of the above

Retrieval of cargo from the Golgi to the ER involves ... *A. COPI coats* B. clathrin coats C. COPII coats D. all of the above

Retromer complexes have proteins with BAR domains. What role do they play? A. cargo binding B. destination membrane targeting C. promotion of membrane curvature

Retromer complexes have proteins with BAR domains. What role do they play? A. cargo binding B. destination membrane targeting *C. promotion of membrane curvature*

What catalyzes carbon fixation?

Rubisco

What enzyme catalyzes fixation of CO2 to ribulose 1,5-bisphosphate?

Rubisco

What is needed for CO2 + ribulose 1,5-bisphosphate to form into an intermediate with 6 carbons?

Rubisco

Cohesins have two _____ domains.

Scc (Scc1 and Scc3)

Sos associates with the Grb2 SH3 domain. That suggests that Sos has ... A. phosphotyrosine motifs B. phosphoinositide groups C. a proline-rich region

Sos associates with the Grb2 SH3 domain. That suggests that Sos has ... A. phosphotyrosine motifs B. phosphoinositide groups *C. a proline-rich region*

The GTPase protein that pinches off a clathrin-coated vesicle from the donor membrane is ... A. clathrin B. phosphoinositide C. adaptin D. cargo receptor E. dynamin

The GTPase protein that pinches off a clathrin-coated vesicle from the donor membrane is ... A. clathrin B. phosphoinositide C. adaptin D. cargo receptor *E. dynamin*

What happens once the STATs dimerize, what happens?

The dimer is translocated to the nucleus where it influences transcription

The electron donated to an electron carrier originates from ... A. chlorophyll B. water C. a quinone

The electron donated to an electron carrier originates from ... *A. chlorophyll* B. water C. a quinone ----- the special pair!!!

The metal ion that is required for chlorophyll function is: A. Mg B. Fe C. S D. O2

The metal ion that is required for chlorophyll function is: *A. Mg* B. Fe C. S D. O2

The nuclear lamins are in what class of cytoskeletal element? A. microtubules B. actin filaments C. intermediate filaments D. all of the above

The nuclear lamins are in what class of cytoskeletal element? A. microtubules B. actin filaments *C. intermediate filaments* D. all of the above

The photoreaction center found in photosystem II absorbs light that is ... A. yellow B. purple C. green D. blue E. red F. yellow and blue G. red and blue H. green and blue I. purple and red

The photoreaction center found in photosystem II absorbs light that is ... A. yellow B. purple C. green D. blue E. red F. yellow and blue *G. red and blue* H. green and blue I. purple and red ----- visible light = 400 (white/purple)-700nm (red)

The specialized soluble t-SNAREs and the complexin protein allow ... A. partial SNARE bundle assembly that allows rapid full assembly and secretion upon a Ca2+ signal B. rapid regeneration of synaptic vesicles after secretion C. constitutive secretion

The specialized soluble t-SNAREs and the complexin protein allow ... *A. partial SNARE bundle assembly that allows rapid full assembly and secretion upon a Ca2+ signal* B. rapid regeneration of synaptic vesicles after secretion C. constitutive secretion

These actin binding proteins can anchor actin filaments to the plasma membrane ... A. fimbrin B. α-actinin C. filamin D. ERMs

These actin binding proteins can anchor actin filaments to the plasma membrane ... A. fimbrin B. α-actinin C. filamin *D. ERMs*

This actin binding protein gives strength and resilience to the plasma membrane of red blood cells ... A. fimbrin B. α-actinin C. spectrin D. both A and B

This actin binding protein gives strength and resilience to the plasma membrane of red blood cells ... A. fimbrin B. α-actinin *C. spectrin* D. both A and B

This actin binding protein organizes filaments in a gel-like network ... A. fimbrin B. α-actinin C. filamin D. both A and B

This actin binding protein organizes filaments in a gel-like network ... A. fimbrin B. α-actinin *C. filamin* D. both A and B

This molecule is rigid in the presence of Ca2+. A. Cadherin B. Adherens C. Desmosome D. Actin

This molecule is rigid in the presence of Ca2+. *A. Cadherin* B. Adherens C. Desmosome D. Actin

What is/are examples of non-ionic detergent(s)?

Triton X-100 and B-octylglucoside

What's "old actin"? A. D-form B. T-form C. both

What's "old actin"? *A. D-form* B. T-form C. both

What's a function of cofilin in the lamellipodium? A. causing myosin contraction B. adhesion to the ECM C. making "old" actin more likely to depolymerize, providing more G-actin for polymerization at the leading edge

What's a function of cofilin in the lamellipodium? A. causing myosin contraction B. adhesion to the ECM *C. making "old" actin more likely to depolymerize, providing more G-actin for polymerization at the leading edge*

What's happening at the beginning of the curve that is seen (flat part) when ~no preformed actin filament seeds are added~? A. nucleation B. polymerization C. treadmilling

What's happening at the beginning of the curve that is seen (flat part) when ~no preformed actin filament seeds are added~? *A. nucleation* B. polymerization C. treadmilling

Where do protons accumulate in chloroplasts? A. stroma B. matrix C. thylakoid space D. intermembrane space E. A and B

Where do protons accumulate in chloroplasts? A. stroma B. matrix *C. thylakoid space* D. intermembrane space E. A and B

Where do protons accumulate in mitochondria? A. stroma B. matrix C. thylakoid space D. intermembrane space E. A and B

Where do protons accumulate in mitochondria? A. stroma B. matrix C. thylakoid space *D. intermembrane space* E. A and B

Which G-α subunit is most likely involved in the Ca2+-dependent contraction of smooth muscle cells? A. Gs B. Gi C. Gq D. Gt

Which G-α subunit is most likely involved in the Ca2+-dependent contraction of smooth muscle cells? A. Gs B. Gi *C. Gq* D. Gt ----- Gq --> PLC-β --> IP3 --> Ca2+ release

Which SMC protein is cleaved by separase at anaphase? A. Cohesin B. Condensin C. Cofilin D. Compactin

Which SMC protein is cleaved by separase at anaphase? *A. Cohesin* B. Condensin C. Cofilin D. Compactin

Which of molecule causes the cell to grow? A. Mitogen B. Growth factor C. Survival factor

Which of molecule causes the cell to grow? A. Mitogen *B. Growth factor* C. Survival factor

Which sequesters actin monomers and suppresses polymerization? A. thymosin B. profilin

Which sequesters actin monomers and suppresses polymerization? *A. thymosin* B. profilin

Whose mitochondrial DNA do Dr. Fisher's sons have? A. their mom's B. their dad's C. both D. neither ... it spontaneously generates

Whose mitochondrial DNA do Dr. Fisher's sons have? *A. their mom's* B. their dad's C. both D. neither ... it spontaneously generates

How does N-linked glycosylation work?

a 14 sugar group is attached to the nitrogen in the N-X-S/T sequence and then some of the sugars are trimmed

What is the output of the Calvin cycle?

a 3 carbon sugar

What can occur as a result of the processing of oligosaccharide chains in the golgi?

a carbohydrate group (CHO)

What is a polarized cell?

a cell that has different membrane domains that are distinct from one side of the cell compared to the other

What does the end capture of a kinetochore?

a kinetochore microtubule

What is mTOR?

a nutrient sensor that responds to the presence/absence of nutrients in the cell by repressing/activating autophagy

What is BiP?

a special hsp70 that is present in the ER lumen and starts to interact with proteins as soon as their chains are emerging

What initiates muscle contraction?

a sudden rise in cytosolic [Ca2+]

What does the JAK-STAT signaling pathway rely on the formation of?

a transcriptional regulatory complex

What is ~JAK~?

a tyrosine kinase

What's the function of pigments in the antenna complex?

absorb light and pass energy to neighboring pigments with ultimate transfer of energy to the photoreaction center special pair and then cause release of an electron from chlorophyll

What allows targeting of proteins to the outer mitochondrial membrane?

accumulation of positive charges on one side of the helix

What does spectrin link to?

actin ... that in turn, links indirectly to proteins that are in the plasma membrane

What plays a key role in the rates of assembly at the plus vs the minus end?

actin being bound to ADP or ATP

What causes organization of actin filaments (into arrays)?

actin binding proteins cause the organization ... they have 2 regions that can bind actin filaments (each one binds 2 filaments)

What has a BAR domain?

adaptin AP2

what does telomerase do?

adds a chunk of another RNA template onto the 3' end of the parent lagging strand and extends the 3' end without this, the DNA strand would get 50-100 nucleotides shorter after every replication of DNA

What does glucosyl transferase do?

adds a glucose back on if the incompletely folded protein still isn't folded right

what is a malignant tumor coming from a gland called?

adenocarcinoma

hemidesmosome transmebrane adhesion protein

alpha6beta4 integrin and type XVII collagen

When the reaction center is in a charge-separated state/the special pair donates an electron to an electron carrier, where does the replacement electron come from?

an electron donor, generally water

What happens when the bonds in the sugar-nucleotide are cleaved?

an exergonic reaction occurs that allows for the transfer of the sugar onto the carbon group (a coupled reaction is driving an unfavorable reaction)

how much genetic stability exists in cells that cause cancer?

an optimum amount!! too much causes the cells to just die and not continue on replication and spreading

What do ERM proteins do?

anchor actin filaments to the plasma membrane

What identifies specific proteins/structures in TEM?

antibodies tagged with heavy metals (ex: gold)

To what amino acid residue is a N-linked oligosaccharide attached?

asparagine (Asn)

How do the 14 gamma-tubulins associate?

assemble in a spiral and one sits right on top of another ... only 13 will be available in the end (because one will be covered)

Which is more likely to occur when nutrients are scarce compared to when they are available?

autophagy is "ramped up"

What was used to see what end microtubules polymerize faster at?

axoneme (core (made up of microtubules) of a flagellum or a cilium) ... the microtubules formed much faster at the plus end than and the minus end

What opens the Sec61 pore?

binding of single (signal? bruh idk) peptide itself

vinculin

binding site for this is reveleaed when alpha-catenin is extended/unfolded

What happens when you have ARP 2/3 and filamin activity together?

branched actin web in lamellipodia - Arp 2/3 = branching nucleator - filamin = causes gel-like stuff lol - good for protruding the leading edge of the lamellipodium!

What pattern does Arp 2/3 associate in?

branched patterns (whenever you see a branched pattern of actin organization, you know its mediated by Arp 2/3 complexes)

What is a complex oligosaccharide?

bunch of different sugars

What is a high-mannose oligosaccharide?

bunch of mannose sugars

How does myosin (II) aid in the development of new tissues?

can exert force on adhesion belts, pulling them together (shortening them) ... actin being contracted causes the epithelial shape to chance

Conversion of a phosphoinositide species that can initiate coat assembly to a different one can ...

cause coat dissociation

Haflic limit

cells have a set number of replications that they undergo before senescence

What kinds of cells have larger regions of SER?

cells that produce high levels of lipid-derived molecules (ex: steroids derived from cholesterol)

Do channel proteins or transporters work faster?

channel proteins! they can flux ions at a much faster rate than transporters because they can flow in a continuous stream

What are the 2 classes of N-linked carbohydrates?

complex oligosaccharide and high-mannose oligosaccharide

What prevents full zipping of the SNARE bundle?

complexin

What does it mean when a secretory pathway is constitutive?

constantly happening in a non-regulated fashion

What kind of signaling is this example involving ephrin?

contact-dependent signaling

How is actin arranged in a stress fiber?

contractile bundle (parallel bundles)

How wide are the RER folds (?)?

cutaway into lumen = 20-30 nm wide

What is the most common CFTR mutation?

deletion of F508 (Phenylalanine)

How is actin arranged in lamellipodium?

dendritic network

intracellular face of desmosome

dense plaque of adaptor proteins that allows interaction with IFs and bind to IFs

What often drives transport in bacterial cells?

differences in [H+] between inside and outside of cells

What often drives transport in animal cells?

differences in [Na+] between inside and outside of cells

What allows for full zipping of the SNARE bundle?

dissociation of complexin due to high Ca2+ levels

What does a phosphoinositide (PI) recruit?

dynamin

What happens when the reduced product (with a very high redox potential) donates to an acceptor?

enough energy is released to pump protons --> generate ATP

Since transmembrane helices are released into the membrane individually, what must their side chains be comprised of?

entirely hydrophobic residues

where do carcinomas originate?

epithelial cells

What does the Nernst equation calculate?

equilibrium potential for an ion

telomere

extra DNA at the end of the chromosome on the leading strand

Where is the only place that proteins and lipids on the plasma membrane are glycosylated?

extracellular face

Intrinsic or extrinsic apoptosis pathway or both?: FADD

extrinsic

Intrinsic or extrinsic apoptosis pathway or both?: FAS receptor

extrinsic

Where are t-SNAREs located in an extracellular vesicle?

facing the inside of the vesicle

Is ~Src~ a tyrosine kinase or a serine/threonine kinase?

first discovered/original cytosolic tyrosine kinase!!!

What do FtsZ proteins do?

form into filaments that mediate a bending force and promote membrane curvature

How are microtubules reorganized during mitosis?

form the mitotic spindle

How do profilin-actin complexes get associated with formin?

formin nucleates these things, and then as it rides along it could be carrying profilin which promotes polymerization

What does transducin (Gt) do?

functions in cells that respond to light/dark

How do proteins move between the cytosol and the nucleus?

gated transport

How are proteins linked to the exoplasmic side of the membrane?

glycophosphatidylinositol (GPI) anchors

What happens in a protein destined for the thylakoid?

goes through TOC, then TIC, and then chloroplast targeting sequence is removed in the stroma, revealing a second signal sequence (thylakoid signal sequence)

What are vesicles on the cis golgi called?

golgi vesicles

Is actin a monomer or a polymer?

hahaha it's a trick question! it's a polymer of individual actin monomers

phosphorylation of condensins by M-cyclin/Cdk

helps condense chromosomes during prophase

What does nidogen do?

helps link collagen and laminin

In the cytosol, [GTP] is _____.

high

When are membranes more fluid: when they are held at high or low temperatures?

high temperatures

Contents of secretory vesicles in the regulated pathway are really _____ (the content of the secretory molecule is _____).

high/large

What does acetylcholine cause in heart pacemaker cells?

hyperpolarization and a decreased firing rate

ok so the next topic is basically like how E1 and the E2/E3 complex transfer ubquitins onto a protein but like here's the tea...... i've been studying for so long i don't even know what i've covered and what i haven't

i learned this process at some point but idk why its not in this notecards or when or why or how i learned it but i know it so i'm going on i cannot do this rn here's a picture

What can make the cytosol of neighboring cells continuous?

if they are joined by gap junctions

Where was GFP first observed?

in jellyfish

Where does DAG go?

in the plasma membrane

What can exocytosis do for a cell?

increased membrane lipids/delivery part of the lipid bilayer

Formation of a particular phosphoinositide species can ...

initiate coat assembly

What normally moves through channel proteins?

inorganic ions (mainly Na+, K+, Ca2+, Cl-)

How does a cytosolic protein reach the peroxisome?

inserted into peroxisome membrane (ex: by tail anchoring)

Where is [K+] high?

inside the cell

Where are GLUTs located in an insulin stimulated cell?

insulin binds to an extracellular insulin receptor and causes an intracellular signal which causes reclocalization of the glucose receptors to the plasma membrane ... this causes more glucose transport (more glucose is brought into the cell)

What is the transmembrane adhesion protein that cell-matrix proteins use?

integrin (hemidesmosomes also use collagen)

Cadherins or integrins?: Are composed of dimers of alpha and beta chain subunits.

integrins

How is a multivescicular body created?

invagination of the early endosome membrane to form many new vesicles that are inside its lumen

How is an intralumenal vesicle created in an endosome?

invagination of the endosomal membrane

What is the role of NSF?

it allows for dissociation of the trans-SNARE complex due to coupling of the reaction with ATP hydrolysis

How does a BAR domain promote membrane curvature?

it has positive charges that are attracted to the negatively charged membrane

What type of protein ~phosphorylates another~?

kinase

Where does macropinocytosis eventually lead to/where does the engulfed material end up?

late endosome

Where does phagocytosis eventually lead to/where does the engulfed material end up?

late endosome

What happens when you have decreased myosin activity?

less stress fiber formation

What do the annular subunits of a nuclear pore do?

line the center of the pore (with "nonsense" extending from the middle of them)

What is the function of the smooth ER?

lipid synthesis (for all of the organelles and the plasma membrane)

In the cytosol, [GDP] is _____.

low

Is the [Ca2+] in the cytosol high or low?

low

What drives creation of a proton gradient by the electron transport chain?

low affinity electron donor donates electron to higher affinity acceptor ... energy of this exergonic is harnessed to pump the protons

M6P receptors release their cargo at what pH?

low pH (~5 ish)

Where does a mannose 6-phosphate tag take things?

lysosome

What regulates autophagy?

mTOR

What do the column subunits of a nuclear pore do?

make ring structure that bridges with both sides

What sorts lysosomal hydrolases in the trans golgi network?

mannose 6-phosphate

basal lamina

mat of ECM that supports dense sheets of epithelial cells and hold them in a sheet

contact-dependent signaling

membrane-bound signals bind to receptors on adjacent target cells

What kinds of residues are seen on proteins that are imported into the ER?

most signal sequences from proteins imported into the ER are rich in hydrophobic residues (8+ in close proximity)

Is ~inactivation of signaling protein~ an example of positive or negative feedback?

negative feedback ... leads to suppression of the very same signal that started the signaling cascade

Does cofilin localize at the leading edge of the lamellipodium?

no! there is only actin at the leading edge, but leading up to it there is actin and cofilin

Are intermediate filament polarized?

no! they have no plus or minus ends

Where does O-linked glycosylation occur?

on Ser or Thr -OH side chains

Where are V-type ATPases found?

on endosomes and lysosomes

Where is a phosphoinositide found?

on the cytosolic side of a membrane

Where is dolichol intially found?

on the cytosolic side of the membrane ... it is flipped to the lumenal side (when phosphates are added)

Where are glycolipids found in a eukaryotic membrane?

on the exterior of the cell and in the lumen of organelles (on the side facing away from the cytosol)

Oncogeneor Tumor Supressor?: Bcr-Abl (Philadelphia chromosome)

oncogene

Oncogeneor Tumor Supressor?: Ras

oncogene

What is coupled transport?

one solute moves down its electrochemical gradient, providing the energy to transport the other solute against its electrochemical gradient - symport and antiport are examples

What does depolarization cause?

opening of voltage-gated channels (probably Na+ ones lol)

what is replicative senescence/senescence?

permanent withdrawal from the cell cycle

What type of protein ~removes a phosphate group from another~?

phosphatase

What is cardiolipan composed of?

phosphatidic acid (2 of these heehee)

What is phosphtaidylglycerol composed of?

phosphatidic acid with a glycerol head

What is a phosphotidylinositol with 2-3 phosphate groups on it called?

phosphoinositide (PI)

What cleaves phosphotidylinositol into DAG and IP3?

phospholipase C

What is the purpose of glycophosphatidylinositol (GPI) anchors?

phospholipase c targets them specifically for cleavage

plasmodesmata

plant version of gap junctions, but are much larger

What is another name for the minus end of actin?

pointed end

How is the BAR domain charged?

positive charges (Arg, Lys, His)

What is an electron donor a source of?

potential energy

Where are ribosomal subunits processed? Where are they exported to?

processed in nucleolus and exported to cytoplasm

What is photosystem II involved in?

producing the p+ gradient

Some formins have structures that act as staging sites for _____.

profilin-actin complexes ----- profilin can bind onto these structures! profilin promotes the assembly of filaments

What does the SH3 domain bind?

proline-rich regions

what class are Ras and Myc in?

proto-oncogenes

How does a F-type ATP synthase work?

protons move down their gradient and this energy is hardness to produce ATP from ADP + Pi

How does a V-type ATP synthase work?

protons moving against their gradient and this requires ATP to be turned into ADP + Pi in order to get chemical energy to fuel it

What function does water serve in photosynthesis?

provides an electron for photosystem II to use to replenish the one lost to photosystem I

What is the relationship between kinesin-14 and kinesin-5?

pull toward each other and separate the spindles

Why don't disulfide bonds form in the cytosol?

reducing environment

What is a myofibril composed of?

repeated contractile units (sarcomeres) of the skeletal muscle

What is dynamic instability?

repeated cycles of catastrophe and rescue in a microtubule ... very dynamic but not very stable

What is the main benefit of using super resolution light microscopy as opposed to regular light microscopy?

resolution is improved 10x to ~ 20nm!!! (instead of 200nm)

What do multinucleated skeletal cells contain?

sarcomeres in series, forming myofibils

How do small uncharged polar molecules (H2O, urea, glycerol, NH3 etc.) get across the lipid bilayer?

some get through, but others are turned back ... membrane is semi-permeable to H2O

What is a proteoglycan?

special class of glycoproteins because they contain GAG chains ... if has GAGs and is part of ECM = proteoglycan

What does the Pleckstrin homology (PH) domain bind?

specific PIs

What does the 14-3-3 domain bind?

specific phosphoserine/phosphothreonine motifs (P-S/T)

What does the SH2 domain bind?

specific phosphotyrosine-containing motifs (/specific AA sequences that contain P-Tyrs) RTK creates P-Tyrs!!! omg cool!!!

What does the Phosphotyrosine binding (PTB) domain bind?

specific phosphotyrosine-containing motifs (different from the ones that SH2 binds)

tell me about MAPs (microtubule associated proteins) pls

stabilize microtubules by binding along the sides

What does a GAP do?

stimulates G protein GTPase activity (G protein hydrolyzes GTP to GDP)

What are the components of a glycolipid?

sugar groups attached to a polar head region

What are the major products of the dark reactions of photosynthesis?

sugars, amino acids, and fatty acids (made from CO2)

What allows an electron from the special pair to be transferred to an electron carrier/the photoreaction center to be ionized?

sunlight

~A neurotransmitter released from a neuron acts on a target cell across a short cleft.~ What kind of signaling is this?

synaptic signaling

What is the chloroplast fission process very similar to?

the bacterial fission process

What part of the cadherin interacts with another one?

the distal part (N ends)

What does intermediate filament structure depend on?

the lateral bundling and twisting of coiled-coils

What has to happen for the membrane of a specialized phagocytic cell to pinch off?

the network has to be dissociated

What is the limiting factor in glucose transport?

the number of transporters on the cell membrane (this is regulated!!!)

What drives ATP synthesis?

the proton gradient generated by the electron transport chain

What does the "z-scheme" refer to?

the shape that the electron travels in when it moves from photosystem II to photosystem I

How does an ion-channel-coupled receptor work?

the signal molecule binds to the receptor, and then the receptor opens and ions flow down their concentration gradient

What is the result of having more EPSPs?

the threshold potential will be larger because they build on each other

What would happen if clathrin were mutated so the triskelions couldn't associate with each other?

there couldn't be a clathrin coat and vesicle

What's the deal with the baby with three parents?

three donors ... two parents are the donors of the nuclear DNA and the third parent donates the mitochondrial DNA

During photosynthesis, where do H+ accumulate?

thylakoid space

What causes different protein localizations on different domains of polarized cells?

tight junctions

What prevents the movement of proteins from one side of a polarized cell to the other?

tight junctions

What do intermediate filaments have a vital function in?

tissues organized in sheets ex: epithelial/endothelial

What does polyubiquitination tag the protein to do?

to be degraded by a proteasome or indicates sites that are requiring DNA repair in the protein

What is the goal of photosystem I?

to donate an electron to the electron carrier (that will then make NADPH out of NADP+ and H+)

How is a microtubule triplet built?

triplet starts with a singlet microtubule and then that has partial microtubules built on top of them

True or false?: Occludin is found in tight junctions.

true

True or false?: Plasmodesmata are larger than gap junction channels.

true even PM and desmotubule of ER can fit through too

True or false: Adherens junctions use cadherins.

true!

aster

tuft of MTs at each pole of the spindle

Oncogeneor Tumor Supressor?: Rb

tumor supressor

What does the 6 carbon intermediate (formed when CO2 and ribulose 1,5-bisphosphate combine) form next?

two 3 carbon sugar molecules (3-phosphoglycerate)

Where can spectrin be found?

under the plasma membrane

glycosaminoglycans (GAGs)

*- unbranched chains of repeating disaccharides* - one sugar is usually a uronic acid and the other is an amino sugar (alternating down the chain) ---> sugars = sulfated *- carry a HUGE overall negative charge* ---> attract positive charges ------> lots of solutes, creates osmotic pressure ---------> creating a very hydrated structure ... gel! ------------> gel fills in all the spaces - main type of GAG = hyaluronan ... no core protein (like normal), so just the sugar chain itself! ---> aggrecan can attach to hyaluronan and make giant space-filling aggregates

*--- Lecture 5: Membrane Transport 1 ---*

*LO1: Categorize the classes of proteins cells use to increase membrane permeability for solutes.* *LO2: Compare/constrast simple diffusion, passive transport, and active transport mechanisms.* *LO3: Define Vmax and Km of a transporter, and describe their relationship.* *LO4: Identify the energy source used in coupled transport.* *LO5: Name and describe examples of symport and antiporters.* *LO6: Compare/contrast mechanisms of cytosolic and lysosomal pH regulation.* *LO7: Describe and compare 3 classes of ATP-powered transport proteins.* *LO8: Define the "problem of osmolarity" and how cells solve it.* *LO9: Describe 2 medical conditions where CTFR transporter plays a mechanistic role.*

*--- Lecture 4: Membrane Structure 2: Membrane Proteins ---*

*LO1: Describe 4 types of membrane proteins.* *LO2: Differentiate alpha-helix (single and multipass) and beta-barrel transmembrane structures.* *LO3: Interpret a hydropathy plot to identify transmembrane alpha-helices.* *LO4: Categorize animo acid sequences by transmembrane structural significance.* *LO5: Identify which classes of membrane proteins are integral vs peripheral.* *LO6: Describe how detergents impact the solubility of membrane components.* *LO7: Predict protein-membrane interaction SDS-PAGE analysis.* *LO8: Relate how (and why) membrane proteins can be restricted into cellular domains.* *LO9: Identify location of membrane carbohydrates and list their functions.*

*--- Lecture 10: Intracellular Compartments 3: Nuclear Transport, ER ---*

*LO1: Describe mechanisms that guide protein folding.* *LO2: Characterize the mechanisms cells use to target proteins for degradation.* *LO3: Describe the proteasome function.* *LO4: Explain the unfolded protein response, listing 3 pathways initiated by the response.* *LO5: Identify the site of plasma membrane lipid synthesis.* *LO6: Interpret in vitro experimental results arising from isolation/disruption of ER.*

*--- Lecture 2: Methods in Cell Biology ---*

*LO1: Distinguish and quantify scale measurements of subcellular objects.* *LO2: Define "resolution".* *LO3: Describe resolution limits of prevalent microscopy techniques.* *LO4: Distinguish 4 kinds of light microscopy.* *LO5: Define fluorescence.* *LO6: Describe benefits of confocal microscopy.* *LO7: Identify applications for fluorescence.* *LO8: Describe uses of FRET and FRAP.* *LO9: Enumerate scale of improvement allowed by superresolution techniques.* *LO10: Distinguish electron microscopy techniques.* *LO11: Identify what kinds of images are produced by different techniques.*

*--- Lecture 8: Intracellular Compartments 1: Introduction to Cellular Organization ---*

*LO1: Explain the benefits of possessing membrane-bound organelles for eukaryotic cells.* *LO2: Identify 3 forms of intracellular transport by mechanism of action and involved organelles.* *LO3: Describe the structure and properties of nucleoporin complexes.* *LO4: Identify the function of the nuclear localization signal and how it interacts with other molecules.* *LO5: Compare and contrast GTP-driven nuclear import and export.* *LO6: Describe a mechanism for transiently regulating transcription factor import.* *LO7: Recognize components of nuclear transport that can be disrupted by viral proteins.* *LO8: Describe 2 instances where RNA is transported out of the nucleus.* *LO9: Describe the sequence of nuclear envelope disassembly and reassembly during mitosis.*

*--- Lecture 9: Intracellular Compartments 2: Nuclear Transport, *ER* ---*

*LO1: Identify the functions of smooth and rough ER.* *LO2: Describe the structure of the ER.* *LO3: Identify and describe functions of components of ER transmembrane transport.* *LO4: List and describe classes of proteins that undergo transport into the ER.* *LO5: Describe insertion methods through/into the ER membrane.* *LO6: List and describe protein modifications that are accomplished in the ER.*

*--- Lecture 3: Membrane Lipids ---*

*LO1: Identify types of membrane lipids.* *LO2: Describe structure of membrane lipids.* *LO3: Define "amphipathic".* *LO4: Describe structure of lipid bilayer.* *LO5: List functions of lipid bilayer.* *LO6: Associate lipids types with location and function.* *LO7: Describe how phospholipid asymmetry is maintained.* *LO8: Describe how lipid rafts are formed.* *LO9: List components of lipid rafts.* *LO10: Explain the relevance of membrane fluidity.*

What is an EPSP?

- "Excitatory Post Synaptic Potential" - excitatory NTs open channels that depolarize the post-synaptic membrane

What does is FRAP and what does it do?

- "Fluorescence Recovery After Photobleaching" - measures the rate of movement of proteins within a cell/on the plasma membrane; change over time! ---> can be used to measure how easily a protein diffuses laterally in a membrane

What does is FRET and what does it do?

- "Fluorescence Resonance Energy Transfer" - measures whether 2 proteins are in contact with each other

What is GFP?

- "Green Fluorescent Protein" - fluorophore that is encoded by a gene (it is a protein)

What is an IPSP?

- "Inhibitory Post Synaptic Potential" - inhibitory NTs open channels that hyperpolarize the post-synaptic membrane

How many microtubules are there for each kinetochore in yeast? What about in mammals?

- 1 microtubule/kinetochore in yeast - many microtubules/kinetochore in mammals

What does the structure of a K+ leak channel look like?

- 4 subunit tetramers ---> each subunit has 2 inner and outer structural helices with a loop in between them that also forms a helix - every helix has a positive and negative end

What is the default receptor used during LTP? What is the special case receptor?

- AMPA - NMDA

What are two forms of energy that can be harnessed to move a protein from the stroma to the thylakoid space?

- ATP - proton gradient

What are some functions of mitochondria?

- ATP synthesis - exportation of citrate to the cytosol (made into acetyl groups there) - heme synthesis - making proteins involved in mitochondrial metabolism - location of the urea cycle - location of amino acid metabolism components - location of gluconeogenesis - key Ca2+ buffer

What happens in bacteria in anaerobic conditions?

- ATPase pumps protons to produce a proton gradient - proton gradient drives uptake of several molecules and export of Na2+ (cotransport bringing H+ and lactose/lysine/succinate/proline into the cell and antiport taking Na+ out and bringing H+ in) - electron transport chain isn't functional!!! no oxygen to act as the final electron acceptor

List 3 proteins, protein complexes, and/or domains that promote membrane curvature.

- BAR domain - clathrin - AP2 - COPI - COPII

What is a single pass type 2 protein and how does it work?

- C-terminus in the lumen (negative end of start-transfer sequence is fed through to lumen side) - negative end of start-transfer sequence is on the C side

p16

- CK1 - inhibits G1-Cdk ... which inhibits Rb ... which releases E2F ... causes transcription of target genes that control entry into S phase

What circumstances inhibit cells from proceeding through the cell cycle?

- DNA damage - lack of stimulatory factors

DNA damage detection at G1/S checkpoint

- DNA damage inhibits cell division by activating p53 - activation of p53 leads to transcription of p21 (CK1), which blocks cell signaling

DNA damage detection at G2/M checkpoint

- DNA damage is detected - breaks can cause inactivation of Cdc25 (prevents activation of M-cyclin/Cdk) - arresting cell division gives cells a chance to repair their DNA

APC/C proteolysis control

- E3-ubiquitin ligase - adds ubiquitin to M-phase cyclins - essential for transition from metaphase --> anaphase - activated by Cdc20, causes polyubiquitination and degradation of M-cyclin

What can create a proton gradient?

- ETC in mitochondria - bacterial ATPase - ETC system in chloroplasts - bacterial ETC system

What types of proteins mediate membrane curvature and pinchase activity for chloroplast fission?

- FtsZ - dynamin

What is treadmilling?

- G-actin monomers are added to plus end at the same rate as other G-actin monomers are removed from the minus end - this happens at Cc

inactivation of Rb and activation of E2F

- G1 to S phase occurs 1. mitogen signaling activates transcription of immediate early gene (ex: Myc) 2. immediate early response gene transcription causes delayed-response gene expression 3. this activates G1-Cdk (phosphorylates it) 4. G1-Cdk phosphorylates and deactivates Rb 5. deactivation of Rb activates/releases E2F protein, which dissociates from Rb 6. E2F causes S-phase gene transcription which causes G1/S cyclin transcription and S cyclin transcription 7. lots of positive feedback that drives the cycle forward

Which GTP gets hydrolyzed in a tubulin dimer?

- GTP of α-tubulin is buried inside and DOESN'T hydrolyze - GTP of β-tubulin DOES hydrolyze (GTP--> GDP)

How is the M6P tag generated?

- GlcNac-phosphate added onto mannose residue - GlcNac removed to expose M6P tag

What are the three components of the unfolded protein response (UPR)?

- IRE1 - PERK - AFT6

question(s) asked at G2-M checkpoint

- Is the environment favorable? - Is all of the DNA replicated?

polar ejection force

- KMTs want to push but AMTs and IMTs want to pull ... these forces are opposing each other until we're ready to actually do the split - if chromosome is cut with a laser, the arm without the kinetochore moves away from the pole but the arm with the kinetochore moves toward the pole - plus-end-directed kinesin-4,10 motor proteins interact with the chromosome and can drive this oscillation force

What are two examples of microtubule binding proteins?

- MAP2 - tau

What is are some examples of ABC transportesr?

- MDR protein - lipid flippases - scramblases - CFTR

What is a single pass type 1 protein and how does it work?

- N-terminus in the lumen - start-transfer sequence and stop-transfer sequence ex: glycophorin

What is a single pass type 3 protein and how does it work?

- N-terminus in the lumen (negative end of start-transfer sequence is fed through to lumen side) - negative end of start-transfer sequence is on the N side

How does the Na+/K+ pump work?

- P-type ATPase - uses ATP hydrolysis to fuel movement of 2 K+ into the cell and 3 Na+ out of the cell (both against their concentration gradients) - causes inside of the cell to become more negative than the outside

What 2 phospholipids are found on the exoplasmic side (outside) of a cell?

- PC - SM

What 2 phospholipids are found on the cytosolic side (inside) of a cell?

- PE - PS - PI

regulation of DNA replication - S phase

- S-cdks phosphorylate Cdc6 ---> Cdc6 is degraded - S-cdks phosphorylate the ORC ---> DNA replication

what are the 2 E3-ubiquitin ligases that are essential for the cell cycle?

- SCF - APC/C

What are the types of Src homology (SH) domains?

- SH2 - SH3 - Pleckstrin homology (PH) - Phosphotyrosine binding (PTB) - 14-3-3

how is Cdk activity inhibited during G1?

- SRF activation - accumulation of CKIs (cyclins prevented from acting) - cyclin transcription is inhibited

What are the translocator proteins that are involved in mitochondrial import and targeting of proteins to various regions?

- TOM complex - SAM complex - TIM22 complex - TIM23 complex - OXA complex

What does the structure of a sarcomere look like?

- Z disc marks the ends of the sarcomere - thin filament (actin) - thick filament (myosin)

What can end a smooth muscle contraction?

- a MLC phosphatase - decrease in cytosolic Ca2+ - GPCR sequestration

What happens when bi-orientation is achieved and a stable conformation occurs?

- a signal that the chromosomes are aligned properly is enabled - mediated by tension sensor at the kinteochore

What do calnexin and calreticulin recognize? What are they?

- a single terminal glucose on incompletely folded proteins and retain them in the ER - they are Ca2+ activated chaperones - they give proteins "second chances" to fold

synaptic signaling

- a type of local signaling specific to neurotransmitters in nerve cells - involves an action potential of a neuron that results in secretion of a neurotransmitter that acts across a synaptic cleft - involvement of a cell-surface receptor

tell me about the kinesin-4,10 that is found in a mitotic spindle pls

- able to move the chromosomes towards the plus ends of the microtubules ---> places them in a better position to be captured by the kinetochore

Traditional/classical cadherins connect the _____ cytoskeletons of two cells to form _____.

- actin - adherens junctions

actin filaments

- actin = thin filament - actin can polymerize and cause movement of the cell - actin can form parallel bundles that link parts of the cell to nodes at the plasma membrane ---> focal adhesions that create stress fibers ... focal adhesions are then linked to ECM - actin helps stabilize microvilli - striated muscle (repeated arrangements of actin and myosin and other proteins)

What are the types of cell-matrix junction?

- actin-linked cell-matrix junction - hemidesmosome

Cdc20

- activates APC/C at metaphase-anaphase transition - stimulated by M-Cdk activity

What does G α-s do?

- activates adenylyl cyclase which activates cAMP - activates Ca2+ channels

what does E6 do?

- acts like Mdm2 - binds p53 and leads to its ubiquitination and proteolysis ---> p53 can't respond to anything!

What does PI 3-kinase do?

- adds a P to PIP2 (makes it into [PI(3,4,5)P3] - because there is less PIP2, there is less IP3 as a result

What are the types of cell-cell anchoring junction?

- adherens junction - desmosome

Under what conditions does a bacterial ATP synthase work both ways?

- aerobic = electron transport system creates a proton gradient taht is harnessed by ATP synthase to produce ATP - anaerobic = ATP synthase pumps protons out of the cell and then that proton gradient is harnessed

How is cellular pH maintained?

- aerobic metabolism of glucose making CO2 which adds H2O to make H2CO3 --> HCO3- and H+ - accumulation of H+ (lowers pH) - transporters can increase/decrease pH ---> ex: Na+/H+ antiporter, Na+ HCO3-/Cl- antiporter, Cl-/HCO3- antiporter

metaphase to anaphase checkpoint

- all kinetochores must be attached to MTs - accumulation of Mad2 protein (key indicator of kinetochore non-attachment) ---> signal may inhibit the anaphase promoting complex/cyclosome (APC/C)

Where do the R groups on a alpha helix face?

- always facing out ---> exposed to hydrophobic chains within the membrane so they have to be nonpolar

What is a myristoyl anchor and where is it found on a protein?

- amide linkage between terminal amino group and myristic acid ---> amide linkage has to be at the N-terminal end

What does the structure of a phospholipid look like?

- amphipathic - at least one of the fatty acid tails if unsaturated ---> kink/bend in the structure of the tail - polar head group (positively charged)

desmosomes

- anchor cells to one another and to IFs - using cadherins

tell me about titin pls

- anchors myosin bundles - spring-like protein - provides muscle some of its stretchability and recoil

What are 3 ways that cells can control the problem of high intracellular osmolarity?

- animal and bacterial cells pump inorganic ions out to keep the osmotic balance - rigid cell walls of plant cells keep the cells from bursting even with high pressures - some protozoans actively extrude H2O through contractile vacuoles

What is a beta-barrel and what does it do?

- antiparallel beta sheets rolled up into a cylindrical barrel shape - barrels can act as pores/channels

What are transmembrane proteins?

- anything that is destined to remain in ER, golgi lysosome, or plasma membranes has to to be transmitted to the ER first - arranged in membrane ex: GPI anchored proteins

What proteins have ER signal sequences?

- anything that needs to live in the ER (soluble/membrane bound): - proteins that are secreted to the extracellular space, then put into a vesicle - any soluble protein that needs to live in an organelle lumen (inside an organelle) - transmembrane proteins for these organelles ... additional sequence added after they're processed sends them to their final destination

What is a lipid raft?

- area of wider membrane - attract transmembrane proteins with longer hydrophobic transmembrane domains - important for cell signaling

what is the role of p53 in cancer?

- at least 50% of human cancers contain mutations in p53 - p53 is necessary to allow the cell to check DNA before proceeding with replication - p53 plays an important role in directing cells with damaged DNA to undergo apoptosis - without pauses for DNA repair, DNA becomes more and more damaged, leading to further oncogenic mutations

At what end does actin tend to polymerize more rapidly?

- at the plus end ---> less rapid/no growth/depolymerizing at the minus end

What is tensile strength?

- being able to pull on something that it resists - due to protein fibers (mainly collagen)

What are some functions of the peroxisome?

- beta-oxidation of fatty acids (into 2 carbon units that get shipped to the cytosol to be used in biosynthetic pathways) - degradation of organic compounds (like ethanol/alcohol) ---> production of H2O2 - peroxidation of organic substrates - synthesis of plasmogen (big lipid component of myelin)

both cohesin and condensins ...

- bind and encircle DNA and require ATP binding - they have similar structures that allow them to bind both ATP and DNA

How do ABC transporters work?

- bind and hydrolyze ATP but they aren't phosphorylated in the process - when they dimerize, a solute is pumped out of the cell - 2 ATPs are hydrolyzed/transport cycle

what do mitogens bind to?

- bind to transmembrane receptors, which lead to activation of Ras, MAP kinase, and the transcription factor Myc

tell me about troponin c pls hehehe

- binds Ca2+ and alters its conformation - calmodulin-related protein

tell me about thymosin pls

- binds subunits, prevents assembly - sequesters free actin so it can't assemble

tell me about profilin pls

- binds subunits, speeds elongation - promotes assembly

Bcl2 (BH 1-4)

- blocks BH123 - anti-apoptotic (prevents cell death) ex: Bcl2, BclXL

BH3-only

- blocks Bcl2 (BH 1-4) - pro-apoptotic (causes cell death) ex: Bad, Bim, Bid, Puma, Noxa

What does proline do when it is present as as side chain?

- breaks an alpha-helix in an aqueous environment - found at very end/turns in between helices - cyclic side chain makes it very rigid and makes it hard for it to have the hydrogen bond interactions to build the helix in the first place - it can be a hinge

What do light and dark responses depend on?

- cGMP - G α-t - effector protein - GPCR

What are the anchoring junction connector types?

- cadherins between cells - integrins for attachment to the ECM

tell me about the kinesin-5 that is found in a mitotic spindle pls

- can move on two different microtubules - moves toward the plus end of one microtubule and towards the plus end of the another microtubule - providing force that forces/pushes the spindles apart

flow-cytometry

- can use Brd-U or just a fluorescent tag for DNA in general - dissociate the cells and run them through the cytometer and look at the amount of fluorescence that each cell is giving off ---> DNA will show up as bright ------> cells with two copies of DNA will be twice as bright as the baseline of brightness

What response does the cell generate in response to these conditions?

- cell cycle arrest - DNA repair

integrins

- cell-matrix anchoring junctions have them - dimers (alpha and beta subunits) ---> beta chain provides a link to the cytoskeleton (on the inside) ---> binding to matrix requires both subunits - binding to matrix is dependent on divalent cations (Mg2+, Ca2+)

How does fluorescence microscopy work?

- cells are illuminated by light at the absorbing wavelength, and are viewed through filters that only let the emitting wavelength through - fluorescent tags on specific molecules allow us to pinpoint their location in the cell

benign tumor

- cells resemble and function like normal cells - encapsulated by fibrous basal lamina - easy surgical targets (because they encapsulated and localized) - can convert into malignant tumors :(

what are the two parts of the mitotic spindle?

- central mitotic spindle - pair of asters

What happens to centrosomes in animal cells during interphase?

- centrosomes (containing centrioles) replicate and become the new spindle poles for mitosis - new centrioles arise de nuovo (reconstructed from scratch) - mitosis = duplication and migration of centrosomes, during which chromosomes are picked up and brought along into separate daughter cells - centrosomes migrate with the spindle apparatus

what are the two multipass transmembrane tight-junction proteins?

- claudin - occludin - their loop domains interact and form the tight junction

What does cAMP phosphodiesterase do?

- cleaves one of the phosphoester bonds to form AMP - can reverse/shut down the signaling pathway by degrading the signaling molecule

what is a tumor?

- clonal mass of cells - cells disregard signals that regulate proliferation - cells avoid suicide by apoptosis - cells escape senescence and differentiation - cells are genetically unstable - growth depends on angiogenesis (can't get bigger than 2mm otherwise) ---> if blood vessels can be recruited as well, they can grow beyond this size

Sister chromatids are held together while they are replicated by _____ and condensed into DNA coils by _____.

- cohesins - condensins

What are the components of a nuclear pore (what are the nucleoporin proteins)?

- column subunits - annular subunits - lumenal subunits - ring subunits - fibrils C-A-R-L-F ?? lol idk

interpolar microtubules

- compose the spindle that runs between the two poles - overlap with microtubules from the opposite pole at the midline

kinetochore microtubules

- composes the spindle that runs between the two poles - attach to sister chromatids of each chromosome at the kinetochore

What influences membrane fluidity?

- composition - temperature

what does M-cyclin/Cdk phosphorylate to promote mitosis?

- condensins - nuclear lamins - MAPs (MT-associated proteins) and catastrophins (kinesin-like proteins) that destabilize the MTs

How do intermediate filament impart mechanical stability to animal cells?

- connecting with contact points of the cell surface and also with the nucleus ---> the intermediate filament network gives structural integrity

cytokinesis in animal cells

- contractile belt of myosin II and actin filaments forms around perimeter of the cell, midway between the poles - belt tightens and the cell is pinched into two daughter cells - spindle asters determine the plane of cleavage in animal cells for even division of the cell

what is absent during cytokinesis in plant cells that is present in animal cell cytokinesis?

- contractile ring - centrosomes - astral MTs

5. telophase

- contractile ring forms and cells begin to pull apart and separate - individual chromosomes have been pulled back to the spindle/centrosome - nuclear envelope reassembles around the individual chromosomes - chromosomes start to dissociate from their most tightly bound state

How do quantum dots work?

- coupled to proteins (ex: antibodies) - allow for long-term tracking of proteins in cells - really useful if you want to take pictures later on - brighter and more stable

What are some ways of fueling active transport?

- coupled transporter - ATP - light

how does cyclin-dependent kinase (Cdk) work?

- cyclin binds to it and allows Cdk to phosphorylate its targets - Cdk is the one that has the active site

what can be left out of the cell cycle to save time and why would this happen?

- cytokinesis can be left out to save time when a lot of cycle have to happen fast - formation of a nuclear syncytium with a shared cytoplasm - minimal G1 - minimal G2 - normal S - quicker mitosis

What direction do ABC transporters transport in eukaryotes? In prokaryotes?

- cytosol to extracellular space - extracellular space to cytosol

necrosis

- death in response to tissue damage/trauma - cell swelling - cells burst - release of intracellular contents into surroundings: ---> inflammation ---> damage to surrounding cells

How can the signaling events caused by the activation of G α-s be terminated?

- degradation of the extracellular signaling molecule - activation of GTPase activity of the G-α subunit - sequestration of the receptor so it can no longer activate G proteins - phosphatase that dephosphorylates the PKA targets - more heeheehee

How does COPII coat dissociation work?

- delayed until the vesicle arrives at the target membrane (keep their coat until they arrive) - GTPase activity of Sar-1 is not sufficient - kinase at the destination membrane phosphorylates coat proteins and causes their dissociation

names of nonclassical cadherin proteins

- desmoglein - desmocolin

names of adaptor proteins that are involved in the plaque of adaptor proteins in the desmosome

- desmoplakin - plakoglobin - plakophilin

How on earth could acetylcholine have such an array of different actions?

- different receptors - same receptors but different intracellular effector proteins

How are intermediate filaments reorganized during mitosis?

- dissociate and later reassociate ---> nuclear lamina (lamins) do this too

p53 pathway

- double strand break detected - 1. Mdm2 (ubiquitin ligase) is sequestering p53 2. p53 is phosphorylated and Mdm2 releases it 3. active p53 binds to regulatory region of p21 gene 4. p21 (CK1) is made 5. p21 CKI inactivates G1/S-Cdk and S-Cdk

How do dyneins in motile cilia/flagella work?

- dynein = motor protein that moved on a microtubule ---> instead of sliding on a microtubule, you get a bending force ------> this causes the flagella to whip back and forth

What does microtubule-interfering molecules do?

- either prevent polymerization or depolymerization - all of the ones we learned are anti-cancer agents

What is the benefit of using immunohistochemistry and how does it work?

- emits light/shines light back at you - you can see the individual filaments because they are far apart from each other and shining

What are the differences between post-translational translocation in eukaryotes and bacteria?

- eukaryotes = sec62, 63, 71, 72 feeds the chaperone-free protein in through sec61 to ER lumen, BiP uses ATP to bind to protein and pull it through to the membrane; lots of chaperones involved - bacteria = secA ATPase (ATP --> ADP) feeding chaperone-free protein through to secY complex to extracellular space; ribosome production isn't pushing it through

What does MDR do?

- expressed at a high level by cancer cells ... pumps out drugs and makes cells resistant to chemotherapy - when expressed by protists that causes malaria, they become resistant to the drug that treats it

How do extracellular signals dictate the direction of cell migration?

- extracellular signaling molecules activate Arp 2/3 mediated polymerization and pushing forward of the leading edge - Rac causes protrusion at the leading edge - Rho causes actin-myosin contraction at the trailing edge

What are 2 ways in which proteins can be attached to the cytosolic face of a membrane?

- fatty acid linkages - prenyl groups ex: myristoyl anchor, palmitoyl anchor, farnesyl anchor

What is a multi-pass type 4 protein and how does it work?

- fed through until we get to the stop-transfer sequence - negative charge oriented towards lumen - number of helices OR start transfer sequences + stop transfer sequences = number of times that the protein is going to pass though the membrane ex: GPCR, GLUTs, VG Ca2+ channels, ABC small molecule pumps, CFTR channel, Sec61

What contributes to integration of cells into tissue and/or cell movement?

- fibronectin and laminin connect cells to ECM (fix cells in place) by binding to integrins in the plasma membrane - ECM provides a lattice along which/through which cells can migrate

What are the organizational proteins?

- fimbin - α-actinin - filamin - spectrin - ERM

What can chlorophyll do after absorbing light?

- fluoresce - produce heat - transfer energy to a neighboring chlorophyll (resonance energy transfer) - transfer an electron to an electron acceptor

How does fluorescent tagging serve as the key means of identifying the plus and determining if the microtubule is polymerizing?

- fluorescent tag is put on a protein - you can look at the location of that protein ... if it is associated with the plus end and the plus end is polymerizing, that proteins moves and you can see it streaking along as the microtubule increases in length ---> "comet" seen under a fluorescent microscope

What are the components super resolution light microscopy?

- fluorophores and lasers - using a process called STED

adherens junction

- form a belt around the outside of the cell - inside the cell, actin bundles are holding the opposite sides of the cell - myosin II can exert force on adhesion belts by moving on actin filaments and pulling them together (shortening them)

astral microtubules

- form the aster - radiate outward from the centrosome toward the cortex of the cell

What are some types of post-translational modifications that proteins go through in the ER lumen?

- formation of disulfide bonds - addition of GPI anchors - N-linked glycosylation - folding (with help of chaperones) - transport out of ER and degradation if proteins don't fold correctly

What is a thick filament?

- formed as myosin tail regions bundle together - made up of many of these units with 2 of the myosin heads

What causes assembly and contraction of the actin-myosin ring?

- formin --> straight actin filament formation - myosin II activation (caused by regulatory myosin light-chain phosphorylation)

Elastin

- forms highly extensible elastic fibers - important in artery walls (50% material), skin, lungs - network of flexible hydrophobic segments joined by alpha-helical cross-links ---> elastin itself is a single hydrophobic protein with alpha-helices coming off of it that can cross-link to other elastin molecules

kinetochore

- forms in prometaphase - multiprotein complex in the form of a trilaminar plate - situated at the centromere of a chromosome

What does a hydropathy index measure?

- free energy change that occurs when a segment of a peptide chain is transferred to water (how hydrophobic the amino acids in the segment are) - each peak on the graph is a transmembrane domain

What are phosphoglycerides derived from? How does this process work?

- from glycerol! 1. free fatty acid trafficked into the membrane 2. CoA added on 3. CoA taken off and two fatty acids are linked together 4. phosphate group removed 5. phosphocholine added

What are two main classes of molecules that make up the ECM?

- glycosaminoglycans (GAGs) - fibrous proteins (collagen, elastin, fibronectin, laminin)

What are some characteristics of phase-contrast microscopy?

- good for measuring cell size and identifying boundaries - heightening of anything that is in contrast - produces sharp edges

How does production of inhibitory protein work?

- happens over a slower time course - changes in gene expression - inhibitory protein stopping the activation of an intermediate protein by the receptor

What are two characteristics that something has to have to be a transmembrane helix?

- has to be at least 20 AAs long - has to have a positive hydropathy index (be made of hydrophobic AAs)

intermediate filaments

- have a role in nuclear lamina, underlying nuclear envelope ---> lamins can be disassociated as a preliminary to mitosis - form bundles that are really resistant to breaking under tensile stress (they're stretchy and hard to break) - often play roles in the mechanical stability of the cell

nucleation

- helical polymer is stabilized by multiple contacts between adjacent subunits - in the case of actin, two actin molecules bind relatively weakly to each other, but addition of a third action monomer to form a trimer makes the entire group more stable

collagen XVII

- hemidesmosome transmembrane adhesion protein - spans membrane and is important in helping bind to laminin of ECM

What are some typical qualities of a signal molecule that is recognized by an intracellular receptor?

- hydrophobic - small (not always)

Talk about the curve that is seen when ~preformed actin filament seeds are added~.

- immediate polymerization! ---> there is no time for random aggregation that had to occur to nucleate these (there was already a filament that could be polymerized!) - there is no lag phase!!!

how can drugs cause death of cancer cells?

- impairment of DNA repair pathways independently ---> there are duplicate pathways ------> cancer cells have frequently obtained a mutation in one pathway to add genetic instability ... so just target the other one! - preserves the integrity of non-cancerous cells since they can still undergo repair by the back-up pathway!

programmed cell death (PCD)

- important role in multicellular development ... involved in deleting entire structures, sculpting of tissues, regulating the number of neurons, and balancing cell division within tissues - essential for eliminating damaged cells - regulated by cellular interactions

caspase pathway

- inactive initiator caspases exist as monomers - inactive executioner caspases exist as dimers 1. an apoptotic signal causes adaptor proteins to interact with inactive initiator caspase monomers and cleave each other ... this causes them to dimerize and activate 2. the active caspase cleaves the protease domain of an inactive executioner caspase and activates it 3. active caspase ---> apoptosis

Rb protein

- inhibitor of cell cycle progression - when phosphorylated, has decreased affinity for E2F

What does G α-i do?

- inhibits adenylate cyclase, which causes lowers [cAMP] ... decreases the rate of depolarization between heartbeats (lowers heart rate) - β-γ complex activates K+ channels (causes outward K+ movement) and causes hyperpolarization, which lowers heart rate

What does the structure of a mitochondrion look like?

- inner membrane - outer membrane - matrix - intermembrane space (space between inner and outer membrane)

What does the structure of a chloroplast look like?

- inner membrane - outer membrane - stroma (similar to mitochondrial matrix) - thylakoid space (space inside thylakoids) - thylakoids (little stack thingies ... photosynthesis takes place here)

What do membranes do for cells?

- insulator - prevents change due to changes in pH and salt concentrations - have associated membrane and transmembrane proteins

1. prophase

- interphase is now done and the cell has passed the G2/M checkpoint! - chromosomes become shorter and more compact ... this requires condensin and ATP - two centrosomes (each with a pair of centrioles) move to opposite poles of the cell - cytosolic network of MTs disappears and the mitotic spindle forms - dynamic instability of MTs increases - motor proteins and ATP hydrolysis contribute to separation and migration of centrosomes - increased MT nucleation at the centrosome - MTs are shorter and more dynamic (more catastrophes) - nuclear envelope still intact

How do intermediate filament monomers arrange?

- into dimers that are of opposite orientations (amino terminal ends = away from each other) - tetramers then link end to end ... thus building up one strand of an intermediate filament - 8 strands twist into a rope-like filament

alpha-catenin

- intracellular adaptin protein that binds actin to cadherin - extended/unfolded by myosin II pulling on actin or by the attached cell pulling on the cadherin ---> this reveals a binding site for vinculin which recruits more actin

how do cellular interactions regulate PCD?

- intrinsic pathway ... most cells require signals (trophic factors) to stay alive and will undergo PCD in the absence of these signals ---> also, DNA damage leads to accumulation of p53, triggering transcription of BH3-only proteins (induce cell to enter into apoptosis) - extrinsic pathway ... some cells are triggered to undergo PCD by specific signals/agents ---> "killer" lymphocyte cells that present a death (Fas) ligand

malignant tumor

- invasive (can break adhesive bonds with other cells) - capable of surviving and proliferating in foreign site (metastasize) - can punch through the basal lamina encapsulation

condensins

- involved in shortening DNA - can form a scaffold of interlocking rings around and through which the chromatin is looped

What are the 3 major classes of cell-surface receptor proteins?

- ion-channel-coupled receptors - G-protein-coupled receptors - enzyme-coupled receptors

Where does estradiol bind on a cell? By looking at a molecule of estradiol how can you tell where it binds?

- it binds via intracellular receptor - without the OHs on it, it is completely composed of Cs and Hs, making it hydrophobic ... this means it can diffuse through the membrane

What are two things that can happen as a result of a power stroke?

- it can create tension (if actin is anchored) - it can move the filament (if actin isn't anchored)

What is special about myosin V?

- it has longer legs ... takes bigger steps (than myosin II) - it's a cargo carrier that takes things to the plus end - doesn't need to generate a lot of tension, but moving quickly is important

What is special about the basal lamina?

- it has specialized regions that are involved in healing ---> can guide regeneration ... BL itself has info that the cell knows this is where you have to target (bc nerve and muscle cell attached to it are depositing components into the BL)

How does the acetylcholine receptor work?

- it is ligand-gated channel - the channel has a selectivity for (+) charged ions because there are (-) charged AAs at either end of the pore - can be unoccupied and closed, occupied and open, or occupied and closed (inactivated)

What is special about myosin VI?

- it is minus end directed - cargo carrier that takes things to the minus end

where is checkpoint 1? what happens there?

- it is right after M phase and right before G1 - cells either go into G0 or go onto G1 ... induced by extracellular signaling molecules ... in yeast/unicellular organisms this is based on favorable environment conditions

tell me about tau pls

- it is smaller than MAP2 - when it forms these structures, the bundles are more closely spaced, just based on the size of the binding protein

How is the RBC membrane different than that of regular cells?

- it needs to be able to be squished/deformed - has a meshwork of spectrin associated with membrane via linkages to transmembrane proteins (instead of a cytoskeleton) - in the two monolayers of the plasma membrane in a human RBC, there are different overall electrical charges with negatively charged phospholipids (PS) normally enriched in the inner monolayer

What does Arp 2/3 do?

- it nucleates actin filament polymerization ... provides the scaffolding onto which actin can associate - provides a binding site for assembly of new actin filaments in that branched pattern

How is an electric potential created across a membrane?

- it only takes a slight difference in ion concentration! - if the cell is at a membrane potential of 0 and a few ions move across the membrane, this can be enough to create a -/+ membrane potential

How fast is plus-end addition? Does hydrolysis lag behind or catch up?

- it's fast! - hydrolysis lags behind

How fast is minus-end addition? Does hydrolysis lag behind or catch up?

- it's slow! - hydrolysis catches up

BH123

- its dimerization causes cytochrome c release from the mitochondria - pro-apoptotic (causes cell death) ex: Bax, Bak

What kinesins are plus-end directed (move towards the plus end)?

- kinesin-1 - kinesin-5 - kinesin-13

How do kinesins and dyneins move in a neuron axon?

- kinesins move cargo from the central area of the axon toward the synapse (anterograde fashion) - dyneins move cargo from the synapse to the central area of the axon (retrograde fashion)

What are some typical qualities of a signal molecule that is recognized by a cell-surface receptor protein?

- large - hydrophilic - polar - charged

What is confocal microscopy?

- laser-based method for obtaining fluorescent micrographs of objects in a single focal plane ---> laser focused at a specific point and depth and detects only light emitted from a single focal plane - series of confocal images are combined to create a 3D image - pinhole barrier

where are the DNA damage checkpoints?

- late G1 phase (before DNA replication) --> start (G1/S) transition - late G2 phase (before mitosis) --> G2/M transition - damaged DNA must be repaired before the cell cycle can continue on

What are some molecules that have effects on actin filaments?

- latrunculin - cytochalasin B - phalloidin

gain of function mutations

- less common than loss of function mutations - dominantly expressed - "better" at causing cancer

What are 5 forms of energy relevant to mitochondria/chloroplasts?

- light - chemical energy (ex: bonds in ATP, nutrients like sugars or fats) - mechanical energy (ex: kinetic energy of ATPase) - proton gradient - reducing potential/electron donor

How does differential-inference-contrast (DIC) or phase-contrast microscopy work? (incident white light)

- light passing through an unstained cell changes phase - utilizing the physics of light's existence as a wave to decide what gets transmitted and what gets bounced off - waves out of phase generate contrast when combined

What is a peripheral membrane protein?

- localized to the membrane by non-covalent interactions with integral membrane protein - can be extracted from membrane with high salt/changes in pH

What kinds of fatty acids chains can generate a wider membrane?

- long - straight - saturated - interacting with cholesterol (strengthens long hydrocarbon chains to straighten them)

What are some characteristics of bright-field microscopy?

- looks flat - see some edges and shapes

Think about DNA replication. What could lead to sister chromosome pairing that isn't Smc protein dependent?

- lot of origin sites where the strand starts to unzip and then replication can continue along both strands and you get two mother and daughter pairs ---> DNA is a bowl of spaghetti after this process ------> cohesins make sure they're held together until the cell says go it's time to make this split happen, but how to overcome knot problem? ---------> catenation? what

what does Myc activate?

- lots of G1-cyclin ... G1-Cdk activation ... Rb phosphorylation and inactivation ... increased E2F activity ... G1/S-cyclin and S-cyclin produced ... entry into S phase - SCF turned on ... p27 degradation ... G1/S-Cdk activation ... Rb phosphorylation and inactivation ... increased E2F activity ... G1/S-cyclin and S-cyclin produced ... entry into S phase - increased E2F synthesis increased E2F activity ... G1/S-cyclin and S-cyclin produced ... entry into S phase

intercellular channels

- made up of connexons - can be homotypic or heterotypic

Laminin

- major organizer of basal lamina underlying epithelia - multidomain heterotrimer (alpha, beta, gamma subunits) binds to other laminins, cell surfaces, and other components of basal lamina such as type IV collagen, forming a sheet - can bind to themselves

aggrecan

- major proteoglycan in cartilage - assemble along a hyaluronan molecule to form a huge aggregate - associates noncovalently into sugar backbone of hyaluronan into a branching tree structure

gap junctions

- make cytosol of neighboring cells continuous - have pores that make a size exclusion limit because of their size ... ---> limit = btw 1 and 5 kDs ... no macromolecules but ions, simple sugars, AAs, nucleotides, vitamins, signaling molecules can go thorugh - gap junctions are made up of many individual tiny pores - transmission through pore can be regulated (phosphorylating them can block the pore) ... they aren't just open all the time

What does cofilin do to actin filaments?

- makes them brittle and subject to severing ... creates new minus ends that could depolymerize - it selectively binds to D-actin ("old actin")

extrinsic activation of caspases

- mediated through receptors such as Fas by Fas ligand 1. killer lymphocyte with trimeric Fas ligands binds to trimeric Fas death receptor on the cell 2. FADD begins to be recruited to receptor 3. FADD binds to receptor and recruits caspases by their death effector domain 4. whole complex, once assembled = DISC (holding everything close to each other so they are forced to interact and cleave the small subunit and active the adaptor protein)

What does low cAMP cause melanosomes to do? What happens to the melanophore as a result?

- melanosomes aggregate ---> cell color goes away (cell is translucent)

What does high cAMP cause melanosomes to do? What happens to the melanophore as a result?

- melanosomes disperse ---> gives color to the cell

Why does phospholipid membrane asymmetry matter?

- membrane charge and cell signaling .... - protein kinase C requires PS for activity - PI binds many proteins and is essential for cell signaling - presence of PS on extracellular side of membrane can signal for cell death and promotes phagocytosis

What does an action potential cause in a T-tubule?

- membrane depolarization ---> opening of a voltage-gated Ca2+ channel - binding of Ca2+ to the SR Ca2+ release channel (Ca2+-induced Ca2+ release)

cytokinesis in plant cells

- membrane-bound cell plate (phragmoplast) forms where the metaphase plate had been ---> phragmoplast (made by the Golgi) supplied the PM that will separate the two daughter cells ---> vesicles line up and start to fuse and form the cell plate at the middle of the cell (------> synthesis of a new cell wall between the two daughter cells will also occur at the phragmoplast)

What is oligosaccharyl transferase?

- membrane-bound enzyme on the lumenal side of the ER - catalyzes the transfer of sugars to asparagine of a protein ---> only AAs on the lumenal side become glycosylated

tell me about the kinesin-14 that is found in a mitotic spindle pls

- minus end directed - when anchored on one microtubule, it moves toward the minus end of another microtubule - pulls the spindles together

How do microtubules grow from the gamma-tubulin ring complexes of the centrosome?

- minus ends are toward the gamma-tubulin ring complexes - plus ends are reaching off toward the plasma membrane

mitosis overview

- mitosis equally partitions newly-replicated chromosomes into two daughter cells - mitotic apparatus = specialized, constantly changing microtubule structure that is designed to capture, align, and then separate the duplicated chromosomes - in a rapidly dividing population of animal cells, mitosis takes about an hour (cell is in interphase for the rest of the time) - 5 steps

Why do membranes form in water?

- mixing hydrophobic molecules with H20 disrupts H2O's ability to hydrogen bond with itself ... causes increased free energy - it's energetically favorable for hydrophobic molecules to segregate as much as possible from water and minimize the disruption of water's structure - H20 makes a "cage" and excludes nonpolar molecules ... it is easier for it to form one big cage

What is long term potentiation (LTP)?

- model for learning and memory - glutamate is released by presynaptic neurons and it causes AMPA channels to open, which allows Na+ influx into the postsynaptic neuron (which depolarizes it)

What are qualities of lipid rafts?

- more cholesterol - more saturated hydrocarbon chains - phospholipids with longer hydrocarbon chains - more glycolipids

tell me about dyneins pls

- motor proteins - minus end-directed - associated with microtubules - unrelated to nucleotide switch proteins

tell me about melanosomes pls

- moved by melanophores - specialized compartments that contain pigment ---> move it out to the periphery = cell is colored ---> aggregated back in the center of the cell = cell is translucent

microtubules

- movement of motor proteins against microtubules causes bending force that moves these structures - form structure of flagella and motile cilia - very dynamic, not rigid, not stable --> growing and shrinking depending on the conditions in the cell - microtubules = network along which vesicular trafficking occurs by movement of motor proteins on the microtubules

fibronectin

- multidomain glycoprotein binds other components of ECM as well as cell surface integrins - each subunit has modular binding domains with many splice variants ---> 2 subunits form a heterodimer (two strands might have different splice variants on them) - binding sites for growth factors, can help establish gradients ---> helpful for fixing a gradient in space so cells can then respond to it ---> useful for helping cell surface interact with the rest of the ECM - help transduce mechanical pull from outside to inside the cell so that it can pull itself along by interacting with the integrins - can exist in soluble/fibrilar form

claudin

- multipass transmembrane tight-junction protein - mostly structural, important in driving assembly of tight junction in the first place

occludin

- multipass transmembrane tight-junction protein - occludes small molecule passage/renders the junction impermeable

What are the components of myosin II?

- myosin heavy chain - myosin light chain - coiled-coil of 2 helices

How does Ca2+ cause muscle contraction?

- myosin on the binding sites on actin filaments is covered by tropomyosin - Ca2+-sensitive troponin is attached to each tropomyosin molecule - when Ca2+ rushes into the cell, it binds to troponin, which moves tropomyosin off the binding sites

What can be assessed with an optical trap assay?

- myosin step length - how far the myosin head is moving the actin - could determine that myosin really WAS moving on the actin and also the step length (which turns out not to be the same for every myosin)

What are the components of the basal lamina?

- nidogen - perlecan - laminin - type IV collagen - integrin

What happens when there is low tension sensed by the tension sensor at the kinetochore?

- no capture means there is no tension ... ---> allows Aurora-B kinase to be very close to proteins that are interacting with the microtubule ------> can phosphorylate them ... it decreases the affinity for microtubule and then they might pop off of the kinetochore

What are the benefits of having myelin sheaths insulating the axon?

- no current leaking - lots of K+ entry in between the nodes that then has to passively flow to the next node to activate the next gate of VG Na+ channels - charges are able to flow more readily - energetically more favorable for APs to be means of propagation (Na+ exchange is only happening at the nodes and not all over the place)

Why are differentiated blood cells the perfect eukaryotic model for studying plasma membrane proteins?

- no membrane bound organelles - everything you get back from this process is plasma membrane associated

Talk about the curve that is seen when ~no preformed actin filament seeds are added~.

- not much is going on until there is an aggregate that can nucleate a filament (it takes a while before actin filament polymerization occurs) - nucleation occurring during a "lag phase" in filament polymerization - after nucleation, the filament rapidly polymerizes and does so until, as it polymerizes, there are fewer and fewer G-actin subunits left in the solution - reaches "critical concentration" at some point

2. prometaphase

- nuclear envelope disintegrates (phosphorylation of lamins leads to disintegration of nuclear membrane and nuclear pores) - kinetochore appears on each chromatid - kinetochore MTs attach to the kinetochores (+ end directly attaches to kinetochore laterally and MT slides until + end attaches to kinteochore end on) - newly condensed and attached chromosomes congress and exhibit saltatory behavior

tell me about formin pls

- nucleates assembly and remains associated with the growing plus end - nucleating formation of straight actin filaments

tell me about gamma-TuRC pls

- nucleates assembly and remains associated with the minus end - allows assembly of the microtubule

tell me about Arp 2/3 complex pls

- nucleates assembly to form a web and remains associated with the minus end - creates branched structures by nucleating new filaments

What organelles have genomes?

- nucleus - mitochondria - chloroplast

How does dark field microscopy work? (oblique incident light)

- oblique light only enters the objective if it is scattered by the cell - only see light that is being reflected off of something in the sample - dark background with a bright image is produced

What are unstable conformations of chromosome capture?

- one spindle attaches on one side - one spindle attaches on two sides - two spindles attach on one side all of these scenarios are unstable because they don't create the tension needed!!!

What are some possible therapies for cystic fibrosis (CF)?

- osmotic therapies (replacing ions to increase osmotic pressure outside of the cells) - gene therapy (expressing the wild type of CFTR)

Immoglobulin (Ig) Superfamily Proteins

- other (non-cadherin or integrin) adhesion protein - structural homology with antibodies - involved in cell sorting interactions ... when missing only subtle deficits (not like with cadherins) - Neural Cell Adhesion Molecules (NCAM) --> homophilic (interacts with another NCAM) - Intercellular Cell Adhesion Molecules (ICAM) --> heterophilic, recognizes integrins

selectins

- other (non-cadherin or integrin) adhesion protein - transient binding of motile cells ---> motile cell can express selectin or another cell can have it and come grab it - lectin domain recognizes a particular oligosaccharide - heterophilic

what happens when Ras/Myc are overactivated?

- overproliferation of cells - can cause cancer! - in most normal cells (non-cancer cells) , overactivation of Ras/Myc can cause cell cycle arrest and/or undergo apoptosis

What is the difference between paracrine signaling and contact-dependent signaling?

- paracrine = involves SECRETION of a signaling mediator that acts locally - contact-dependent = direct interaction of membrane proteins on opposite cells

How is a new MTOC generated?

- part of the cell somehow is separated from the rest of the cell ... - within that part of the cell, there are organizing proteins (maybe even motor proteins) that can create a new MTOC - the microtubules project out towards the cell periphery from the new MTOC

What are some lipids that mitochondria can synthesize?

- phosphatidic acid - phosphatidylethanolamine - phophatidylglycerol - cardiolipin

What are the 4 kinds of phosphoglyceride?

- phosphatidylcholine (PC) - phosphatidylserine (PS) - phosphatidylethanolamine (PE) - phosphatidylinositol (PI)

What are the 2 kinds of phospholipid?

- phosphoglycerides - sphingomyelin

What are the 3 components of a membrane?

- phospholipids - glycolipids - cholesterol (only in animal membranes)

how does M-cyclin/Cdk phosphorylation of the APC set up a negative feedback loop?

- phosphorylates APC, which allows Cdc20 to bind - Cdc20 binding activates the APC - active APC degrades M-cyclin

What does cytoplasmic tyrosine kinase do?

- phosphorylates tyrosines - activates Rho-GEF which activates RhoA (-GDP --> -GTP)

how can a fully active Cdk be deactivated?

- phosphorylation by Wee1 kinase at the inhibitory phosphorylation site - up-regulation of CKIs like p27

What causes the lamins to disassemble and the nuclear envelope to break down? When does this happen?

- phosphorylation of lamins causes this - this happens when the cell is preparing to divide

List at least 3 characteristics of modern mitochondria and chloroplasts that are consistent with the endosymbiotic hypothesis regarding their origins.

- photoreaction centers in bacteria are similar to those in photoreaction centers of eukaryotic cells - assembly process for insertion of porins into the outer membrane is similar in bacteria and in mitochondria - mitochondrial and chloroplastic gene sequences are more similar to bacterial gene sequences than to nuclear genome sequences - certain bactericides that stop protein synthesis in bacteria also do the same in mitochondria and chloroplasts (but not in ribosomes in the cytosol of eukaryotic cells)

What is the purpose of the signal-sequence binding pocket on the SRP?

- portion of the molecule that's going to bind to the signal peptide of the protein ... causes translocation to pause and association of the ribosome to a SRP receptor on the ER membrane - has a lot of Met residues (unbranched, largely hydrophobic AAs)

thymosin

- prevents polymerization and promotes instability - regulated by phosphorylation - actin-binding protein - when it is actin, it can bind free-actin and sequester it, preventing its assembly into filaments - negative effects on filament growth because it binds up all the free actin

How do kinesins move along microtubules?

- processively, step by step along the microtubule - when bound to the microtubule, the head is bound to an ATP - nucleotide exchange triggers the neck linker to zipper on to the catalytic core ---> this brings the second head forward

tell me about interpolar microtubles pls

- project out from one spindle and interact with microtubules from another spindle

tell me about astral microtubules pls

- project out towards the plasma membrane - have an important role in anchoring the spindle and later reeling it in to that end of the cell

tell me about kinetochore microtubules pls

- project up and eventually capture the chromosomes - dynamic instability is important here ... side/end capture of chromosomes at the kinetochore as they are growing/shrinking relies on it

profilin

- promote polymerization when it binds actin subunits and causes filament assembly - regulated by phosphorylation

What are the functions of membrane carbohydrates?

- protection from harsh extracellular conditions - cell to cell recognition events (based on identity of their glycolipids and sugars)

What are 4 common ways in which membrane protein diffusion is restricted?

- protein self-aggregation - binding of protein to molecules in the extracellular matrix - binding of proteins to intracellular molecules (Ex: cytoskeleton) - binding of proteins to molecules on other cells (ex: tight junctions)

How can membrane protein and lipid composition influence the curvature of the membrane?

- protein with hydrophobic domain inserted into only one side of the membrane (ex: amphipathic helix) - curved protein complexes can bind to lipid head groups/other proteins - lipids with larger head groups (ex: PI) inserted into only one side of the membrane

How does assembly of a signaling complex on phosphoinositide docking sites work?

- proteins are inactive and unable to bind to the specific PIs in the plasma membrane - signal molecule binds to the receptor activates a kinase that can create a different kind of PI (adds another P on) ... this species of PI can now recruit the proteins and allow them to be associated with the PM ... downstream signals

What are soluble proteins?

- proteins destined for lumen of ER, golgi, lysosomes or secretion - synthesized with N-terminal SS that is later clipped off - paperclip inserting of SS (+ end of SS orients towards cytosol ... allows cleavage by signal peptidase)

What is the difference between a proteoglycan and a glycoprotein?

- proteoglycan = mostly sugar, found in the ECM - glycoprotein = mostly protein, found on the surface of cells - both = made in golgi and ER (hyaluronan is the exception because it has no protein so it isn't made here!)

what kinds of mutations cause cancer?

- proto-oncogenes --> oncogenes [ex: ras or myc] (activation of genes responsible for cell division and growth) - inactivation of tumor-suppressor genes (genes that normally suppress/restrict growth and proliferation) [ex: Rb, p53]

What happens in bacteria in aerobic conditions?

- proton gradient drives ATP synthesis - proton gradient drives uptake of several molecules and export of Na2+ (cotransport bringing H+ and lactose/lysine/succinate/proline into the cell and antiport taking Na+ out and bringing H+ in) - electron transport chain generates the proton gradient (pumps protons out and produces the gradient)

kinetechore generated forces

- pull of MTs attached to kinetochore pulls the chromatids apart ---> they are already kind of pulling apart, but cohesins keep them from fully doing so

what are three kinds of non-dividing cell?

- quiescent (waiting to cycle) - senescent (dying) - differentiated (exited cycle entirely)

How does COP1 coat dissociation work?

- rapid dissociation - ARF GAP (inactive)

How does clathrin coat dissociation work?

- rapid dissociation ... naked vesicle - phosphoinositide phosphatase removes phosphate group from PI - Hsp 70 might be involved as a chaperone protein

How does a G-protein-coupled receptor work?

- receptor (7 TMS) and G-protein are inactive (receptors are coupled to heterotrimeric G-proteins - signal molecule attaches to receptor and causes it to activate and join with the G-protein to activate it as well ... this complex can now activate/suppress effector proteins - enzyme is activated idk about this order and how this works exactly tbh i'm kinda confused

How does receptor sequestration work?

- receptor and signal molecule endocytosed - ligand is dissociated in the endocome so the signal is shut off

How does an enzyme-coupled receptor work?

- receptors have catalytic domains on the cytosolic side - intracellular domain = Tyrosine-Kinase ... can catalyze a transfer of a phosphate group onto a Tyrosine residue of a protein - receptor tyrosine kinase (RTK) - big class of these = growth receptors

What could cause the cessation of the movement of proteins from the stroma to the thylakoid space?

- reduced ATP synthesis - destruction of the proton gradient (ex: by an uncoupler)

What are some benefits of confocal microscopy?

- reduced background by fluorescence activation only in the focal - 3D reconstruction of structures from stacks of images (BUT ... data files are large and hard to process) - protection from photobleaching of molecules outside the focal plane

What does IRE1 do in the UPR?

- reduces amount of proteins entering the ER - increases the production of chaperones - activates mRNA splicing enzyme ---> intron is excised in the cytosol, not the nucleus (WEIRD!!!)

What does PERK do in the UPR?

- reduces amount of proteins entering the ER - makes more chaperones

What happens when PKA is activated? How does it get activated?

- regulatory subunits suppress the activity of the catalytic subunit when it is inactive - when cAMP binds, this allows dissociation of the catalytic subunits - catalytic subunits become active and phosphorylate their targets

tell me about +TIPs pls

- remain associated with growing plus ends and can link them to other structures such as membranes - might bind a protein of the plasma membrane and anchor the microtubule

What are some special qualities of beta-barrels?

- rigid, can't undergo conformational changes like alpha-helices - generally restricted to outer membranes of mitochondria, chloroplasts, and bacteria - center of barrel can open and allow for the passage of hydrophilic molecules

How does a safranin and fast green stain work?

- safranin binds xylem - fast green binds cellulose

endocrine signaling

- secreted molecules diffuse into the bloodstream and trigger responses in target cells anywhere in the body - most long-distance signaling - moves through bloodstream to a distant target cell where it can bind a cell-surface receptor

paracrine signaling

- secreted molecules diffuse locally and trigger a response in neighboring cells - signaling over a short distance - secretes an extracellular signaling molecule to a neighboring cell

autocrine signaling

- secreted molecules diffuse locally and trigger a response in the cells that secrete them - secreted molecule acting on the same cell that it came from

What are some other (non-cadherin or integrin) adhesion proteins?

- selectins - immunoglobulin superfamily proteins

What is the purpose of the selectivity filter in the K+ leak channel? How does it work/why don't other positively charged ions also pass through?

- selective for K+ and not Na+ - selectivity filters are oriented to the negative end of the helix is pointing into the central vestibule ---> oxygen molecules that are facing into the central canal allow K+ to energetically ditch its water shell, but the oxygens are placed a bit too far apart for the Na+ with its H2O shell to be able to interact in the same way ... Na+ can't ditch its shell and is therefore too large to pass through the pore

tell me about stathmin pls

- sequesters tubulin dimers - binds up free dimers, decreases concentration, this suppresses the rate of polymerizing of the microtubule - because the microtubule isn't polymerizing, it is less likely to have a GTP cap and is more likely to undergo catastrophe - interferes with gamma-TuRC (by binding up all of the free tubulin and preventing polymerization)

tell me about gelsolin pls

- severs filaments and binds to plus end - directly cleaves up actin

What AFT6 do in the UPR?

- shuttled to golgi, protease there clips of its extracellular domain - makes more chaperones

How does signaling by GTP binding work?

- signal comes in ... GTP binding occurs and GDP gets kicked off and replaced by GTP ... protein (+ GTP) gets turned on ... signal goes out - signal goes out ... GTP hydrolysis occurs and a P is taken off ... protein (+ GDP) is turned off ... signal comes in and the cycle starts all over again

How does signaling by phosphorylation work?

- signal comes in ... protein kinase turns ATP into ADP by removing a P and adding it onto the Ser/Thr/Tyr of a protein ... this causes the protein (+ P) to be turned on ... signal goes out - signal goes out ... protein phosphatase takes P off of the protein and causes it to be turned off ... signal comes in and the cycle starts all over again *** some proteins can be turned off by phosphorylation too; and some just have their structure/function altered

Why do proteins produced in the absence of microsomes appear larger?

- signal sequences! ---> glycosylation ---> GPI anchors ---> SS cleavage

How does assembly of a signaling complex on an activated receptor work?

- signaling proteins are not associated with the receptor and are inactive without a signal molecule bound to the receptor - once signal molecule is bound to receptor, phosphotyrosines are created that act as sites of recruitment for proteins that are now associated with the receptor ... downstream signals

What is α-actinin?

- similar protein to fimbrin, but it is much longer, spaced further apart so myosin can fit in there and move toward the plus end and provide some contractile force - loose packing allows myosin II to enter bundle

What are the 2 classes of transmembrane proteins?

- single pass - multi-pass

3. metaphase

- sister chromatids line up along the equator (metaphase plate) - kinetochore MTs and asters are fully formed and ready to be pulled apart - P (poleward) and AP (away from pole) saltatory forces result in chromosome oscillations ... but the forces are smaller than in prometaphase - multiple mechanisms contribute to the lining up of chromosomes at metaphase plate: coupling of MT dynamics and MT motors keep chromosomes positioned at the equator ... these forces include: ---> 1. kinetochore generated ---> 2. MT flux ---> 3. polar ejection

4. anaphase

- sister chromatids suddenly separate and each moves to its respective pole dragging its attached chromatid behind it - anaphase A: ---> kinteochore MTs shorten ------> depolym at + ends ------> MT flux-like movement but without + end polym - anaphase B: ---> spindle elongates and the two poles move further apart ---> requires motor proteins like the ones required to establish the first bipolar spindle (the motor proteins are no longer being held in check and will push the spindles apart) ------> PM astral MT dyneins ------> interpolar MT kinesins

What drives passive transport across a membrane?

- solutes move in the direction that leads to a decrease in free energy - uncharged solutes moving based on a chemical concentration gradient - charged solutes moving based on an electrochemical gradient, affected by concentration gradient of solute and membrane potential

What contributes to cell-cell signaling?

- some ECM components bind diffusible signaling molecules and "regulate" the diffusion and distribution of the signals - some ECM components can directly trigger intracellular signal transduction cascades and changes in cell behavior (sensor for physical and chemical components) ---> ex: integrins molecules in the PM that then are actually bound physically to the ECM ... can transduce pull/sheer force to the inside of a cell and will eventually upregulate actin polymerization so it has more tensile strength in response to a pull

What is an integral membrane protein?

- spans all/part of the membrane or has a covalent attachment to a lipid group in the membrane - can't be extracted from membrane by high salt/changes in pH - transmembrane proteins fall into this category

Basal lamina

- specialized ECM - extracellular architectural component of epithelia - surrounds muscle, fat, and Schwann cells - 40-120nm thick - barrier, mechanical, and filtration roles ---> physical barrier ... can keep cells contained within it inside and prevent others from getting inside ---> has a lot of tensile strength ... mechanical resistance and reinforcement of the cytoskeleton ---> filtration role in the kidney

how does proteolysis of cyclins occur?

- specific E3 liagases - ubiquitination of proteins - destruction in proteasomes

tell me about XMAP215 pls

- stabilizes the microtubule and prevents catastrophe - technically, it's a "rescue factor"

How does an H&E stain work?

- stands for Hematoxylin and Eosin stain - hematoxylin binds acidic molecules - eosin binds basic molecules

What does a GEF do?

- stimulates exchange of GDP for GTP - causes G protein to open its nucleotide binding pocket, GDP diffuses out, GTP diffuses in

What is good about the rope-like organization of intermediate filaments?

- stretchable - resistant to being pulled/pried apart - if they are anchored to anchoring points of cells with other cells or with the extracellular matrix, they provide great resistance to cells being pulled apart from each other

apoptosis

- strict cellular control mechanism - cell shrinkage - DNA condensation - DNA fragmentation - membrane-bound apoptotic bodies - no release of intracellular contents - PS flipping ---> recognition of surface PS on a apoptotic cell (fragments) prevents inflammation - laddering seen on gel (endonuclease cuts in spaces between nucleosomes)

extracellular matrix (ECM)

- structural elements of cytoskeleton can interact with these structures - secreted and created by cells - highly structured - used as a scaffold by some molecules

important functions of ECM in animals

- structural integrity/strength in tissue - integration of cells into tissue and/or cell movement - cell-cell signaling

Why does the proton ionophore dinitrophenol inhibit mitochondrial protein import?

- suppresses ATP synthesis (ATP is required for chaperones in the mitochondrial import process) - is dissipates the proton gradient across the mitochondrial membrane that would normally attract positive charges on the mitochondrial targeting sequence toward the matrix

How does a classic light microscope work?

- targets light so it will hit your retina and be in focus ---> works via a series of lenses that channel the light into your eye - objective magnifies the image - condenser focuses the light and makes it brighter and more targeted

What are the 3 microtubule-interfering molecules?

- taxol (paclitaxel) - nocodazole - colchicine

phosphorylation of APC "by M-cyclin/Cdk"

- technically M-Cdk phosphorylates other proteins that lead to activation of APC - phosphorylation of APC allows it to bind to Cdc20, which leads to activation of separase and proteolysis of cohesins

What things determine the point at which CMC transitions?

- temperature - pH - amount of salt in solution

What are the two factors that contribute to the structural integrity of the ECM?

- tensile strength - compression resistance

What happens when there is high tension sensed by the tension sensor at the kinetochore?

- tension stretches the kinetochore away from Aurora-B kinase ---> no longer phosphorylates those regulatory proteins

How does a Phe deletion impact CFTR?

- the Phe that gets deleted is close to the ATP binding domain ... now the cell can't use ATP to drive and pump Cl- out of the membrane and a sticky and thick mucus forms ---> Cl- stays in the cells and this increases Na+ transport into the cells ... this causes H2O to be pulled into cells and increases the viscosity of the mucus on the surface

What happens at checkpoint 2 (G2-M phase checkpoint)?

- the cell has already undergone all of its replication - checking if conditions are still favorable and also checking to see that all the DNA was replicated and there were no errors in the replication

What is the main advantage to using GFP tagging as opposed to antibody staining?

- the cell remains alive!!! ---> you can look at how it behaves in real time ------> ex: GFP-fusion proteins can be used to track the movement of proteins over time

What is critical concentration (Cc)?

- the concentration of monomers at steady state = Cc - rate of polymerization exactly equals the rate of depolymerization ---> no change in net length - subunits are added and removed at the same rate ---> this is called "treadmilling"

Why are sarcomeres special and quickly able to pass along action potentials?

- the extracellular fluid is very nearby every part of the cell ---> changes that occur in response to an AP are very rapidly transmitted to every part of the cell because of the structure of the T-tubules

What happens when no Ca2+ is bound to the hinge region of a cadherin?

- the hinge region is floppy - this decreases adhesive strength because the terminal domains are less able to interlock amongst that space

What happens when Ca2+ is bound to the hinge region of a cadherin?

- the hinge region is taught - terminal regions closer to each other! more adhesion

How do aquaporins prevent H+ from passing through and allow H2O to flow thorough?

- the polar face of the aquaporin has a bunch of oxygen molecules that cause an interaction with the dipoles on Hs of the water as it is traveling through - Asn residues can interact with both of the dipoles on both of the H atoms on the water molecule ... extra dipole force that H+ could use will stop at this point

How do kinesins and dyneins move in a neuron dendrite?

- there can antiparallel arrangement of microtubules in dendrites! ---> kinesins and dyneins could be moving both ways

What do DAG and IP3 both do?

- they are both second messengers - they are both involved in the activation of protein kinase C

How do the channels in the hair cells of the cochlea work?

- they are mechanically-gated channels - when sound comes into the ear, the basilar membrane is vibrated and this causes the channel to be ripped open and ions to be able to low through - the fluid of the inner ear is K+ rich (channel is cation-selective ... K+ and Ca2+)

What is a palmitoyl anchor and where is it found on a protein?

- thioester linkage between cysteine and palmitic group ---> can be anywhere on the whole length of the protein as long as a cysteine residue exists there

What is a farnesyl anchor and where is it found on oa protein?

- thioester linkage between cysteine and prenyl group ---> c terminal end of protein ---> have to have a cysteine to make the link ---> cysteine 3-4 AAs from the c-terminal end

E2F

- transcription factor - when released from Rb, can drive transcription of G1/S and S cyclins

How does cell-free translation without microsomes work?

- translation occurs before microsomes are added ... no proteins in microsomes - bunch of free soluble proteins

How does cell-free translation with microsomes work?

- translation occurs with microsomes ... proteins are found inside the microsomes - proteins appear larger

What happens when troponin C binds Ca2+?

- tropomyosin normally blocks myosin from interacting with actin ... ---> it moves when Ca2+ is present, and now allows myosins to get in there, get to actin, and cause power strokes

microtubule flux force

- tubulin moves poleward (away from the chromosome) - doesn't contribute to MT shortening because growing and shrinking at same rate but provides a treadmill pull outwards

spindle attachment/metaphase-anaphase checkpoint

- unattached kinetochores release a signal that blocks APC ... this signal appears mediated through MAD2, which is localized to proteins that have not yet attached to spindle MTs - non-spindle attached kinetochores convert MAD2 to a Cdc20 inhibitor ... APC remains active ... chromatids can't be separated

How do actin-filament-binding cap proteins alter filament dynamics?

- uncapped population of filaments = growth at plus and minus ends - capped population of filaments = growth at minus end only! (no plus end polymerization)

what is cancer?

- unregulated cell division ... cells divide in the absence of growth signals, and are not inhibited by normal system checks - usually arises from a single abnormal proliferating cell that creates a primary tumor

In the example of the solubilization of the Na+/K+ pump, how do you differentiate between inward and outward facing proteins?

- use antibodies selected for one of the faces ("affinity selection") - tag antibody with a fluorescence molecule and use all sorter to direct which colors go into which buckets

Brd-U labeling

- used for DNA - Brd-U is a T analog (used in the place of T in DNA)

intrinsic activation of caspases

- usually involves release of cytochrome C from mitochondria, leading to activation of Apaf-1 1. apoptotic stimulus causes mitochondria to release cytochrome C from the mitochondria 2. cytochrome C interacts with Apaf-1 (now = CARD) and self-assembles into a heptomeric apopotosome (7 CARDs) 3. CARD domain wants to interact with procaspases ... causes them to come into contact with each other and causes autoproteolysis and activation 4. executioner caspases are activated

How are most lipids delivered to other organelles in the cell? What happens in organelles that don't use this mechanism?

- vesicular transport - lipids delivered by phospholipid exchange proteins (deliver each lipid individually)

How do we know where cells are in the cycle?

- visually - Brd-U labeling and flow-cytometry

What are some examples of gated channel proteins?

- voltage gated - ligand gated - mechanically gated

What do mutations in the intermediate filament network cause?

- weakens the cell layer - ex: in caratin ... causes lesions of the skin layer in this case

What are consequences of taking an uncoupling drug?

- weight loss and heat-related liver damage

tel me about nebulin pls

- when actin filaments assembly, they assembly on the nebulin ... the actin filament will become the same size as nebulin ---> depending on the length of the nebulin molecule, the length of actin is set

catenation

- where adjacent replication forks meet during replication: DNA strands wind up looped/crossed at each site. this is resolved during S phase and G2 to prevent M phase segregation errors. - issue of catenation needs to be solved chromatid A and chromatid B are separated from each other

What is the issue with fluorescence/indirect immunohistochemistry microscopy?

- white light from the sun can bleach the fluorescent molecules so you need to take the picture right away!! - molecules get stuck in a higher energy state break (stop fluorescing permanently)

What does a G protein look like?

- α domain = GTPase switch/Ras domain and G-protein/GTPase domain (? i didn't understand how he explained this?) - β and γ domain stay together as a pair, but can be dissociated from α - two lipid anchors (one on α and one on γ)

Do kinesins rely on nucleotide switch proteins to function?

yes

is hyaluronan a GAG?

yes

Can ~JAK~ create binding sites for proteins with SH2 or PTB domains?

yes ... tyrosine kinase!!!

Do misfolded proteins ever leave the ER? If so, how?

yes! through a translocon ... they are translocated out (as opposed to being trafficked in vesicles)

Does a bacterial ATP synthase work both ways?

yes!!

Can a proton gradient drive things other than ATP synthesis?

yes!!!

In the example of the solubilization of the Na+/K+ pump, why do you add phospholipids mixed with detergent as a step?

you want to see how the protein functions, so you want it to exist as a vesicle in this case

How often do lipids flip-flop?

~ 1 time/month

What is the resolution of TEM?

~ 10 A

How long is a typical beta strand?

~ 10 AAs

How fast do lipids move through a membrane?

~ 2 μm/second

What is the diameter of a typical eukaryotic cell?

~ 20 nm

How many carbons are in CO2?

1 carbons

How many heads does myosin I have?

1 head

How does the Ca2+ ATPase work?

1. 2 H+ leave and 2 CA2+ enter the transporter from the cytosol 2. ATP hydrolyzed 3. 2 Ca2+ leave and 2H+ enter the transporter from the lumen of the sarcoplasmic reticulum 4. resphosphorylation

How does the creation of an action potential and contraction happen in a skeletal muscle cell?

1. Ach binds to Ach receptor 2. ligand gated ion channel 3. channel opens and Na+ ions flood inside the cell 4. action potential 5. contraction

what happens when there are high levels of Ras/Myc?

1. Arf is activated 2. Arf binds Mdm2-inactive p53 and inactivates it 3. p53 is released 4. active p53 causes cell-cycle arrest or apoptosis (BH3-only proteins are made (Puma and Noxa))

order of Bcl2 family proteins

1. BH3-only 2. Bcl2 (BH 1-4) 3. BH123

Order of components of the intrinsic apoptosis pathway?

1. Bcl2-family proteins 2. cytochrome c 3. apoptosome 4. caspase cascade

What are the steps of ATP synthesis in the mitochondria?

1. H+ are pumped from the matrix out into the intermembrane space 2. H+ return into the matrix through an ATP synthase, producing ATP in the matrix

What are the steps of ATP synthesis in the chloroplast?

1. H+ are pumped from the stroma into the thylakoid space 2. H+ return into the stroma through an ATP synthase, producing ATP in the stroma

how is entry into M-phase regulated (G2-M checkpoint)?

1. M-cyclin joins with Cdk to make inactive M-Cdk 2. CAK adds an activating phosphate to M-Cdk and Wee1 adds an inhibitory phosphate at the same time ... M-Cdk is still inactive, but is now phosphorylated 3. Cdc25 (has to be phosphorylated to be active) removes the inhibitory phosphate ... M-Cdk is now active 4. active M-Cdk phosphorylates more Cdc25 and also inhibits Wee1 (positive feedback)

How does the spindle assemble (steps)?

1. MT nucleation near chromosomes ... condensed chromatin is locally driving this process (binds and accumulates a GEF which activates a Ran-GTPase that selectively cleaves protein complexes to release MT stabilizing proteins) 2. assembly of antiparallel MT bundles (driven by kinesin-5, which crosslinks between 2 MTs in opposite polar orientation (+/- opposing)) 3. pushing minus MT ends away from the chromosomes (outward) (kinesin-4 and kinesin-10) 4. gathering minus ends (dynein and kinesin-14 pull the minus ends together toward the spindle poles) 5. ready to interact with the centrioles

What happens to the PI-3-kinase-Akt signaling pathway with growth factor?

1. Rheb-GAP activates PI-3-kinase 2. active PI-3-kinase activates Akt 3. active Akt inactivates Rheb-GAP 4. active Rheb (Rheb-GTP) activates mTOR 5. active mTOR stimulates cell growth

What does the activation of a G protein cause?

1. activated G α-s stimulates adenyl cyclase to make cAMP from ATP 2. cAMP activates PKA 3. PKA activates CREB 4. CREB-binding protein (CBP) binds to CREB and the cyclic AMP response element (CRE) 5. gene transcription is increased

Bcl2 (BH 1-4) pathway

1. active Bcl2 (BH 1-4) protein inactivates effector

What happens to the PI-3-kinase-Akt signaling pathway without growth factor?

1. active Tsc 2 (this is a Rheb-GAP) 2. active Rheb-GAP inactivates Rheb (Rheb-GDP) MTOP is inactive ... so no cell growth!!!!

BH3-only pathway

1. apopototic stimulus activates BH3-only protein ... 2. BH3-only protein inactivates Bcl2 (BH 1-4) protein and activates BH123 protein 3. cytochrome C and other mitochondrial proteins are released from the mitochondrial intermembrane space

BH123 pathway

1. apoptotic stimulus activates BH123 protein and causes it to aggregate 2. cytochrome C and other mitochondrial proteins are released from the mitochondrial intermembrane space

How does a "ball and chain" model of a voltage-gated channel work?

1. channel is closed 2. inside of the membrane is depolarized (made more +) 3. channel opens 4. since the NH2 "ball" is slightly negatively charged, and the inner surface of the membrane now has a positive charge, the "ball" enters into the channel and blocks it 5. channel is inactivated 6. membrane repolarizes (inside gets negative again) 7. "ball" dissociates and opens up the inner pore again 8. channel is now closed again, but able to be activated

How does APC/C regulation prevent progression into anaphase?

1. cohesin is the only thing still linking the chromosomes together at this point 2. Cdc20 activates APC/C 3. active APC/C-Cdc20 complex acts as polyubiquitin ligase and targets securin-inactive separase complex 4. securin gets degraded and now separase is active 5. separase targest the Scc subunit on cohesin 6. the chromosomes can no longer withstand the pulling forces of the mitotic spindle and pull apart

How do you run an SDS-PAGE?

1. denature proteins 2. load into gel wells 3. run electrical current through 4. proteins get separated by mass (larger molecules move slower)

How are tissues prepared for microscopy?

1. fixation with formaldehyde cross-links adjacent proteins so everything int he cell will stay in the same place 2. microtome is used to section tissue into small (1 μm) slices

How does a protein get to the inner mitochondrial membrane without using TIM23?

1. goes in from cytosol through TOM 2. ends up in intermembrane space 3. inserted into the membrane by TIM22

How does a protein get to the outer mitochondrial membrane?

1. goes in from cytosol through TOM 2. enters intermembrane space 3. inserted into the outer membrane by SAM

How does a protein get to the inner mitochondrial membrane?

1. goes in from cytosol through TOM 2. goes partially through TIM23 3. released laterally 4. becomes a protein of the inner mitochondrial membrane

How does a protein get to the mitochondrial matrix?

1. goes in from cytosol through TOM 2. goes through TIM23 3. enters into the matrix where it can then fold up

What does the path to the inner membrane through TOM and TIM23 look like?

1. goes through TOM into intermembrane space 2. goes through TIM23 and stops at stop transfer sequence 3. TIM23 releases protein into the inner membrane

What does the path to the matrix via TOM and TIM23 look like?

1. goes through TOM into intermembrane space 2. goes through TIM23 into matrix 3. signal sequence is cleaved off 4. protein folds up

What does the path to the outer membrane via TOM and SAM look like?

1. goes through TOM into intermembrane space 2. insertion into outer membrane by SAM

What does the path to the inner membrane through TOM and TIM22 look like?

1. goes through TOM into the intermembrane space 2. goes through TIM22 and gets inserted into inner membrane

survival factor pathway

1. growth factor binds to RTK receptor 2. receptor is activated 3. PI3-kinase is activated 4. PIP3 5. PDK1 and Akt joins with PIP3 6. active Akt phosphorylates Bad-inactive apoptosis inhibitory protein 7. Bad is inactive, so it can no longer cause apoptosis and apoptosis inhibitory protein is released from Bad-inactive apoptosis inhibitory protein complex, and is active 8. apoptosis is inhibited

growth factor pathway

1. growth factor binds to RTK receptor 2. receptor is activated 3. PI3-kinase is activated 4. PIP3 5. PIP3 activates TOR 6. gene regulatory factors are made 7. ribosome synthesis 8. protein synthesis and cell growth

How does transducin (Gt) work?

1. high [cGMP] in the dark activates cGMP-gated cation channels (opens them) 2. Na2+ rushes into the channels and the cell is depolarized 3. light activates the GPCR rhodopsin 4. rhodopsin activates Gt 5. Gt activates a cGMP phosphodiesterase 6. cation channels close 7. cell is hyperpolarized (shuts down secretion by the cell)

Name 5 signaling molecules that are secreted by one cell and act on another. Indicate whether they act on cell surface or intracellular receptors.

1. insulin --> it's a protein, so cell-surface receptor 2. estrogen (estradiol) --> intracellular receptor 3. acetylcholine --> cell-surface receptor 4. epinephrine --> cell-surface receptor (... acts on a GPCR that is coupled to G α-s ... activates cyclase ... activates PKA) 5. cortisol --> intracellular receptor 6. testosterone --> intracellular receptor 7. platelet derived growth factor --> cell-surface receptor 8. TGF(β) --> cell-surface receptor

What are the steps involved in the deliverance of misfolded proteins to the proteasome?

1. lectin binds to glucoses 2. protein targeted to translocator complex 3. ubiquitin is added onto the protein chain, AAA-ATPase pulls the protein through, N-glycanase deglycosylates the protein, ATP is hydrolyzed to ADP 4. more ubiquitins added onto the protein, forming a polyubiquitin chain 5. protein taken to proteasome and chewed up

Name 5 things that can turn off the Gs signaling pathway.

1. ligand degradation 2. GPCR kinases that can phosphorylate the receptor and recruit arrestin (it blocks interaction with the G-α subunit or can even lead to endocytosis and degradation of the receptor) 3. G-α ATPase activity will eventually hydrolyze the GTP and turn it off ... RGS will stimulate this 4. second messenger could be degraded by a cAMP phosphodiesterase 5. PKA phosphorylates its targets ... the phosphate that connects CBP and CRE (?) could be removed by a phosphatase

What are the steps of photosynthesis?

1. light hits photoreaction center and excites it so much that it is ionized and gives up an electron 2. this photoreaction center is so ionized that it can strip electrons from H2O and produced O2 as a byproduct 3. the electron is transferred through an ETC that allows pumping of protons into the thylakoid space 4. another photoreaction center is being excited by light while this is going on which allows transfer of another electron to an electron carrier (forming NADPH) 5. proton gradient is driving ATP synthesis 6. chemical energy of ATP and redox potential of NADPH are involved in carbon fixation (C from CO2 used to make sugars) idk about the order of these steps but ya :) <3

What are the steps of an action potential?

1. membrane gets depolarized and VG Na+ channels open and Na+ rushes in 2. Na+ going in depolarizes the membrane more, which causes more VG Na+ channels to open and the signal to be amplified 3. depolarization spreads to neighboring regions of the membrane, which causes VG Na+ channels to open there ... after a while Na+ channels deactivate and close 4. depolarization causes VG K+ channels to open and K+ begins to flow out 5. flow of K+ out of the cell and inactivation of VG Na+ channels causes repolarization of the membrane (moving towards negative value) 6. Na+/K+ pump moves Na+ and K+ back across the plasma membrane

What are the steps of myosin using the coupling of ATP hydrolysis to conformational changes to generate force?

1. myosin head has bound ATP and P and have weak affinity for actin 2. once one of the heads docks onto the actin subunit, P is released ... 3. this strengthens the binding of the myosin head to actin ... 4. this triggers the first generating power stroke that moves the actin filament 5. ADP dissociates and ATP binds to the empty nucleotide binding site 6. myosin head detaches from actin filament 7. on the detached head, ATP is hydrolyzes and this recocks the lever arm back to its pre-stroke state

If you keep adding detergent to a solution what will happen?

1. number of monomers will increase, number of micelles will stay the same 2. CMC is reached 3. number of monomers stays the same, number of micelles will increase

In what order do the steps of mitochondrial fusion occur?

1. outer membranes fuse 2. inner membranes fuse

Tell me 5 things about this (Ach signaling).

1. positive charge on N in Ach ... this means it probably isn't going to go across the PM, and is probably working through cell-surface receptors 2. on a muscle cell ... when Ach binds, it causes depolarization bc it's a Na+ channel and Na+ can rush in and depolarize the cell ... this can lead to muscle contraction 3. Ach has different receptors and different cell types that could mediate different responses (different receptor in skeletal muscle cell vs salivary gland cell) 4. same receptor but different responses (different responses in salivary gland cell vs heart pacemaker cell) 5. In a heart pacemaker cell, the Ach receptor is coupled to G α-i ... β/γ subunits dissociates and activates K+ channels which causes hyperpolarization 6. in an salivary gland cell, the Ach receptor is coupled to G α-q ... leads to generation of IP3 and causes ER Ca2+ release ... which causes secretion

How does indirect immunohistochemistry work when used with fluorescence microscopy?

1. primary antibody is directed against antigen 2. secondary marker-coupled antibodies (more general) are directed towards the antibodies - antibodies are specific and bind tightly - tag isn't put on the primary antibody because you get more fluorophores by using the secondary antibodies and it makes it more flexible/shine more - antibodies can be generated against any target by introducing antigen to an animal system and harvesting the antibodies back off - different primary antibodies and fluorescence tagged secondary antibodies can be used to visualize different proteins/structures in the same cell

How does a protein get to the inner mitochondrial membrane without TIM22 OR TIM23?

1. protein in matrix gets inserted into inner membrane by OXA complex - occurs for any protein that came from the cytosol or a protein that was translated from the mitochondrial genome

How are second messengers and enzymatic cascades used to amplify signals?

1. rhodopsin molecule (GPCR) absorbs a photon 2. G-protein (transducin) molecules are activated 3. cGMP phosphodiesterase molecules are activated 4. cGMP molecules are hydrolyzed 5. cation channels close 6. Na+ ions are prevented from entering the cell 7. membrane potential is altered

What are the steps of Gq signaling?

1. signal molecule activates GPCR 2. Gq protein gets activated and α and β/γ subunits split 3. activated Gq protein activates phospholipase C 4. phospholipase splits PIP2 into DAG and IP3 5. PIP2 binds to a Ca2+ release channel 6. Ca2+ is released into the cytosol 7. the high level of Ca2+ in the cytosol along with the presence of DAG activates protein kinase C 8. protein kinase C phosphorylates target proteins

What are the steps of RTK activation?

1. signal protein binds 2. RTKs dimerize and trans-autophosphorylation activates kinase domains 3. trans-autophosphorylation generates binding sites for signaling proteins 4. activated signaling proteins relay signal downstream

What are the steps of the PI-3-kinase-Akt signaling pathway?

1. survival signal (GF) activates RTK 2. RTK activates PI 3-kinase 3. PI 3-kinase turns PI(4,5)P2 (PIP2) into PI(3,4,5)P3 4. PI(3,4,5)P3 activates PH domains 5. Akt (same as PKB) is phosphorylated and activated 6. active Akt phosphorylates and inactivates Bad (+ apoptosis inhibitory protein complex) 7. inactive/phosphorylated Bad binds to 14-3-3 protein 8. Apoptosis-inhibitory protein dissociates from Bad and is now activate 9. Apoptosis is inhibited and the cell survives

What does the path from the matrix to the inner membrane look like?

1. unfolded protein from matrix inserted into membrane via OXA

What are 3 ways for proteins to reach the peroxisome?

1. vesicular trafficking 2. SKL motif 3. insertion/tail anchoring into peroxisomal membrane

How do voltage-gated Na+ channels function?

1. voltage sensitive helices (+ charge) are closer to the inside of the membrane because it is negatively charged ... the channel is closed 2. membrane depolarization causes the inside of the membrane to become positively charged and the helices shift towards the negative charge on the outside of the membrane, opening the channel 3. the ball fits into the channel, inactivating it while the membrane repolarizes (during refractory period) 4. when the inside of the membrane becomes negatively charged again, the ball leaves the channel, allowing it to be in an closed, but active position

What is the limit of resolution of light microscopy?

1/2 of the wavelength of light used to illuminate the object

How much faster does water move across a lipid membrane than a charged ion?

10^9x faster

What is the expected mass of a nuclear pore complex?

125 million daltons

How many gamma-tubulins in a gamma-tubulin small complex spiral are available for binding to a tubulin dimer?

How many protofilaments are in a microtubule?

How many protofilaments make up a microtubule?

How many gamma-tubulins will be available for the binding of a tubulin dimer?

13 because one will be covered

How many available gamma-tubulins are in the gamma-tubulin ring complex?

13 gamma-tubulins are available

How many proteins are encoded by human mitochondrial DNA?

13 proteins

How many proteins are found in the mitochondrial genome (in a human)?

13 proteins

What do alpha/beta-tubulin dimers have to turn into in order to be made into microtubules?

13 protofilaments

How long is a typical phospholipid fatty acid tail?

14-24 carbons long

What domain binds ~phosphoserine/phosphothreonine motifs~?

14-3-3

What is diacylglycerol composed of?

2 fatty acid tails and a glycerol backbone

What does the structure of diacylglycerol look like?

2 fatty acids and a glycerol

What does the structure of phosphatidylglycerol look like?

2 fatty acids, a glycerol, a phosphate group, and a glycerol head group

What does the structure of phosphatidic acid look like?

2 fatty acids, a glycerol, and a phosphate group

What is myosin composed of?

2 identical motor heads that act independently ... each head has a catalytic core and an attached lever arm

Where are the mitotic spindles of a cell? How many are there?

2 opposite mitotic spindles (one at each pole of the cell)

What does the structure of cardiolipin look like?

2 phosphatidic acids and a glycerol head (4 fatty acids and 2 glycerols and 2 phosphates attached to a glycerol head)

What is the size of a typical eukaryotic cell?

20 microns in diameter (10-20 μm)

How far can 2 proteins be in order for FRET to work?

20-30 A apart

How many amino acids are needed in the transmembrane domain in a lipid raft?

20-30 amino acids

How many AAs make up a typical alpha-helical transmembrane domain? Are they polar or nonpolar?

20-30 nonpolar AAs

What is the resolution limit of a light microscope?

200 nm (.2 μm)

What are the 2 subunits that make up the proteasome?

20S core and two 19S caps on each end

How many H+ ions does it take to make a lysosome acidic?

252 H+s

How many CO2s actually go into the Calvin cycle?

3 CO2s (3 total carbons)

What's a product of the Calvin cycle? How many carbons does it have?

3 carbon sugar

How many intermediates are actually formed when CO2 and 1,5-bisphosphate combine during the Calvin cycle?

3 intermediates (18 carbons)

How many membranes can potentially be crossed in the chloroplast?

3 membranes (outer, inner, and thylakoid)

How many conformations does an ion channel have?

3! closed, open, and inactivated

About how thick is a lipid bilayer?

5 nm

How many 3-phosphoglycerate molecules are actually produced in the Calvin cycle?

6 3-phosphoglycerates (and then 1 goes to biosynthetic pathways, so really 5 heehee)

How many carbons are in the intermediate formed when CO2 and ribulose 1,5-bisphosphate are combined?

6 carbons

Photosystem II absorbs light at what wavelength?

680 nm

How many different phosphoinositides are there?

What is the width of the nuclear pore opening?

9 nm-26 nm

A KDEL receptor binds proteins with KDEL motifs in compartments such as the Golgi and releases them in the ER. What is the basis for this? A. receptor-cargo binding at the lower pH in the Golgi lumen B. receptor-cargo disassociation at the higher pH in the ER lumen C. both of the above

A bacteria goes from a warm to a cold environment. What change does it make to its membrane? A. increases HC tails with no double bonds in membrane phospholipids B. decreases amount of glycolipids in membrane C. increases amount of cholesterol in membrane D. increases unsaturated HC tails in membrane phospholipids E. increases length of HC tails in its membrane phospholipids

A bacteria goes from a warm to a cold environment. What change does it make to its membrane? A. increases HC tails with no double bonds in membrane phospholipids B. decreases amount of glycolipids in membrane C. increases amount of cholesterol in membrane *D. increases unsaturated HC tails in membrane phospholipids* E. increases length of HC tails in its membrane phospholipids ----- technically both C and D will help, but bacteria doesn't have cholesterol teehee

A benign neoplasia of cartilage is called a ... A. Chondroma B. Chondromelanoma C. Chondrocarcinoma D. Chondrosarcoma E. Adenochondroma

A benign neoplasia of cartilage is called a ... *A. Chondroma* B. Chondromelanoma C. Chondrocarcinoma D. Chondrosarcoma E. Adenochondroma ----- Benign and malignant tumors of cartilage are termed chondroma and chondrosarcoma, respectively.

A certain cell lacks the enzyme that would normally phosphorylate the 3 position of a phosphoinositol/phosphoionsitide. How many different phosphopinositides could there be in that cell? A. one B. two C. three D. three E. seven

A general role of protein coats that assemble around budding/pitting vesicles is to ... A. protect the vesicle from acid hydrolases B. keep the cargo warm C. promote membrane curvature D. all of the above

A general role of protein coats that assemble around budding/pitting vesicles is to ... A. protect the vesicle from acid hydrolases B. keep the cargo warm *C. promote membrane curvature* D. all of the above

A microtubule-severing protein such as katanin increases depolymerization by ... A. capping minus ends B. capping plus ends C. creating a minus end that isn't capped

A microtubule-severing protein such as katanin increases depolymerization by ... A. capping minus ends B. capping plus ends *C. creating a minus end that isn't capped*

A monomeric GTPase protein (G protein) is "activated" by ... A. a GTPase activating protein (GAP) that promotes the G protein to hydrolyze its bound GTP B. a guanine nucleotide exchange protein (GEF) that causes the G protein to release its bound GDP and bind a GTP C. a GDP dissociation inhibitor protein (GDI) which prevents the G protein from releasing its bound GDP

A monomeric GTPase protein (G protein) is "activated" by ... A. a GTPase activating protein (GAP) that promotes the G protein to hydrolyze its bound GTP *B. a guanine nucleotide exchange protein (GEF) that causes the G protein to release its bound GDP and bind a GTP* C. a GDP dissociation inhibitor protein (GDI) which prevents the G protein from releasing its bound GDP

A mutated peroxisomal lumen protein that lacks a peroxisomal targeting motif will most likely end up ... A. secreted B. in the ER C. in the lysosome D. in the cytosol

A mutated peroxisomal lumen protein that lacks a peroxisomal targeting motif will most likely end up ... A. secreted B. in the ER C. in the lysosome *D. in the cytosol*

A nuclearly-encoded mitochondrial gene is mutated so that it no longer encodes an N-terminal mitochondrial targeting sequence. What will be this protein's subcellular location? A. mitochondria B. chloroplasts C. ER D. cytosol E. plasma membrane

A nuclearly-encoded protein of the thylakoid space must cross ____ membranes to reach its destination. A. 0 B. 1 C. 2 D. 3

A nuclearly-encoded protein of the thylakoid space must cross ____ membranes to reach its destination. A. 0 B. 1 C. 2 *D. 3*

A pair of otherwise identical mammalian cells includes one in G1 and the other in G0 (stationary) phase. Both receive a transient extracellular proliferation signal sufficient to pass the restriction point, at which point the signal is removed. What is likely to happen? A. Neither of the cells will replicate their DNA. B. Only the G1 cell will replicate its DNA. C. Only the G1 cell will start to replicate its DNA, but will stop halfway through the replication and will not reach G2. D. Only the G0 cell will replicate its DNA. E. Both cells will replicate their DNA.

A phosphatidylinositol looks like ... A. a phospholipid B. a component of the cytosolic leaflet of the plasma membrane C. both of the above

A phosphatidylinositol looks like ... A. a phospholipid B. a component of the cytosolic leaflet of the plasma membrane *C. both of the above* ----- - 2 fatty acid tails - glycerol backbone - phosphate group - inositol group on top

A protein on the lumenal face of an endosome engulfed by an intralumenal vesicle. This protein now ... A. faces the interior of the vesicle B. faces the lumen of the endosome

A protein on the lumenal face of an endosome engulfed by an intralumenal vesicle. This protein now ... A. faces the interior of the vesicle *B. faces the lumen of the endosome*

A proton gradient across the inner bacterial membrane can drive ... A. nutrient uptake B. Na+ export C. flagellar turning D. all of the above

A proton gradient across the inner bacterial membrane can drive ... A. nutrient uptake B. Na+ export C. flagellar turning *D. all of the above*

A receptor tyrosine kinase (RTK) directly produces binding sites for proteins with the following domain A. PH B. SH3 C. 14-3-3 D. PTB E. SH2 F. both D and E

A receptor tyrosine kinase (RTK) directly produces binding sites for proteins with the following domain A. PH B. SH3 C. 14-3-3 D. PTB E. SH2 *F. both D and E*

A regulator of G protein signaling (RGS) can speed up deactivation of a G-α subunit. Thus, its role is similar to the role of a ... A. GEF B. GAP C. GPCR D. G-β/γ complex

A regulator of G protein signaling (RGS) can speed up deactivation of a G-α subunit. Thus, its role is similar to the role of a ... A. GEF *B. GAP* C. GPCR D. G-β/γ complex

A role of myosin II at the retracting end suggests a role of _____ there. A. alpha-actinin (parallel actin bundles) B. Arp 2/3 (branched actin network)

A role of myosin II at the retracting end suggests a role of _____ there. *A. alpha-actinin (parallel actin bundles)* B. Arp 2/3 (branched actin network) ----- myosins working on actins = moving working on actins = moving on a straight filament (which would be bundled together by alpha-actinin --> myosin can fit in!)

A secretory vesicle might bud off from ... A. the ER B. mitochondria C. the Golgi D. lysosomes E. all of the above

A secretory vesicle might bud off from ... A. the ER B. mitochondria *C. the Golgi* D. lysosomes E. all of the above

A signaling complex recruits Sos to the plasma membrane. Why is Sos's G protein target also at the plasma membrane? A. a phosphoinositide recruits it B. it binds a phosphotyrosine motif C. it binds a phosphoserine motif D. it binds a proline-rich motif E. the G protein is localized to the plasma membrane by a lipid anchor

A signaling complex recruits Sos to the plasma membrane. Why is Sos's G protein target also at the plasma membrane? A. a phosphoinositide recruits it B. it binds a phosphotyrosine motif C. it binds a phosphoserine motif D. it binds a proline-rich motif *E. the G protein is localized to the plasma membrane by a lipid anchor*

A soluble tyrosine kinase such as Src is ... A. a transmembrane protein B. a protein in the cytoplasm

A soluble tyrosine kinase such as Src is ... A. a transmembrane protein *B. a protein in the cytoplasm*

A t-SNARE in the plasma membrane would face ... A. the cytosol B. the extracellular space

A t-SNARE in the plasma membrane would face ... *A. the cytosol* B. the extracellular space

A transmembrane protein of a donor compartment is trafficked to a target compartment, where it is in ... A. The target compartment lumen B. The cytosol C. The target compartment membrane

A transmembrane protein of a donor compartment is trafficked to a target compartment, where it is in ... A. The target compartment lumen B. The cytosol *C. The target compartment membrane*

what are three ways in which a survival factor can block apoptosis?

A. increased production of anti-apoptotic Bcl2 family protein 1. survival factor activates the receptor 2. transcription regulator is activated 3. Bcl2 protein is made 4. apoptosis blocked B. inactivation of pro-apoptotic BH3-only protein 1. survival factor activates the receptor 2. receptor activates Akt kinase 3. Akt kinase phosphorylates the Bad (inactivates it) on the active Bad-inactive Bcl2 4. Bcl2 protein blocks apoptosis C. inactivation of anti-IAPS 1. survival factor activates the receptor 2. receptor activated MAP kinase 3. activated MAP kinase phosphorylates and inactivates Hid 4. Hid normally inhibits IAPs (inhibitors of apoptosis), so when Hid is inactivated IAPs function and prevent apoptosis 5. apoptosis is blocked

APC and SCF are examples of what type of proteins? A. proteases B. protein phosphatases C. protein kinases D. ubiquitins E. ubiquitin ligases

APC and SCF are examples of what type of proteins? A. proteases B. protein phosphatases C. protein kinases D. ubiquitins *E. ubiquitin ligases*

What is required for myosin motors to move actin filaments?

ATP

When individual monomers polymerize (usually at the plus end) they come in bound to _____.

ATP

What are the major products of the light reactions of photosynthesis?

ATP and NADPH

Is ADP or ATP more negative?

ATP is more negative (it has 3 negatively charged phosphate groups vs to 2 in ADP)

ATP synthase responds to proton transport down an electrochemical gradient to phosphorylate ADP to ADP. What would happen if the ATP synthase were to run in reverse? A. ATP synthase would hydrolyze ATP to ADP + Pi B. a proton gradient would be generated C. both

What is the normal function of an F-type ATPase?

ATP synthesis

What is photosystem I involved in?

ATP synthesis and production of NADPH from NADP+

Accessory pigments (P450, P470, P480, P500, P510, P650, etc.) allow ... A. carbon fixation B. uncoupling C. absorbance of light at other wavelengths than just the red and blue range D. pumping protons against a gradient E. dark reactions

Accessory pigments (P450, P470, P480, P500, P510, P650, etc.) allow ... A. carbon fixation B. uncoupling *C. absorbance of light at other wavelengths than just the red and blue range* D. pumping protons against a gradient E. dark reactions

Actin rearrangement is a feature of ... A. macropinocytosis B. phagocytosis C. endocytosis D. receptor mediated endocytosis E. both A and B

Actin rearrangement is a feature of ... A. macropinocytosis B. phagocytosis C. endocytosis D. receptor mediated endocytosis *E. both A and B*

Actin related proteins 2 and 3 ... A. nucleate new actin filaments B. generate branched organization of actin filaments C. cap the minus end of new actin filaments D. all of the above

Actin related proteins 2 and 3 ... A. nucleate new actin filaments B. generate branched organization of actin filaments C. cap the minus end of new actin filaments *D. all of the above*

Adaptin DOES NOT bind: A. cargo B. cargo receptors c. clathrin triskelion

Adaptin DOES NOT bind: *A. cargo* B. cargo receptors c. clathrin triskelion

Adhesion between cells at desmosomes is mediated by: A. Integrins B. Cadherins C. Proteoglycans D. Collagen fibrils E. Glycosaminoglycans

Adhesion between cells at desmosomes is mediated by: A. Integrins *B. Cadherins* C. Proteoglycans D. Collagen fibrils E. Glycosaminoglycans

After catastrophe, when a microtubule polymerizes rapidly enough to regain a GTP cap, this ... A. causes new catastrophe B. rescues the microtubule C. allows rapid growth at the GTP-capped end D. both B and C

After neurosecretion, a rapid means of synaptic vesicle regeneration involves ... A. formation of new synaptic vesicles from plasma membrane endocytosis B. rapid refilling of new synaptic vesicles by neurotransmitter uptake driven by a proton gradient C. both of the above

All of the following are phosphorylated by active M-cyclin/Cdk EXCEPT: A. condensins B. cohesins C. APC-activating kinases D. lamins E. MAPs

All of the following are phosphorylated by active M-cyclin/Cdk EXCEPT: A. condensins *B. cohesins* C. APC-activating kinases D. lamins E. MAPs ----- cohesins aren't a target ... they're the ones that are targeted by the APC

All of the following factors help regulate Cdk activity EXCEPT: A. Binding to cyclins B. Binding to GTP C. Binding to CKIs D. Phosphorylation by wee-1 E. Phosphorylation by CAK

All of the following factors help regulate Cdk activity EXCEPT: A. Binding to cyclins *B. Binding to GTP* C. Binding to CKIs D. Phosphorylation by wee-1 E. Phosphorylation by CAK

All of these are cell surface receptor proteins EXCEPT ... A. ligand-gated ion channels B. G protein coupled receptors (GPCRs) C. enzyme-coupled receptors D. monomeric G proteins

All of these are cell surface receptor proteins EXCEPT ... A. ligand-gated ion channels B. G protein coupled receptors (GPCRs) C. enzyme-coupled receptors *D. monomeric G proteins*

All of these have proteins that are similar to mitochondrial ATP synthase EXCEPT ... A. archaea B. bacteria C. chloroplasts D. there are no exceptions

All of these have proteins that are similar to mitochondrial ATP synthase EXCEPT ... A. archaea B. bacteria C. chloroplasts *D. there are no exceptions* ----- (they all have proteins that are similar to mitochondrial ATP synthase)

Among the following cancers, one is currently leading to the most number of deaths in the United States and in the rest of the world. In the United States, it contributes to cancer mortality more than the next three killing cancers combined. Worldwide, it claims more than 1.5 million lives every year. Which cancer is this? A. Pancreatic cancer B. Breast cancer C. Stomach cancer D. Lung cancer E. Colon cancer

An ECM protein contains multiple binding domains for matrix structural components, cell surface proteins, and growth factors. It forms a dimer. It is: A. Laminin B. Elastin C. Fibronectin D. Collagen

An ECM protein contains multiple binding domains for matrix structural components, cell surface proteins, and growth factors. It forms a dimer. It is: A. Laminin B. Elastin *C. Fibronectin* D. Collagen ----- laminin = trimer, elastin = bc forms a big sheet, collagen = bundles with three alpha helices so trimer

An RTK signaling cascade brings a Ras GEF in close proximity to Ras. This will ... A. activate Ras B. inactivate Ras

An RTK signaling cascade brings a Ras GEF in close proximity to Ras. This will ... *A. activate Ras* B. inactivate Ras

An actin capping protein A. prevents depolymerization at the capped end B. causes depolymerization at the capped end

An actin capping protein *A. prevents depolymerization at the capped end* B. causes depolymerization at the capped end

An electrochemical gradient formed by pumping protons across a membrane can play a role in all of these EXCEPT ... A. translocation of the positively-charged mitochondrial targeting region of a protein across the inner mitochondrial membrane B. ADP phosphorylation by ATP synthase C. nutrient or Na+ transport across a bacterial membrane D. rotary motion of a bacterial flagellum E. direct transfer of an electron from donor to an acceptor

An electrochemical gradient formed by pumping protons across a membrane can play a role in all of these EXCEPT ... A. translocation of the positively-charged mitochondrial targeting region of a protein across the inner mitochondrial membrane B. ADP phosphorylation by ATP synthase C. nutrient or Na+ transport across a bacterial membrane D. rotary motion of a bacterial flagellum *E. direct transfer of an electron from donor to an acceptor*

An enzyme on the cytosolic face of the endosome is generating cytosolic signals. If it is endocytosed and is now on the membrane of an intralumenal vesicle, what does that do to the cytosolic signaling? A. prevents it B. augments it

Apoptotic cells are efficiently phagocytosed by neighboring cells or macrophages. Which of the following DOES NOT normally happen in this process? A. The apoptotic cell releases some of its cytoplasmic content to induce a local inflammatory response. B. The apoptotic cell loses or inactivates "don't eat me" signals. C. The apoptotic cell rounds up and detaches from its neighbors, which facilitates phagocytosis. D. The apoptotic cell exposes phosphatidylserine at its surface, which interacts with receptor proteins on the surface of phagocytes via "bridging" proteins.

Apoptotic cells are efficiently phagocytosed by neighboring cells or macrophages. Which of the following DOES NOT normally happen in this process? *A. The apoptotic cell releases some of its cytoplasmic content to induce a local inflammatory response.* B. The apoptotic cell loses or inactivates "don't eat me" signals. C. The apoptotic cell rounds up and detaches from its neighbors, which facilitates phagocytosis. D. The apoptotic cell exposes phosphatidylserine at its surface, which interacts with receptor proteins on the surface of phagocytes via "bridging" proteins. ----- Apoptosis is carried out in a remarkably tidy process and the cell is phagocytosed without triggering an inflammatory response.

question(s) asked at metaphase-anaphase checkpoint

Are all of the chromosomes attached to the spindle?

Are all the myosins plus-end directed? A. yes B. nope! Myosin VI moves toward the minus end

Are all the myosins plus-end directed? A. yes *B. nope! Myosin VI moves toward the minus end*

Arp 2/3-nucleated actin filaments are: A. straight B. branched network

Arp 2/3-nucleated actin filaments are: A. straight *B. branched network*

Binding a GPCR to its ligand causes a change in its cytosolic domain that stimulates ... A. GTPase activity B. release of GDP and binding of GTP to a G-α subunit C. inactivation of a heterotrimeric G protein

Binding a GPCR to its ligand causes a change in its cytosolic domain that stimulates ... A. GTPase activity *B. release of GDP and binding of GTP to a G-α subunit* C. inactivation of a heterotrimeric G protein

Bone or tendon is a specialized example of ... A. Basal lamina B. Connective tissue C. Epithelial cell layer

Bone or tendon is a specialized example of ... A. Basal lamina *B. Connective tissue* C. Epithelial cell layer

Both cadherins and integrins are expressed by cells in the ... A. Basal lamina B. Connective tissue C. Epithelial cell layer

Both cadherins and integrins are expressed by cells in the ... A. Basal lamina B. Connective tissue *C. Epithelial cell layer*

What are the products of respiration?

CO2 and H2O

Where is the carbon that is fixed into carbohydrate molecules come from?

CO2 in the atmosphere

Once localized to the membrane, what does SAR1 recruit?

COPII inner coat proteins

ER/mitochondrial contacts can mediate the transfer of ...

Ca2+ and lipids

What is the name of the protein that moves Ca2+ from the cytosol to inside the sarcoplasmic reticulum lumen?

Ca2+ pump / Ca2+ ATPase / SR Ca2+ ATPase

Caffeine and theobrommine (from tea and cacao) inhibit cAMP phosphodiesterase. These would cause melanosomes to ... A. disperse B. aggregate C. both

Caffeine and theobrommine (from tea and cacao) inhibit cAMP phosphodiesterase. These would cause melanosomes to ... *A. disperse* B. aggregate C. both ----- cAMP --(PDE)--> AMP ... when PDE is inhibited, there is more cAMP built up in the cell and high cAMP levels cause melanosomes to disperse

Can an extracellular virus particle rely on SNAREs for fusion w/a target plasma membrane? A. no, because the SNAREs face the wrong way B. yes

Can an extracellular virus particle rely on SNAREs for fusion w/a target plasma membrane? *A. no, because the SNAREs face the wrong way* B. yes

Can myosins carry cargo, especially in the cortical actin network? A. no way, that's a role for kinesins and dyneins that carry cargo on microtubules B. yes, that myosin V is a good carrier, and probably myosin VI can move the other way

Can myosins carry cargo, especially in the cortical actin network? A. no way, that's a role for kinesins and dyneins that carry cargo on microtubules *B. yes, that myosin V is a good carrier, and probably myosin VI can move the other way*

Caspase activation involves _____ proteolysis to become an active _____. A. inhibition of, kinase B. inhibition of, phosphatase C. Inhibition of, protease D. Auto-, protease E. Auto-, kinase

Caspase activation involves _____ proteolysis to become an active _____. A. inhibition of, kinase B. inhibition of, phosphatase C. Inhibition of, protease *D. Auto-, protease* E. Auto-, kinase

Cdc20 is involved in the _____ checkpoint, while Cdc25 regulates the _____ checkpoint. A. metaphase-anaphase, G2-M B. Start, G1-S C. G2-M, start D. start, metaphase-anaphase

Cdc20 is involved in the _____ checkpoint, while Cdc25 regulates the _____ checkpoint. *A. metaphase-anaphase, G2-M* B. Start, G1-S C. G2-M, start D. start, metaphase-anaphase

regulation of DNA replication - G1

Cdc6 binds to ORC, which allows formation of Mcm complex ... preRC is complete

Cell divison is controlled in two ways. First, by genes that promote cell division, and second, by genes that monitor and suppress cell division. This supports the idea that: A. Cancer can be benign or malignant. B. Different cancer arise from different tissues. C. Multiple mutations are required for cancer. D. Cancer can become invasive. E. Benign tumors are usually a compact cell mass.

Cell divison is controlled in two ways. First, by genes that promote cell division, and second, by genes that monitor and suppress cell division. This supports the idea that: A. Cancer can be benign or malignant. B. Different cancer arise from different tissues. *C. Multiple mutations are required for cancer.* D. Cancer can become invasive. E. Benign tumors are usually a compact cell mass.

Cellular uptake of low density lipoprotein particles is an example of ... A. micropinocytosis B. receptor-mediated endocytosis C. phagocytosis D. autophagy

Cellular uptake of low density lipoprotein particles is an example of ... A. micropinocytosis *B. receptor-mediated endocytosis* C. phagocytosis D. autophagy

Centriole replication happens at the same time as: A. Cell growth, G1 B. DNA replication C. Cell growth, G2 D. Mitotic separation of chromosomes E. Cytokinesis

Centriole replication happens at the same time as: A. Cell growth, G1 *B. DNA replication* C. Cell growth, G2 D. Mitotic separation of chromosomes E. Cytokinesis

Chlorophyll special pairs (P680 and P700) in the photoreaction centers of photosystems I and II absorb ... A. red and blue B. infrared C. ultraviolet D. green E. all of the above

Chlorophyll special pairs (P680 and P700) in the photoreaction centers of photosystems I and II absorb ... *A. red and blue* B. infrared C. ultraviolet D. green E. all of the above

Chloroplast fission involves ... A. membrane curvature caused by FtsZ-like proteins B. dynamin-like proteins C. both of the above

Chloroplast fission involves ... A. membrane curvature caused by FtsZ-like proteins B. dynamin-like proteins *C. both of the above*

Cofilin ... A. binds to actin filaments, making them more likely to break B. caps the plus end C. nucleates actin D. stimulates polymerization

Collagen in the ECM: A. Is secreted by fibroblasts B. Forms a network of cross-linked elastic segments C. Has a double-stranded helical structure D. Is found in connective tissue but not basal lamina

Collagen in the ECM: *A. Is secreted by fibroblasts* B. Forms a network of cross-linked elastic segments C. Has a double-stranded helical structure D. Is found in connective tissue but not basal lamina ---- B = elastin, C is wrong bc triple stranded, D is wrong bc collagen IV is in basal lamina

Consider a healthy adult animal in which 1015 cell divisions have taken place since birth. Spontaneous mutations can occur at a rate of approximately one nucleotide out of about ten billion nucleotides every time DNA is replicated. The animal has a diploid genome size of about 2 billion nucleotide pairs. Assuming that only about 5% of mutations occur within genes or gene regulatory sequences, and further assuming that about 0.1% of those may cause cancer, how many potential cancer-causing mutations has the animal been able to successfully suppress (i.e. has been able to survive) during its lifetime? A. Ten thousand B. One hundred thousand C. Ten million D. One billion *E. Ten billion* ----- The number of cancer-related mutations is calculated from these assumptions as: (1015 cell divisions) × (10-10 mutations/nucleotide/division) × (2 × 109 nucleotides/genome) × (5 × 10-2 genic mutation/mutation) × (10-3 cancerous mutations/genic mutations) = 1010 cancerous mutations/genome

Conversion of a PI(3)P to a PI(3,5)P2 indicates the action of a ... A. Kinase B. Phosphatase C. Both

Conversion of a PI(3)P to a PI(3,5)P2 indicates the action of a ... *A. Kinase* B. Phosphatase C. Both ----- kinase puts Ps on

Cytosolic chaperones that prevent folding of mitochondrial proteins and matrix chaperones that help pull proteins through the TIM do so ... A. without energy input B. in a fashion dependent on ATP hydrolysis C. both

Direct transcriptional regulation by steroid molecules is generally mediated by ... A. nuclear receptors B. cell surface receptors

Direct transcriptional regulation by steroid molecules is generally mediated by ... *A. nuclear receptors* B. cell surface receptors

Disassembly of the "old" actin in an Arp2/3 branched organization in a lamellipodium is mediated by ... A. Arp2/3 B. formin C. fimbrin D. cofilin

Disassembly of the "old" actin in an Arp2/3 branched organization in a lamellipodium is mediated by ... A. Arp2/3 B. formin C. fimbrin *D. cofilin*

ESCRT complexes ... A. escort lysosomal proteins B. are involved in membrane deformation C. contribute to intralumenal or extracellular vesicle formation D. all of the above E. only B and C

ESCRT complexes ... A. escort lysosomal proteins B. are involved in membrane deformation C. contribute to intralumenal or extracellular vesicle formation D. all of the above *E. only B and C*

Executioner caspases: A. Induce Bcl2-family protein activation B. Cleave DNA into laddered fragments C. Are monomeric when inactive D. Are activated by initiator caspases in a cascade

Executioner caspases: A. Induce Bcl2-family protein activation B. Cleave DNA into laddered fragments C. Are monomeric when inactive *D. Are activated by initiator caspases in a cascade*

What do nuclear import proteins bind to on nucleoporin proteins?

FG (Phe Gly) repeats

How can Ras-GTP be detected experimentally?

FRET stuff aw cute ... it can be used to measure how much of the G protein is bound to GTP

For V-type ATPases of the lysosomal membrane, ATP is hydrolyzed A. on the cytosolic side B. on the side facing the lysosomal lumen C. both

For V-type ATPases of the lysosomal membrane, ATP is hydrolyzed *A. on the cytosolic side* B. on the side facing the lysosomal lumen C. both

Formins nucleate actin filaments that are ... A. straight B. branched C. gel-like

Formins nucleate actin filaments that are ... *A. straight* B. branched C. gel-like

From which is O2 derived during photosynthesis? A. sunlight B. proton gradient C. water D. CO2 E. photosystem I F. photosystem II G. a photoreaction center H. electrons

From which is O2 derived during photosynthesis? A. sunlight B. proton gradient *C. water* D. CO2 E. photosystem I F. photosystem II G. a photoreaction center H. electrons

From whom did Dr. Fisher's sons inherit their nuclearly-encoded mitochondrial genes? A. their mom B. their dad C. both

From whom did Dr. Fisher's sons inherit their nuclearly-encoded mitochondrial genes? A. their mom B. their dad *C. both*

G-actin binds ATP toward the ________ end. A. minus (pointed) B. plus (barbed) C. both

G-actin binds ATP toward the ________ end. *A. minus (pointed)* B. plus (barbed) C. both

Is aggrecan a GAG or a fibrous protein?

GAG

What does a GDI do?

GDP disassociation inhibitor!! inhibits dissociation of GDP from its G protein (keeps G protein turned off)

What activates a Rho?

GEF

What type of protein ~activates a monomeric G protein~?

GEF

What type of protein ~activates a G-α subunit~?

GPCR (that is coupled to G-α)

How is a GPCR desensitized?

GPCR kinase (GPCRK) phosphorylates the receptor ... arresting binds to the phosphorylated GPCR and blocks the receptor from binding to G α subunits (this is negative feedback!) idk how tho ?

What is the microtubule cap?

GTP-bound portion of the microtubule

Generation of a mannose 6-phosphate (M6P) tag requires a GlcNac phosphotransferase and then a GlcNacase that removes the GlcNac and reveals the M6P. What would happen if the GlcNac phosphotransferase were inhibited? A. there would be no specific targeting or retrieval of lysosomal resident proteins to the endosome/lysosome B. lysosomal proteins would be secreted C. undigested materials would accumulate in the endosomes D. all of the above

What targets proteins with a signal sequence at the C-terminus to be inserted into the ER membrane?

Get3 ATPase and Get1-Get2 1. C-terminal signal sequence binds to pre-targeting complex 2. new protein associated with Get3 ATPase 3. Get3 ATPAse carries the protein to the membrane and associates with Get1-Get2 complex 4. ATP on Get3 ATPase hydrolyzed and protein released and inserted into the membrane 5. Get3 ATPase releases Get1-Get2 complex 6. it combines with ATP agin and gets recycled

Given what you know about monomeric G proteins, what do you suppose deactivates a G-α subunit ... A. GTPase activity of the G-α subunit that hydrolyzes GTP to GDP B. GTP binding C. association with the GPCR D. association with effector proteins

Given what you know about monomeric G proteins, what do you suppose deactivates a G-α subunit ... *A. GTPase activity of the G-α subunit that hydrolyzes GTP to GDP* B. GTP binding C. association with the GPCR D. association with effector proteins

Which sugar does a glycosidase remove to reveal the M6P tag?

GlcNac (???)

How does a V-type proton pump work?

H+ pump (into acidic organelles)

If fat is the oxidative fuel, where does almost all of the oxygen in CO2 produced come from?

H2O

In what molecule does oxygen consumed by mitochondria end up?

H2O

The electron released by a chlorophyll in a special pair of photosystem II is essentially replaced by an electron from what molecule?

H2O

What is a source of oxygen atoms in CO2 produced by mitochondria?

H2O

What is needed for the 6 carbon intermediate (formed when CO2 and ribulose 1,5-bisphosphate combine) to form into 2 molecules of 3-phosphoglycerate?

H2O

What is oxygen derived from during photosynthesis?

H2O

How are gap junctions different from adherens junctions? A. Gap junctions are between two cells, while adherens junctions are between cells and the extracellular matrix. B. Gap junctions are found in plant cells, while adherens junctions are not. C. Gap junctions allow direct flow of solutes from one cell to another, while adherens junctions do not. D. Gap junctions contain proteins undergoing homophilic interactions, while adherens junctions don't.

How are gap junctions different from adherens junctions? A. Gap junctions are between two cells, while adherens junctions are between cells and the extracellular matrix. B. Gap junctions are found in plant cells, while adherens junctions are not. *C. Gap junctions allow direct flow of solutes from one cell to another, while adherens junctions do not.* D. Gap junctions contain proteins undergoing homophilic interactions, while adherens junctions don't. ----- A. adherens are cell-cell B. this is talking about plasmodesmata D. connexons are homophilic for gap junctions, cadherins are homophilic for adherens junctions

How are mitochondria and the ER similar? A. Both are derived from invagination of the cell's plasma membrane B. Both evolved from engulfment of a bacterium C. Both have their own DNA D. Both have membranes continuous with the nuclear membrane E. All of the above

How are mitochondria and the ER similar? *A. Both are derived from invagination of the cell's plasma membrane* B. Both evolved from engulfment of a bacterium C. Both have their own DNA D. Both have membranes continuous with the nuclear membrane E. All of the above ----- A. :) B. only mitochondria C. only mitochondria D. only ER E. no lol

How can actin-related protein 2 and 3 nucleate actin filament formation? A. Their structures are similar to actin. B. They sequester G-actin and prevent polymerization. C. They depolymerize at the minus end.

How can actin-related protein 2 and 3 nucleate actin filament formation? *A. Their structures are similar to actin.* B. They sequester G-actin and prevent polymerization. C. They depolymerize at the minus end.

How can the same GPCR have different actions in different cells? A. it can't B. it might be coupled to different G-α subunit types in different cells C. it takes different strokes to move the world D. the world don't move to the beat of just one drum

How can the same GPCR have different actions in different cells? A. it can't *B. it might be coupled to different G-α subunit types in different cells* C. it takes different strokes to move the world D. the world don't move to the beat of just one drum

How do mitochondrial proteins get into the matrix? A. through transporters of the outer membrane B. through transporters of the inner membrane C. both

How do mitochondrial proteins get into the matrix? A. through transporters of the outer membrane B. through transporters of the inner membrane *C. both*

How does a growing protein become associated with the ER membrane? (the very first step) A. emerging signal sequence binds directly to a binding pocket on Sex61 complex B. emerging signal sequence binds directly to a binding pocket on SRP complex C. ribosomes producing the protein are permanently associated with the ER membrane D. mRNA being translated beings to the RNA in the the SRP complex E. All of the above.

How does a growing protein become associated with the ER membrane? (the very first step) A. emerging signal sequence binds directly to a binding pocket on Sex61 complex *B. emerging signal sequence binds directly to a binding pocket on SRP complex* C. ribosomes producing the protein are permanently associated with the ER membrane D. mRNA being translated beings to the RNA in the the SRP complex E. All of the above.

How does an antibody in a mother's milk make it toward a baby's bloodstream? A. through transcytosis B. by protease action C. it doesn't

How does an antibody in a mother's milk make it toward a baby's bloodstream? *A. through transcytosis* B. by protease action C. it doesn't

How does assembly of a clathrin coat drive vesicle formation? A. It utilizes ATP to assemble the membrane. B. It relies on motor proteins to initiate vesicle formation. C. It promotes membrane curvature.

How does assembly of a clathrin coat drive vesicle formation? A. It utilizes ATP to assemble the membrane. B. It relies on motor proteins to initiate vesicle formation. *C. It promotes membrane curvature.*

How does binding by p27 affect Cyclin-Cdk activity? A. increase B. decrease C. neither

How does binding by p27 affect Cyclin-Cdk activity? A. increase *B. decrease* C. neither

How does cyclin binding affect Cyclin-Cdk activity? A. increase B. decrease C. neither

How does cyclin binding affect Cyclin-Cdk activity? *A. increase* B. decrease C. neither

How does cyclin degradation affect Cyclin-Cdk activity? A. increase B. decrease C. neither

How does cyclin degradation affect Cyclin-Cdk activity? A. increase *B. decrease* C. neither

How does dephosphorylation by Cdc25 affect Cyclin-Cdk activity? A. increase B. decrease C. neither

How does dephosphorylation by Cdc25 affect Cyclin-Cdk activity? *A. increase* B. decrease C. neither

How does hydrolysis of GTP to GDP affect Cyclin-Cdk activity? A. increase B. decrease C. neither

How does hydrolysis of GTP to GDP affect Cyclin-Cdk activity? A. increase B. decrease *C. neither*

How does phosphorylation by CAK affect Cyclin-Cdk activity? A. increase B. decrease C. neither

How does phosphorylation by CAK affect Cyclin-Cdk activity? *A. increase* B. decrease C. neither

How does phosphorylation by Wee1 affect Cyclin-Cdk activity? A. increase B. decrease C. neither

How does phosphorylation by Wee1 affect Cyclin-Cdk activity? A. increase *B. decrease* C. neither

How does phosphorylation of Rb affect Cyclin-Cdk activity? A. increase B. decrease C. neither

How does phosphorylation of Rb affect Cyclin-Cdk activity? *A. increase* B. decrease C. neither ----- released E2F that leads to cyclin expression

How does phosphorylation of p53 affect Cyclin-Cdk activity? A. increase B. decrease C. neither

How does phosphorylation of p53 affect Cyclin-Cdk activity? A. increase *B. decrease* C. neither ----- results in expression of p21

How does ubiquitylation of cyclin by APC affect Cyclin-Cdk activity? A. increase B. decrease C. neither

How does ubiquitylation of cyclin by APC affect Cyclin-Cdk activity? A. increase *B. decrease* C. neither

How is ATP produced when it's dark? A. catabolism of stored fuel B. photosynthesis C. both

How is ATP produced when it's dark? *A. catabolism of stored fuel* B. photosynthesis C. both

How is M-cyclin rapidly degraded? A. It phosphorylates APC. B. Cdc20 binding activates APC. C. APC polyubiquitylates the cyclin. D. The cyclin is targeted to the proteasome. E. All of the above

How is M-cyclin rapidly degraded? A. It phosphorylates APC. B. Cdc20 binding activates APC. C. APC polyubiquitylates the cyclin. D. The cyclin is targeted to the proteasome. *E. All of the above*

How is hyaluronic acid different from other glycosaminoglycans (GAGs) of the extracellular matrix (ECM)? A. All of these statements describe hyaluronan. B. It is generally not covalently linked to proteins. C. It is not assembled in the Golgi apparatus. D. It can be several megadaltons in mass. E. It lacks sulfate groups.

How is hyaluronic acid different from other glycosaminoglycans (GAGs) of the extracellular matrix (ECM)? *A. All of these statements describe hyaluronan.* B. It is generally not covalently linked to proteins. C. It is not assembled in the Golgi apparatus. D. It can be several megadaltons in mass. E. It lacks sulfate groups. ----- Being the simplest of the GAGs, hyaluronan chains can be remarkably long. Not typical of GAGs, it contains no sulfated sugars, is not generally linked to proteins covalently, and is synthesized and spun out directly from the cell surface by a transmembrane enzyme.

How many different doubly-phosphorylated PI forms are there? A. 1 B. 2 C. 3

How many different doubly-phosphorylated PI forms are there? A. 1 B. 2 *C. 3* ------ 3 and 4, 3 and 5, 4 and 5

How many different phosphoinositides are there, keeping in mind that a phosphoinositide contains at least one phosphate group (phosphatidylinositol itself is not a phosphoinositide), and there are three positions on which the molecule can be phosphorylated? A. 3 phosphoinositide monophosphates B. 3 phosphoinositide bisphosphates C. one phosphoinositide trisphosphate D. seven in total

How many different singly-phosphorylated PI forms are there? A. 1 B. 2 C. 3

How many different singly-phosphorylated PI forms are there? A. 1 B. 2 *C. 3* ----- 3, 4, and 5

How many protofilaments are in a microtubule? A. 1 B. 7 C. 13 D. 14

How many protofilaments are in a microtubule? A. 1 B. 7 *C. 13* D. 14

How would you describe actin at a new minus end after gelosin acts there (look at pic lol)? A. pretty stable B. subject to depolymerization

How would you describe actin at a new minus end after gelosin acts there (look at pic lol)? A. pretty stable *B. subject to depolymerization* ----- the thing that he circled in the picture was like a little bit up from the third cap along the bottom idk it's confusing sorry just look at ur lecture slides from 3/27)

How would you describe actin at this capped end? (look at pic lol) A. pretty stable B. rapidly depolymerizing

How would you describe actin at this capped end? (look at pic lol) *A. pretty stable* B. rapidly depolymerizing ----- the thing that he circled in the picture was like the cap of the strand at the right upper corner like if you follow it down idk it's confusing sorry just look at ur lecture slides from 3/27)

If a cell is injected with a factor that prevents XMAP215 from acting, microtubules will be ... A. more stable B. less stable C. rescued

If a cell is injected with a factor that prevents XMAP215 from acting, microtubules will be ... A. more stable *B. less stable* C. rescued

If a gene that would normally encode a KDEL sequence of an ER resident protein is mutated so that its protein product no longer contains the KDEL sequence ... A. the protein would no longer be cotranslationally inserted into the ER lumen B. the protein would be retained in the ER C. the protein would eventually be secreted into the extracellular fluid

If a gene that would normally encode a KDEL sequence of an ER resident protein is mutated so that its protein product no longer contains the KDEL sequence ... A. the protein would no longer be cotranslationally inserted into the ER lumen B. the protein would be retained in the ER *C. the protein would eventually be secreted into the extracellular fluid*

If a phospholipid is diffusing in a straight line ... how long does it take for it to diffuse across the diameter of a typical cell? A. 10 microseconds B. 10 seconds C. 10 hours D. 10 days E. 10 weeks

If a phospholipid is diffusing in a straight line ... how long does it take for it to diffuse across the diameter of a typical cell? A. 10 microseconds *B. 10 seconds* C. 10 hours D. 10 days E. 10 weeks ----- moving a couple of microns/second so the scale is seconds

If a vesicle buds off from a donor compartment carrying a protein that had been in the lumen of the donor compartment, where will the protein be after the vesicle fuses with a target compartment? A. target compartment lumen B. cytosol C. both of the above

If a vesicle buds off from a donor compartment carrying a protein that had been in the lumen of the donor compartment, where will the protein be after the vesicle fuses with a target compartment? *A. target compartment lumen* B. cytosol C. both of the above

If a vesicle or compartment with a set of v- and t-SNAREs fuses with a vesicle or compartment with an identical set of v- and t-SNAREs, this is ... A. heterotypic fusion B. homotypic fusion

If a vesicle or compartment with a set of v- and t-SNAREs fuses with a vesicle or compartment with an identical set of v- and t-SNAREs, this is ... A. heterotypic fusion *B. homotypic fusion*

If an activated RTK recruits and activates a GTPase activating protein (GAP), that will directly ... A. activate a G protein B. inactivate a G protein C. create new binding sites for SH2 or PTB domains D. generate specific species of phosphoinositide E. generate second messengers that cause Ca2+ release from the ER and activation of protein kinase C (PKC)

If an activated RTK recruits and activates a GTPase activating protein (GAP), that will directly ... A. activate a G protein *B. inactivate a G protein* C. create new binding sites for SH2 or PTB domains D. generate specific species of phosphoinositide E. generate second messengers that cause Ca2+ release from the ER and activation of protein kinase C (PKC)

If an activated RTK recruits and activates a phospholipase C, that will directly ... A. activate a G protein B. inactivate a G protein C. create new binding sites for SH2 or PTB domains D. generate specific species of phosphoinositide E. generate second messengers that cause Ca2+ release from the ER and activation of protein kinase C (PKC)

If an activated RTK recruits and activates a phospholipase C, that will directly ... A. activate a G protein B. inactivate a G protein C. create new binding sites for SH2 or PTB domains D. generate specific species of phosphoinositide *E. generate second messengers that cause Ca2+ release from the ER and activation of protein kinase C (PKC)*

If an activated RTK recruits and activates phosphatidylinositol 3-kinase (PI3K), that will directly ... A. activate a G protein B. inactivate a G protein C. create new binding sites for SH2 or PTB domains D. generate specific species of phosphoinositide E. generate second messengers that cause Ca2+ release from the ER and activation of protein kinase C (PKC)

If an activated RTK recruits and activates phosphatidylinositol 3-kinase (PI3K), that will directly ... A. activate a G protein B. inactivate a G protein C. create new binding sites for SH2 or PTB domains *D. generate specific species of phosphoinositide* E. generate second messengers that cause Ca2+ release from the ER and activation of protein kinase C (PKC)

If part of a transmembrane protein that faces the cytosol in one compartment is trafficked to a target compartment, there it will face ... A. The target compartment lumen B. The cytosol C. The target compartment membrane

If part of a transmembrane protein that faces the cytosol in one compartment is trafficked to a target compartment, there it will face ... A. The target compartment lumen *B. The cytosol* C. The target compartment membrane ----- if it has a cytosolic face in one compartment, it will have a cytosolic face in another compartment

If securin were mutated and unrecognizable by the APC, where in the cell cycle would cells become stalled? A. prophase B. interphase C. prometaphase D. G1-phase E. metaphase

If securin were mutated and unrecognizable by the APC, where in the cell cycle would cells become stalled? A. prophase B. interphase C. prometaphase D. G1-phase *E. metaphase*

If the gene encoding a normally secreted protein is mutated so that encodes a protein with a KDEL sequence ... A. the protein would no longer be cotranslationally inserted into the ER lumen B. the protein would be retained in the ER or trafficked back to the ER if it escapes C. the protein would eventually be secreted into the extracellular fluid

If the gene encoding a normally secreted protein is mutated so that encodes a protein with a KDEL sequence ... A. the protein would no longer be cotranslationally inserted into the ER lumen *B. the protein would be retained in the ER or trafficked back to the ER if it escapes* C. the protein would eventually be secreted into the extracellular fluid

If the protein kinase A (PKA) regulatory subunit is mutated so that it cannot associate with the catalytic subunit, A. PKA will always be inactive B. cAMP production will cease C. PKA will be active even in the absence of cAMP

If the protein kinase A (PKA) regulatory subunit is mutated so that it cannot associate with the catalytic subunit, A. PKA will always be inactive B. cAMP production will cease *C. PKA will be active even in the absence of cAMP*

If the signaling receptor is an active enzyme, what does its sequestration in an intralumenal vesicle do? A. increases the enzyme activity in the cytosol B. prevents the enzyme activity in the cytosol

If the signaling receptor is an active enzyme, what does its sequestration in an intralumenal vesicle do? A. increases the enzyme activity in the cytosol *B. prevents the enzyme activity in the cytosol*

If β-tubulin cannot hydrolyze GTP to GDP, what does that do to microtubules ... A. stabilizes B. causes depolymerization C. catastrophe

If β-tubulin cannot hydrolyze GTP to GDP, what does that do to microtubules ... *A. stabilizes* B. causes depolymerization C. catastrophe

In a pedigree, a certain condition in an affected mother could be present in all of her children and in her daughters' children but not in her sons' children. This is most likely ... A. autosomal recessive B. autosomal dominant C. X-linked D. related to a mutation in the mitochondrial genome

In a pedigree, a certain condition in an affected mother could be present in all of her children and in her daughters' children but not in her sons' children. This is most likely ... A. autosomal recessive B. autosomal dominant C. X-linked *D. related to a mutation in the mitochondrial genome*

In a photosynthetic plant cell, how is ATP generated when it's dark? A. catabolism of stored fuel (e.g. oxidation of sugars or fats) B. photosynthesis C. both

In a photosynthetic plant cell, how is ATP generated when it's dark? *A. catabolism of stored fuel (e.g. oxidation of sugars or fats)* B. photosynthesis C. both

In addition to favorable chemical gradients, what drives exchange of ATP and ADP across the inner mitochondrial membrane? A. electrical gradient B. ATP synthase C. ATP just needs to get out and get things done D. ADP loves to hang out with Keanu Reaves in the matrix

In addition to favorable chemical gradients, what drives exchange of ATP and ADP across the inner mitochondrial membrane? *A. electrical gradient* B. ATP synthase C. ATP just needs to get out and get things done D. ADP loves to hang out with Keanu Reaves in the matrix ----- ADP moves into the matrix in exchange for the more negatively charged ATP entering into the positively charged intermembrane space

In an example Rab cascade, activation of Rab A might recruit ________, resulting in a change in the Rab form associated with the membrane from Rab A to Rab B. A. A Rab A GAP B. A Rab B GEF C. both of the above

In an example Rab cascade, activation of Rab A might recruit ________, resulting in a change in the Rab form associated with the membrane from Rab A to Rab B. A. A Rab A GAP B. A Rab B GEF *C. both of the above*

In mode of actin, stathmin (for tubulin dimers) is most similar to _____ (for actin filaments). A. Thymosin B. Profilin C. Cofilin D. Gelsolin E. Arp 2/3

In mode of actin, stathmin (for tubulin dimers) is most similar to _____ (for actin filaments). *A. Thymosin* B. Profilin C. Cofilin D. Gelsolin E. Arp 2/3 ----- stathmin is a protein that is sequestering something - thymosin = binding up free monomers of actin - profilin = promotes polymerization

In mode of actin, the gamma-tublin ring complex is most similar to _____. A. Thymosin B. Profilin C. Cofilin D. Gelsolin E. Arp 2/3

In mode of actin, the gamma-tublin ring complex is most similar to _____. A. Thymosin B. Profilin C. Cofilin D. Gelsolin *E. Arp 2/3* ----- - gamma-tubulin ring complex = nucleation factor ... what nucleates actin filaments?

In mode of actin, the microtubule severing katanin (for tubulin dimers) is most similar to _____ (for actin filaments). A. Thymosin B. Profilin C. Cofilin D. Gelsolin E. Arp 2/3

In mode of actin, the microtubule severing katanin (for tubulin dimers) is most similar to _____ (for actin filaments). A. Thymosin B. Profilin *C. Cofilin* D. Gelsolin E. Arp 2/3 ----- - cofilin = binds to old actin-ADP filament and makes it more susceptible to breakage - gelsolin = bonafide severing protein this was a bad question lol

In plants and animals, inheritance of mitochondria is ... A. paternal B. maternal C. both of the above

In plants and animals, inheritance of mitochondria is ... A. paternal *B. maternal* C. both of the above

In smooth muscle, activation of myosin light chain kinases stimulate contraction after an increase in cytosolic Ca2+ initiated by ... A. plasma membrane Na+/Ca2+ exchange B. acetylcholine-gated Ca2+ channels C. activation of a Gq-linked GCPR, generation of IP3, and activation of ER Ca2+ channels

In smooth muscle, activation of myosin light chain kinases stimulate contraction after an increase in cytosolic Ca2+ initiated by ... A. plasma membrane Na+/Ca2+ exchange B. acetylcholine-gated Ca2+ channels *C. activation of a Gq-linked GCPR, generation of IP3, and activation of ER Ca2+ channels*

In the sliding filament assay ... A. myosin moves actin B. actin moves myosin

In the sliding filament assay ... *A. myosin moves actin* B. actin moves myosin

In the sliding filament assay, nothing moves until ... A. myosin does its dynamic warmup B. morning coffee C. ATP is added to the solution

In the sliding filament assay, nothing moves until ... A. myosin does its dynamic warmup B. morning coffee *C. ATP is added to the solution*

In which model of organization of the Golgi are compartments relatively stable and maintained by influx of vesicular cargo and efflux of specific cargo. A. cisternal maturation model B. vesicle transport model

In which of the following have most of the non-resident contents been digested? A. late endosome B. endolysosome C. lysosome

In which of the following have most of the non-resident contents been digested? A. late endosome B. endolysosome *C. lysosome*

In which phase of mitosis does the nuclear envelope break down? A. prophase B. prometaphase C. metaphase D. anaphase E. telophase

In which phase of mitosis does the nuclear envelope break down? A. prophase *B. prometaphase* C. metaphase D. anaphase E. telophase

Initiator and executioner caspases share all of the following features EXCEPT that ... A. they are cysteine proteases (they have a cysteine residue at their active site). B. they undergo cleavage during activation. *C. their inactive form is a monomer.* D. they are inhibited by IAPs. E. their active form is a dimer. ----- Caspases are cysteine proteases that are normally activated in apoptosis through proteolytic cleavage by other caspase molecules and formation of active dimers. Both initiator and executioner caspases can be inhibited by inhibitors of apoptosis (IAPs). While inactive initiator caspases are monomers, inactive executioner caspases are dimers.

Is STAT1/STAT2 association is mediated by SH2 domains? A. Yes B. No

Is STAT1/STAT2 association is mediated by SH2 domains? *A. Yes* B. No

What determines the resting membrane potential?

K+ equilibrium potential (due to K+ leak channels)

What kinds of channels play the largest role in determining membrane potential?

K+ leak channels

What is the soluble ER resident protein retrieval signal?

KDEL (lysine-aspartate-gluatamate-leucine)

KDEL receptors bind proteins with KDEL sequences when pH is lower than the pH of the ER lumen. What causes the lower pHs of compartments from which proteins with KDEL sequences are retrieved? *A. An ATP-dependent proton pump that moves protons from the cytosol to the compartment lumen* B. An ATP-dependent proton pump that moves protons from the compartment lumen to the cytosol C. Facilitated diffusion of proton down an electrochemical gradient ----- golgi = acidic environment ... protons are moved against the gradient ... not (B) bc that would de-acidify and not (C) bc it isn't diffusion! the protons are moving against their gradient

Knowing that the electrical gradient across the inner mitochondrial membrane provides some motive force for translocation of proteins across the inner mitochondrial membrane, you can figure out that ... A. a mitochondrial targeting sequence has positive charges B. a mitochondrial targeting sequence has negative charges C. a mitochondrial targeting sequence is hydrophobic

Knowing that the electrical gradient across the inner mitochondrial membrane provides some motive force for translocation of proteins across the inner mitochondrial membrane, you can figure out that ... *A. a mitochondrial targeting sequence has positive charges* B. a mitochondrial targeting sequence has negative charges C. a mitochondrial targeting sequence is hydrophobic

Lamellipodia have _____ at the leading edge and _____ protruding toward the leading edge.

Lamellipodia have *nucleated actin growth* at the leading edge and *actin filaments* protruding toward the leading edge.

Laminin is the primary component of ... A. Basal lamina B. Connective tissue C. Epithelial cell layer

Laminin is the primary component of ... *A. Basal lamina* B. Connective tissue C. Epithelial cell layer

Large polar and/or charged extracellular signaling molecules generally act ... A. by diffusing across the plasma membrane of a target cell and binding an intracellular receptor B. by binding the extracellular portion of a receptor, which transduces a change to the intracellular portion of the receptor

Large polar and/or charged extracellular signaling molecules generally act ... A. by diffusing across the plasma membrane of a target cell and binding an intracellular receptor *B. by binding the extracellular portion of a receptor, which transduces a change to the intracellular portion of the receptor*

Loss of function mutations in tumor suppressor proteins cause: A. apoptosis B. cancer C. arrest of cell cycle in G1 D. arrest of cell cycle in G2 E. cell differentiation

Loss of function mutations in tumor suppressor proteins cause: A. apoptosis *B. cancer* C. arrest of cell cycle in G1 D. arrest of cell cycle in G2 E. cell differentiation ----- - these tumor suppressor proteins can normally lead to apoptosis or cell cycle arrest when they are functional

Lysosomal hydrolases are functional ... A. at neutral pH B. at cytosolic pH C. at extracellular pH D. under acidic conditions

Lysosomal hydrolases are functional ... A. at neutral pH B. at cytosolic pH C. at extracellular pH *D. under acidic conditions* (he never said what the answer was but I'm pretty sure it's D)

In regard to the MAP-kinase pathway, ~what phosphorylates a MAPK~?

MAPKK

Microtubule-interfering molecules can interfere with mitosis by ... A. Affecting dynamic instability of microtubules B. Affecting actin polymerization C. Affecting intermediate filament network D. All of the above

Microtubule-interfering molecules can interfere with mitosis by ... *A. Affecting dynamic instability of microtubules* B. Affecting actin polymerization C. Affecting intermediate filament network D. All of the above ----- - the compounds can wipe out rapidly dividing cells - they prevent dynamic instability which is important for mitosis - not dealing with actin or intermediate filaments, so B and C are wrong

Mitochondria are thought to have been derived from a endosymbiosis between an ancestral archaeal cell and ... A. an ancestral alpha-proteobacterium B. an ancient photosynthetic proto-cyanobacterium C. both

Mitochondria are thought to have been derived from a endosymbiosis between an ancestral archaeal cell and ... *A. an ancestral alpha-proteobacterium* B. an ancient photosynthetic proto-cyanobacterium C. both

Mitochondria have roles in ... A. oxidative phosphorylation B. respiration C. heme synthesis D. the urea cycle E. amino acid catabolism F. gluconeogenesis G. synthesis of phospholipids H. Ca2+ buffering I. ...and it goes on and on and on and on

Mitochondrial fission involves ... A. cytosolic dynamins B. a mitotic spindle C. both of the above

Mitochondrial fission involves ... *A. cytosolic dynamins* B. a mitotic spindle C. both of the above

Mitochondrial proteins that are encoded by the nuclear genome are synthesized ... A. on ribosomes at the rough ER B. on free, cytosolic ribosomes C. on ribosomes in the mitochondrial matrix D. both B and C

Mitochondrial proteins that are encoded by the nuclear genome are synthesized ... A. on ribosomes at the rough ER *B. on free, cytosolic ribosomes* C. on ribosomes in the mitochondrial matrix D. both B and C

Mitogens: A. Activate RTKs, which leads to phosphatidylinositol activity via PI-3 kinase B. Activate Ras signaling, which activates MAP kinase C. Increase ribosome synthesis D. Inactivate BH3-only proteins

Mitogens: A. Activate RTKs, which leads to phosphatidylinositol activity via PI-3 kinase *B. Activate Ras signaling, which activates MAP kinase* C. Increase ribosome synthesis D. Inactivate BH3-only proteins

Most genes encoding mitochondrial proteins are ... A. in the nuclear genome B. in the mitochondrial genome C. in cytosolic ribosomes

Most genes encoding mitochondrial proteins are ... *A. in the nuclear genome* B. in the mitochondrial genome C. in cytosolic ribosomes

Multivesicular bodies can fuse with the plasma membrane, releasing vesicles into the extracellular space. They can fuse with the plasma membrane of target cells, delivering their cargo. This fusion likely requires ... A. the SNAREs on the vesicles B. some protein that takes the place of SNARE function

Multivesicular bodies can fuse with the plasma membrane, releasing vesicles into the extracellular space. They can fuse with the plasma membrane of target cells, delivering their cargo. This fusion likely requires ... A. the SNAREs on the vesicles *B. some protein that takes the place of SNARE function*

Mutations in two important cancer-critical genes, encoding p53 and Rb, respectively, are commonly found in cancers. What type of mutations are these expected to be? A. Gain-of-function mutations in both genes B. Loss-of-function mutation in p53 and gain-of-function mutation in Rb C. Gain-of-function mutation in p53 and loss-of-function mutation in Rb D. Loss-of-function mutations in both genes

Myosin II assembles with ... A. two myosin heavy chains B. two myosin light chain dimers C. both!

Myosin II assembles with ... A. two myosin heavy chains B. two myosin light chain dimers *C. both!*

Myosin II can assemble into thick bundles through association of ... A. myosin heads B. myosin tails

Myosin II can assemble into thick bundles through association of ... A. myosin heads *B. myosin tails*

Myosin is a nucleotide switch protein. What is it evolutionarily related to (i.e. other nucleotide switch proteins)? A. kinesins B. monomeric G proteins C. α subunits of heterotrimeric G proteins D. all of the above, and more!

Where is the mitochondrial targeting sequence found?

N terminal of proteins going to mitochondria

What is the motif for the attachment of a N-linked oligosaccharide/glycosylation?

N-X-S/T

N-linked oligosaccharides are ... A. first transferred to asparagine side chains in the ER B. trimmed in the ER and then the Golgi to form high-mannose oligosaccharides C. trimmed but then modified by addition of sugars in the ER to become complex oligosaccharides D. destined to face the lumen of intracellular compartments or the extracellular space E. all of the above

What is the potential energy product of photosystem I?

NADPH

How can a T-antigen get into/out of the nucleus?

NLS (nuclear localization sequence) used for import

Where are soluble cytosolic proteins targeted to?

NOT THE ER!!! they go to ribosomes in the cytosol to be translated

Dissociation of a trans-SNARE complex requires ...

NSF and ATP (energy source)

How are Na+ and K+ concentrations re-established after an action potential?

Na+/K+ pump pumping 3 Na+ out of the cell, and bringing 2 K+ into it

Neuromuscular junctions of vertebrates are special types of chemical synapses formed from close association between motor neuron axon terminals and muscle fibers. A thin layer of basal lamina separates the two cell membranes at the neuromuscular junction and is important for its organization and maintenance. Which of the following would you NOT expect to find in the basal lamina in these structures? A. Perlecan B. Nidogen C. Laminin D. Type I collagen E. Type IV collagen

O-linked glycosylation occurs in ... A. the ER B. the Golgi C. both of the above

O-linked glycosylation occurs in ... A. the ER *B. the Golgi* C. both of the above

What is a byproduct of the use of H2O to obtain a replacement electron for photosystem II?

One extracellular signaling molecule might have different effects on different target tissues. Explanations for this include all EXCEPT ... A. different cell types might express different receptor proteins for that signaling molecule B. different tissues have different functions, so they respond however they want to in order to get the job done C. intracellular effector proteins might be different in different tissue types, even if the receptors are the same

One extracellular signaling molecule might have different effects on different target tissues. Explanations for this include all EXCEPT ... A. different cell types might express different receptor proteins for that signaling molecule *B. different tissues have different functions, so they respond however they want to in order to get the job done* C. intracellular effector proteins might be different in different tissue types, even if the receptors are the same

One of those six 3-carbon molecules is bled off as a biosynthetic precursor, leaving ______ for regeneration of _____ 5-carbon ribulose 1,5 bisphosphate molecules. A. 5, 3 B. 5, 5 C. 3, 5 D. 3, 3

One of those six 3-carbon molecules is bled off as a biosynthetic precursor, leaving ______ for regeneration of _____ 5-carbon ribulose 1,5 bisphosphate molecules. *A. 5, 3* B. 5, 5 C. 3, 5 D. 3, 3

Organelle identity in the Rab A/Rab B example seen in class refers to: A. the particular type of Rab recruited to the membrane B. endocytosis or exocytosis

Organelle identity in the Rab A/Rab B example seen in class refers to: *A. the particular type of Rab recruited to the membrane* B. endocytosis or exocytosis

Oxygen consumed by respiration ends up in: A. water B. CO2 C. NADH D. the citric acid cycle

Oxygen consumed by respiration ends up in: *A. water* B. CO2 C. NADH D. the citric acid cycle

How does dissociation of the network vesicle and its uptake occur with specialized phagocytic cells?

PI 3-kinase adds another phosphate group to the initial phosphoinositide (PI(4,5)P2 --> PI (3,4,5)P3)

PI3K produces 3-phosphoinositides. What does PTEN do to these? A. creates more B. removes the phosphate group from the third position of the phosphoinositide C. creates PH domain binding

PI3K produces 3-phosphoinositides. What does PTEN do to these? A. creates more *B. removes the phosphate group from the third position of the phosphoinositide* C. creates PH domain binding

Which phospholipid is negatively charged?

Why does the inside of the plasma membrane have a net negative charge?

PS is negatively charged and it is found on the inside of the cell membrane (cytosolic side)

What can reverse the effects of PI 3-kinase?

PTEN (it is a PIP 3 phosphatase)

Phosphorylation of Bad by Akt creates binding sites for ... A. PH domains B. SH2 domains C. 14-3-3 domains D. SH3 domains E. PTB domains

Phosphorylation of Bad by Akt creates binding sites for ... A. PH domains B. SH2 domains *C. 14-3-3 domains* D. SH3 domains E. PTB domains

Place the cell cycle checkpoints in order: A. Start, G1-S, metaphase-anaphase B. G1-S, metaphase-anaphase, G2-M C. metaphase-anaphase, G2-M, G1-S D. Start, G2-M, metaphase-anaphase

Place the cell cycle checkpoints in order: A. Start, G1-S, metaphase-anaphase B. G1-S, metaphase-anaphase, G2-M C. metaphase-anaphase, G2-M, G1-S *D. Start, G2-M, metaphase-anaphase*

Plus-end tracking proteins (+TIPs) can ... A. ride along on growing microtubules B. anchor the plus ends at sites such as plasma membrane proteins C. both

Plus-end tracking proteins (+TIPs) can ... A. ride along on growing microtubules B. anchor the plus ends at sites such as plasma membrane proteins *C. both*

Proteins bind the phosphotyrosine-containing motifs on the RTK via ... A. SH2 domains B SH3 domains C. both

Proteins bind the phosphotyrosine-containing motifs on the RTK via ... *A. SH2 domains* B SH3 domains C. both

Proteins of the peroxisomal lumen generally ... A. are synthesized and folded in the cytosol B. are targeted to the peroxisome by a receptor that binds a peroxisome targeting motif C. contain a C-terminal peroxisomal targeting motif such as serine-lysine-leucine (SKL) D. all of the above

Proteins of the peroxisome membrane can be ... A. trafficked in vesicles from the ER to the peroxisome B. directly inserted from the cytosol into the peroxisome membrane by a tail anchor C. either of the above

Proteoglycans contain all EXCEPT: A. Branching polysaccharides B. Sulfated sugars C. A protein backbone D. Repeating disaccharides

Proteoglycans contain all EXCEPT: *A. Branching polysaccharides* B. Sulfated sugars C. A protein backbone D. Repeating disaccharides

Proton pumping processes in chloroplasts develop a proton gradient ... A. across the outer chloroplast membrane B. across the inner chloroplast membrane C. across the thylakoid membrane D. all of the above

Proton pumping processes in chloroplasts develop a proton gradient ... A. across the outer chloroplast membrane B. across the inner chloroplast membrane *C. across the thylakoid membrane* D. all of the above

What kind of receptor is EphA4?

RTK (dimer is phosphorylating itself on tyrosines)

Is ~RTK~ a tyrosine kinase or a serine/threonine kinase?

RTK stands for "receptor tyrosine kinase" heehee

Tethering proteins are recruited by ...

Rab

Name one G protein involved in vesicular trafficking.

Rab (involved in targeting), ARF, Sar1

What keeps Rab sequestered in the cytosol?

Rab GDI

If activation of one Rab at a membrane leads to recruitment and activation of a different Rab, what's that called?

Rab cascade (/compartment maturation) ... different pool of Rabs is associated with that particular membrane

What can change the identity of an organelle?

Rab cascades

How is the direction of transport through nuclear pores maintained?

Ran-GTPase

In regard to the MAP-kinase pathway, ~what activates a MAPKKK~?

Ras

what does G1-Cdk phosphoryate?

Rb protein

Rheb-GTP activates mTOR, stimulating cell growth and survival. What does a Rheb GAP do to this? A. stops the growth and survival signal B. augments the growth and survival signal

Rheb-GTP activates mTOR, stimulating cell growth and survival. What does a Rheb GAP do to this? *A. stops the growth and survival signal* B. augments the growth and survival signal

Rubisco catalyzes fixation of three CO2 molecules onto three 5-carbon molecules of ribulose 1-,5 bisphosphate. How many six-carbon molecules does that make? A. 3 B. 4 C. 5 D. 6

Rubisco catalyzes fixation of three CO2 molecules onto three 5-carbon molecules of ribulose 1-,5 bisphosphate. How many six-carbon molecules does that make? *A. 3* B. 4 C. 5 D. 6

what prevents additional pre-Rcs from reforming at the origins?

S-cdk persisting until the metaphase-->anaphase

What happens to SAR1 as a result of GTP binding?

SAR1 becomes ER membrane anchored and recruits Sec23 and Sec24 (inner coat proteins) and then COPII (outer coat protein) ... coat proteins then bind cargo receptors (which then buy cargo)

What is/are examples of ionic detergent(s)?

SDS

What domain binds ~phosphotyrosine-containing motif~?

SH2 and PTB

What domain binds ~proline-rich regions~?

SH3

What targets proteins to the peroxisome?

SKL motif on the C-terminus

How does a lumenal protein reach the peroxisome?

SKL motifs at the C-terminus targeting them to the lumen of the peroxisome

Sar1 is a small G protein that plays a role in COPII vesicle formation. When Sar1 is activated by its ____, it anchors to the donor membrane and binds inner COPII coat proteins. A. GEF B. GDI C. GAP

Sar1 is a small G protein that plays a role in COPII vesicle formation. When Sar1 is activated by its ____, it anchors to the donor membrane and binds inner COPII coat proteins. *A. GEF* B. GDI C. GAP

Sometimes epithelial cells are called "polarized" because ... A. they have positive and negative charges B. they have abundant hydrophilic molecules C. they have distinct membrane domains with different protein and lipid constituents D. all of the above

Sometimes epithelial cells are called "polarized" because ... A. they have positive and negative charges B. they have abundant hydrophilic molecules *C. they have distinct membrane domains with different protein and lipid constituents* D. all of the above

Soon after the discovery of nerve growth factor (NGF), researchers injected newborn mice with rabbit antiserum (i.e. serum that contains antibodies) against NGF. They observed massive nerve cell death compared to appropriate control injections. Up to 99% of the neurons in some parts of the developing peripheral nervous system died after about a week of daily injections. These results suggest that ... A. NGF signaling is sufficient for survival of the developing neurons. B. NGF signaling sensitizes developing nerve cells to apoptotic signals. *C. developing neurons undergo cell death in the absence of NGF.* D. developing neurons undergo apoptosis in the presence of rabbit proteins. E. developing neurons require NGF for apoptosis. ----- The antiserum injection results in the perturbation of NGF function, which is similar to knocking-down NGF using genetic techniques. The increase in cell death after injection suggests that NGF is important for nerve cell survival. We now know that the cells undergo apoptosis in the absence of the survival factor.

Suppose that a cell has overactive Sar1 GAPs. What would this do to COPII coat formation? A. rate of formation would increase B. no effects on coat formation C. it would promote Sar1 dissociation from the membrane and reverse coat assembly

Suppose that a cell has overactive Sar1 GAPs. What would this do to COPII coat formation? A. rate of formation would increase B. no effects on coat formation *C. it would promote Sar1 dissociation from the membrane and reverse coat assembly*

Tethering together of microtubules in the flagellar axoneme ... A. causes filament sliding when dynein acts B. prevents filaments from sliding when dynein acts, causing bending instead

Tethering together of microtubules in the flagellar axoneme ... A. causes filament sliding when dynein acts *B. prevents filaments from sliding when dynein acts, causing bending instead*

The "proton pump" of photosystem II is ... A. cytochrome b6-f complex B. chlorophyll C. special pair D. photoreaction center E. plastoquinone

The "proton pump" of photosystem II is ... *A. cytochrome b6-f complex* B. chlorophyll C. special pair D. photoreaction center E. plastoquinone

The ATP generated by photosystem II is synthesized in ... A. the thylakoid space B. the stroma C. the intermembrane space between the outer and inner chloroplast membranes

The ATP generated by photosystem II is synthesized in ... A. the thylakoid space *B. the stroma* C. the intermembrane space between the outer and inner chloroplast membranes

The G-α subunit in a cell type that uses Ach as a signal on a GPCR that activates IP3, then Ca2+, then NO, then guanylyl cyclase which causes smooth muscle relaxation is ... A. Gs B. Gi C. Gq D. Gt E. all of the above

The G-α subunit in a cell type that uses Ach as a signal on a GPCR that activates IP3, then Ca2+, then NO, then guanylyl cyclase which causes smooth muscle relaxation is ... A. Gs B. Gi *C. Gq* D. Gt E. all of the above ----- Gs turns AC on Gi turns AC off Gq turns PLC on

The LDL receptor releases its cargo under ... A. acidic conditions B. basic conditions

The LDL receptor releases its cargo under ... *A. acidic conditions* B. basic conditions

The Ndc80 complex's firm contact with polymerized MT might be most important when a _____ MT needs to _____ and pull a sister chromatid pole-ward. A. astral, polymerize B. interpolar, polymerize C. kinetochore, polymerize D. kinetochore, depolymerize E. interpolar, depolymerize

The Ndc80 complex's firm contact with polymerized MT might be most important when a _____ MT needs to _____ and pull a sister chromatid pole-ward. A. astral, polymerize B. interpolar, polymerize C. kinetochore, polymerize *D. kinetochore, depolymerize* E. interpolar, depolymerize ----- pulling towards the pole would mean we want the MT to shorten

The adaptin adaptor protein AP2 can bind ... A. clathrin triskelions B. transmembrane cargo receptors C. both of the above

The adaptin adaptor protein AP2 can bind ... A. clathrin triskelions B. transmembrane cargo receptors *C. both of the above*

The chloroplast ATP synthase is ... A. V-type B. F-type C. C-type D. T-type

The chloroplast ATP synthase is ... A. V-type *B. F-type* C. C-type D. T-type

The critical actin concentration (Cc) for a given end of an actin filament is the concentration of free actin ... A. at which the rate of polymerization equals the rate of depolymerization B. below which actin depolymerizes at that end C. above which actin polymerizes at that end D. all of the above

The electron that replaces the electron that had been separated from chlorophyll generally comes from ... A. chlorophyll B. water C. a quinone

The electron that replaces the electron that had been separated from chlorophyll generally comes from ... A. chlorophyll *B. water* C. a quinone

The electron transferred from a photoreaction center to an electron carrier in photosystem II is from ... A. water B. H+ C. CO2 D. chlorophyll

The electron transferred from a photoreaction center to an electron carrier in photosystem II is from ... A. water B. H+ C. CO2 *D. chlorophyll*

The gene encoding a lysosomal hydrolase is mutated so that it no longer encodes an ER signal sequence, but instead encodes a mitochondrial targeting sequence. What will be this protein's subcellular localization? A. lysosomes, because the hydrolases only function under acidic conditions B. the thylakoid space because the protein is drawn to the low pH C. mitochondria

The machinery for insertion of beta-barrel pore proteins into the outer bacterial membrane is similar to ... A. the sorting and assembly machinery of the mitochondrial outer membrane B. protein translocators of the outer membrane C. both

The machinery for insertion of beta-barrel pore proteins into the outer bacterial membrane is similar to ... *A. the sorting and assembly machinery of the mitochondrial outer membrane* B. protein translocators of the outer membrane C. both

The monomeric G protein Rho is activated by ... A. a Rho GAP B. a Rho GDI C. a Rho GEF

The monomeric G protein Rho is activated by ... A. a Rho GAP B. a Rho GDI *C. a Rho GEF*

The nucleotide switch action of kinesin-13 (a "catastrophe factor) ... A. stabilizes microtubules B. destabilizes microtubules

The nucleotide switch action of kinesin-13 (a "catastrophe factor) ... A. stabilizes microtubules *B. destabilizes microtubules*

The outer membrane of a bacterium is topologically equivalent to: A. the thylakoid membrane B. the chloroplast inner membrane C. the chloroplast outer membrane D. the mitochondrial inner membrane

The outer membrane of a bacterium is topologically equivalent to: A. the thylakoid membrane B. the chloroplast inner membrane *C. the chloroplast outer membrane* D. the mitochondrial inner membrane

The pH of the cytosol is about _____, while the pH of the lysosomal lumen is about _____. A. 5.0, 7.2 B. 7.2, 5.0 C. 7.2, 7.2 D. 5.0, 5.0

The pH of the cytosol is about _____, while the pH of the lysosomal lumen is about _____. A. 5.0, 7.2 *B. 7.2, 5.0* C. 7.2, 7.2 D. 5.0, 5.0

The photoreaction center found in photosystem II absorbs like that is ... A. ultraviolet B. visible C. infrared

The photoreaction center found in photosystem II absorbs like that is ... A. ultraviolet *B. visible* C. infrared ----- visible light = 400-700nm

The photosystem I photoreaction center absorbs light that is ... A. yellow B. purple C. green D. blue E. red F. yellow and blue G. red and blue H. green and blue I. purple and red

The photosystem I photoreaction center absorbs light that is ... A. yellow B. purple C. green D. blue E. red F. yellow and blue *G. red and blue* H. green and blue I. purple and red

The potential for Ras and Myc to drive cell proliferation classifies them as: A. growth factors B. proto-oncogenes C. tumor supressors D. oncogenes E. caspases

The potential for Ras and Myc to drive cell proliferation classifies them as: A. growth factors *B. proto-oncogenes* C. tumor supressors D. oncogenes E. caspases

The process by which specialized phagocytic cells ingest large particles is initiated by a monomeric G protein named Rho. What activates this process? A. a GAP B. a GEF C. a GDI

The process by which specialized phagocytic cells ingest large particles is initiated by a monomeric G protein named Rho. What activates this process? A. a GAP *B. a GEF* C. a GDI

The purpose of tight junctions is to: A. Allow the flow of solutes through the space between cells B. Keep cells from pulling away from each other C. Permit direct trafficking of molecules from one cell cytoplasm to another D. Create another barrier for solutes in the space between cells E. None of the above

The purpose of tight junctions is to: A. Allow the flow of solutes through the space between cells B. Keep cells from pulling away from each other C. Permit direct trafficking of molecules from one cell cytoplasm to another *D. Create a barrier for solutes in the space between cells* E. None of the above

The rate-limiting step in formation of new actin filaments is ... A. depolymerization B. catastrophe C. dynamic instability *D. nucleation*

This actin binding protein organizes filaments in parallel bundles ... A. fimbrin B. α-actinin C. filamin D. spectrin E. both A and B

This actin binding protein organizes filaments in parallel bundles ... A. fimbrin B. α-actinin C. filamin D. spectrin *E. both A and B*

This cell cycle checkpoint requires confirmation of the completion of DNA duplication as well as favorable environment for division. A. G2-M B. metaphase-anaphase C. G1-S

This cell cycle checkpoint requires confirmation of the completion of DNA duplication as well as favorable environment for division. *A. G2-M* B. metaphase-anaphase C. G1-S

This contributes to formation of the proton gradient across the thylakoid membrane: A. the "water splitting" that produces protons in the thylakoid space B. cytochrome b-6-f complex contributing to movement of protons from the stroma into the thylakoid space C. both

This junction connects to a network of IFs. A. Cadherin B. Adherens C. Desmosome D. Actin

This junction connects to a network of IFs. A. Cadherin B. Adherens *C. Desmosome* D. Actin

This junction senses tension via alpha-catenin. A. Cadherin B. Adherens C. Desmosome D. Actin

This junction senses tension via alpha-catenin. A. Cadherin *B. Adherens* C. Desmosome D. Actin

This molecule is recruited by vinculin to strengthen the epithelial adhesion belt. A. Cadherin B. Adherens C. Desmosome D. Actin

This molecule is recruited by vinculin to strengthen the epithelial adhesion belt. A. Cadherin B. Adherens C. Desmosome *D. Actin*

This molecule's homophylic associations enable "sorting out" of cell types in development. A. Cadherin B. Adherens C. Desmosome D. Actin

This molecule's homophylic associations enable "sorting out" of cell types in development. *A. Cadherin* B. Adherens C. Desmosome D. Actin

Topologically speaking, one of these things is not like the others, one of these things is not the same... A. ER lumen B. interior of vesicle C. Golgi lumen D. extracellular space E. cytosol

Topologically speaking, one of these things is not like the others, one of these things is not the same... A. ER lumen B. interior of vesicle C. Golgi lumen D. extracellular space *E. cytosol*

True or False: Drugs that interfere with the function of Bcl2 family proteins such as Bax and Bak may treat cancers by stimulating apoptosis. A. True B. False

True or False: Drugs that interfere with the function of Bcl2 family proteins such as Bax and Bak may treat cancers by stimulating apoptosis. A. True *B. False* ----- Bax and Bak are pro-apoptotic effector Bcl2 proteins, so their disruption will prevent apoptosis and potentially drive further cancer growth. Interfering with the anti-apoptotic Bcl2 family members (e.g. Bcl2, BclXL) are appropriate anti-cancer, pro-apoptotic targets.

True or False: Excessive apoptosis, in many cases, leads to autoimmune disease and cancer. A. True B. False

True or False: Excessive apoptosis, in many cases, leads to autoimmune disease and cancer. A. True *B. False* ----- Contribution to disease can come from either excessive apoptosis (e.g. in strokes) or insufficient apoptosis (e.g. in some autoimmune disease and cancers).

True or False: In about half of human cancers, the tumor suppressor protein p53 is mutated. A. True B. False

True or False: In about half of human cancers, the tumor suppressor protein p53 is mutated. *A. True* B. False ----- The p53 protein normally arrests the cell cycle or initiates apoptosis in response to DNA damage, which explains why the loss of p53 function is of benefit to, and is widely observed in, cancer cells.

True or False: The earlier a cancer is diagnosed, the better the chances are for a cure. A. True B. False

True or False: The earlier a cancer is diagnosed, the better the chances are for a cure. *A. True* B. False ----- Most cancers develop gradually from a single aberrant cell by the accumulation of a number of genetic and epigenetic changes over time. Treatment is generally easier if the cancer is diagnosed at earlier stages.

True or False: Unlike in normal tissues, cell death is extremely rare in tumors. A. True B. False

True or False: Unlike in normal tissues, cell death is extremely rare in tumors. A. True *B. False* ----- Cells within a tumor still die in large numbers, typically undergoing necrosis as may cancers render cells resistant to apoptosis.

True or false: Glycosaminoglycan chains in the extracellular matrix consist of highly branched, negatively-charged polysaccharides. A. True B. False

True or false: Glycosaminoglycan chains in the extracellular matrix consist of highly branched, negatively-charged polysaccharides. A. True *B. False* ----- Glycosaminoglycans (GAGs) are unbranched and highly anionic.

Unfolded or misfolded proteins in the ER are ... A. retained by binding to chaperone proteins until properly folded or translocated out of the ER B. bound to cargo receptors C. removed from the ER by vesicular trafficking

Unfolded or misfolded proteins in the ER are ... *A. retained by binding to chaperone proteins until properly folded or translocated out of the ER* B. bound to cargo receptors C. removed from the ER by vesicular trafficking

Do the products of photosynthesis have a low or a high redox potential?

VERY HIGH!!! (he said this so many times! know this!)

Vesicles containing M6P receptors ... A. sometimes are trafficked to the plasma membrane B. can bud from the trans-Golgi network and move to the endosome C. can bud from the endosome and move to the trans-Golgi network D. all of the above

Vesicular trafficking is ... A. associated with a microtubule network B. reliant on microtubule-associated motor proteins C. a process in which vesicles migrate in random directions until they encounter a target membrane D. only in one direction (i.e. from ER to Golgi, but not the other way around) E. both A and B

What are energy sources for the dark reactions of photosynthesis? A. potential energy in the electron carrier NADPH B. chemical energy of ATP C. sunlight D. a proton gradient E. all of the above F. A and B, but not the other stuff

What calmodulin-related protein causes a shift in tropomyosin that allows myosin to change its binding position on actin? A. troponin C B. SR Ca2+ ATPase C. IP3-activated Ca2+ channel

What calmodulin-related protein causes a shift in tropomyosin that allows myosin to change its binding position on actin? *A. troponin C* B. SR Ca2+ ATPase C. IP3-activated Ca2+ channel

What causes the target membrane Rab to dissociate from the membrane and tethering protein? A. Rab GEF B. Rab GAP C. Rab GDI

What causes the target membrane Rab to dissociate from the membrane and tethering protein? A. Rab GEF *B. Rab GAP* C. Rab GDI

What clears Ca2+ out of the cytosol? A. GPCR B. MLCK C. myosin D. actin E. SR/ER Ca2+ ATPase

What clears Ca2+ out of the cytosol? A. GPCR B. MLCK C. myosin D. actin *E. SR/ER Ca2+ ATPase*

What clears cytosolic Ca2+ back into the sarcoplasmic reticulum? A. voltage gated calcium channels B. IP3 activated calcium channels C. sarcoplasmic reticulum Ca2+ ATPases (Ca2+ pumps)

What clears cytosolic Ca2+ back into the sarcoplasmic reticulum? A. voltage gated calcium channels B. IP3 activated calcium channels *C. sarcoplasmic reticulum Ca2+ ATPases (Ca2+ pumps)*

What could inactivate or prevent actions of a MAPK signaling cascade such as in figure 15-49? A. a Ras GAP B. dephosphorylation of a MAP kinase kinase C. dephosphorylation a MAP kinase D. dephosphorylation of MAP kinase substrates E. All of the above

What could inactivate or prevent actions of a MAPK signaling cascade such as in figure 15-49? Selected Answer: E. All of the above Answers: A. a Ras GAP B. dephosphorylation of a MAP kinase kinase C. dephosphorylation a MAP kinase D. dephosphorylation of MAP kinase substrates *E. All of the above*

What do you think the little yellow dynamin protein does (it's dynamin lol)? A. recruits cargo B. binds cargo receptors C. recruits the clathrin coat D. pinches off the vesicle from the donor membrane

What do you think the little yellow dynamin protein does (it's dynamin lol) ? A. recruits cargo B. binds cargo receptors C. recruits the clathrin coat *D. pinches off the vesicle from the donor membrane*

What does adaptin bind in the LDL pathway? A. LDL receptor B. clathrin triskelion C. apolipoprotein D. LDL particle E. A and B

What does adaptin bind in the LDL pathway? A. LDL receptor B. clathrin triskelion C. apolipoprotein D. LDL particle *E. A and B*

What does the ORC do? A. Phosphorylates p53 B. Binds to DNA prior to replication at origin sites C. Adds polyubiquitin residues to p21 D. Receptor for growth factors

What does the ORC do? A. Phosphorylates p53 *B. Binds to DNA prior to replication at origin sites* C. Adds polyubiquitin residues to p21 D. Receptor for growth factors

What domain of son of sevenless (Sos) recruits it to the plasma membrane, where it is then in close proximity to Grb2? A. PH B. SH3 C. 14-3-3 D. PTB E. SH2

What domain of son of sevenless (Sos) recruits it to the plasma membrane, where it is then in close proximity to Grb2? *A. PH* B. SH3 C. 14-3-3 D. PTB E. SH2

What end os the microtubule does catastrophe/rescue occur at? A. plus end B. minus end C. both

What end os the microtubule does catastrophe/rescue occur at? *A. plus end* B. minus end C. both ------ polymerizes more rapidly and is more likely to have a GTP cap

What happens if a protein's KDEL sequence is blocked by a drug? A. The protein won't bind KDEL receptors B. The protein won't be retrieved to the ER C. The protein will likely be secreted, though slowly, because aggregation of ER resident proteins is another mechanism for retention D. All of the above

What happens if dynamin can't hydrolyze GTP? A. Premature pinching off of a vesicle B. Prevention of vesicles from pinching off C. Membrane doesn't curve D. Vesicle doesn't form

What happens if dynamin can't hydrolyze GTP? A. Premature pinching off of a vesicle *B. Prevention of vesicles from pinching off* C. Membrane doesn't curve D. Vesicle doesn't form

What happens if the actin concentration is greater than Cc(T), but equal to Cc(D)? A. polymerization at both ends B. polymerization at the plus end, and no net polymerization at the minus end C. depolymerization at both ends

What happens if the actin concentration is greater than Cc(T), but equal to Cc(D)? A. polymerization at both ends *B. polymerization at the plus end, and no net polymerization at the minus end* C. depolymerization at both ends

What is a common feature of purple nonsulfur bacteria, plant chloroplasts and cyanobacteria, and mitochondria? A. all involve electron transfer that result in formation of a proton gradient B. all require O2 C. all produce H2O

What is a common feature of purple nonsulfur bacteria, plant chloroplasts and cyanobacteria, and mitochondria? *A. all involve electron transfer that result in formation of a proton gradient* B. all require O2 C. all produce H2O

What is a pathway for delivery of material to the lysosome? A. endocytosis B. phagocytosis C. autophagy D. macropinocytosis E. all of the above

What is a pathway for delivery of material to the lysosome? A. endocytosis B. phagocytosis C. autophagy D. macropinocytosis *E. all of the above*

What is an example of a mechanism for desensitization to an extracellular signaling molecule? A. receptor sequestration by endocytosis B. receptor degradation after endocytosis C. receptor inactivation D. inactivation of an effector protein of the receptor E. production of an inhibitory protein that suppresses the receptor's actions F. all of the above

What is the basis of M6P receptor binding to and release of M6P-tagged proteins? A. binding at pH 6.5-6.7 B. release at pH 6.0 C. both

What is the basis of M6P receptor binding to and release of M6P-tagged proteins? A. binding at pH 6.5-6.7 B. release at pH 6.0 *C. both*

What is the biggest consumer of ATP via ATP hydrolysis during skeletal muscle contractions? A. myosin B. SR Ca2+ C. protein synthesis D. vesicular transport

What is the biggest consumer of ATP via ATP hydrolysis during skeletal muscle contractions? *A. myosin* B. SR Ca2+ C. protein synthesis D. vesicular transport

What is the mode of potential energy that is transformed into the kinetic energy of turning of the ATP synthase rotor? A. chemical gradient B. electrical gradient C. both of the above (i.e. an electrochemical gradient)

What is the mode of potential energy that is transformed into the kinetic energy of turning of the ATP synthase rotor? A. chemical gradient B. electrical gradient *C. both of the above (i.e. an electrochemical gradient)*

What is the role of cohesin in the cell cycle? A. Binding sister chromatids together during S-phase. B. Securing the origin recognition complex to the DNA helicase during replication. C. Triggering anaphase by targeting M-cyclin for degradation. D. Verifying the cell is ready to enter the cycle at the restriction point.

What is the role of cohesin in the cell cycle? *A. Binding sister chromatids together during S-phase.* B. Securing the origin recognition complex to the DNA helicase during replication. C. Triggering anaphase by targeting M-cyclin for degradation. D. Verifying the cell is ready to enter the cycle at the restriction point. ----- Cohesin is a large protein complex that forms a coiled-coil ring structure, linking sister chromatids and enabling them to be attached correctly to the poles of the mitotic spindle.

What is the second biggest consumer of ATP via ATP hydrolysis during skeletal muscle contractions? A. myosin B. SR Ca2+ C. protein synthesis D. vesicular transport

What is the second biggest consumer of ATP via ATP hydrolysis during skeletal muscle contractions? A. myosin *B. SR Ca2+* C. protein synthesis D. vesicular transport

What is the target of SCF? A. APC/C B. CKIs C. Securin D. M-Cdk

What is the target of SCF? A. APC/C *B. CKIs* C. Securin D. M-Cdk

What is true of ATPases? A. they can pump protons B. they can harness a proton gradient to drive ATP synthesis C. both

What is true of ATPases? A. they can pump protons B. they can harness a proton gradient to drive ATP synthesis *C. both*

What makes up the mitotic spindles? A. microtubules B. actin filaments C. intermediate filaments D. all of the above

What makes up the mitotic spindles? *A. microtubules* B. actin filaments C. intermediate filaments D. all of the above

What plays a role in retracting a motile cell at the trailing side? A. actin polymerization B. attachment of the cell to the substratum at focal adhesions C. actin depolymerization D. myosin action on actin E. all except A

What process returns glucose transporters from the plasma membrane to intracellular storage vesicles? A. exocytosis B. endocytosis C. transcytosis D. sequestration E. all of the above

What process returns glucose transporters from the plasma membrane to intracellular storage vesicles? A. exocytosis *B. endocytosis* C. transcytosis D. sequestration E. all of the above

What process takes glucose transporters to the plasma membrane from intracellular storage vesicles? A. exocytosis B. endocytosis C. transcytosis D. sequestration E. all of the above

What process takes glucose transporters to the plasma membrane from intracellular storage vesicles? *A. exocytosis* B. endocytosis C. transcytosis D. sequestration E. all of the above

What produced the phosphoinositides shown in fig 15-11? A. phosphatidylinositol and phosphoinositide kinases B. phosphoinositide phosphatases C. an RTK D. a GEF E. a GAP

What produced the phosphoinositides shown in fig 15-11? *A. phosphatidylinositol and phosphoinositide kinases* B. phosphoinositide phosphatases C. an RTK D. a GEF E. a GAP

What protein "unzips" the SNARE bundle? A. synaptotagmin B. synaptobrevin C. complexin D. syntaxin E. NSF

What protein "unzips" the SNARE bundle? A. synaptotagmin B. synaptobrevin C. complexin D. syntaxin *E. NSF* ----- NSF is used for the dissociation of every SNARE bundle (ATP-dependent process)

What protein is responsible for the lower pH in the Golgi lumen compared to the ER lumen? A. a proton channel B. a proton carrier that allows transmembrane proton movement down an electrochemical gradient C. ATP-dependent proton pumping into the Golgi lumen by a V-Type ATPase

What protein is responsible for the lower pH in the Golgi lumen compared to the ER lumen? A. a proton channel B. a proton carrier that allows transmembrane proton movement down an electrochemical gradient *C. ATP-dependent proton pumping into the Golgi lumen by a V-Type ATPase*

What is protruding the leading edge of a cell? A. myosin B. actin polymerization C. integrins

What protrudes the leading edge of a cell? A. myosin *B. actin polymerization* C. integrins

What pushes a motile cell forward at the leading edge? A. actin polymerization B. attachment of the cell to the substratum at focal adhesions C. actin depolymerization D. myosin action on actin E. all except A

What pushes a motile cell forward at the leading edge? *A. actin polymerization* B. attachment of the cell to the substratum at focal adhesions C. actin depolymerization D. myosin action on actin E. all except A

What role does NSF play? A. selection of the target compartment B. release of cargo C. ATP-dependent disassociation of v-SNAREs and t-SNAREs

What role does NSF play? A. selection of the target compartment B. release of cargo *C. ATP-dependent disassociation of v-SNAREs and t-SNAREs*

What side of G-actin does ATP bind? A. plus B. minus

What side of G-actin does ATP bind? A. plus *B. minus*

What type of receptor binds resident lysosomal proteins? A. KDEL receptor B. KKXX-binding proteins C. mannose 6-phosphate (M6P) receptors

What type of receptor binds resident lysosomal proteins? A. KDEL receptor B. KKXX-binding proteins *C. mannose 6-phosphate (M6P) receptors*

What will AP2 bind? A. cargo receptor B. clathrin triskelion C. both

What will AP2 bind? A. cargo receptor B. clathrin triskelion *C. both*

What would a Ras-Gef do to the FRET signal? A. increase B. decrease C. both D. none of the above

What would a Ras-GEF do to the FRET signal? *A. increase* B. decrease C. both D. none of the above ----- GEF causes Ras to give up GDP and bind the fluorescent GTP

What would a SAR1 GAP do to a partially-assembled COPII coat? A. Cause coat dissociation B. Speed up coat formation

What would a SAR1 GAP do to a partially-assembled COPII coat? *A. Cause coat dissociation* B. Speed up coat formation

What would an inhibitor of cGMP phosphodiesterase do? A. nada B. cause smooth muscle cell relaxation C. make Pfizer beaucoup bucks D. B and C

What would an inhibitor of cGMP phosphodiesterase do? A. nada B. cause smooth muscle cell relaxation C. make Pfizer beaucoup bucks *D. B and C* ----- beaucoup means "a lot" in french lol ... basically he's hinting at Pfizer making a lot of money off of Viagra bc it uses this pathway and causes smooth muscle cell relaxation

What would an uncoupling drug do to ATP synthesis? A. decrease it B. increase it

What would an uncoupling drug do to ATP synthesis? *A. decrease it* B. increase it

What would an uncoupling drug to do heat production? A. decrease it B. increase it

What would an uncoupling drug to do heat production? A. decrease it *B. increase it*

What would an uncoupling drug to do respiration? A. decrease it B. increase it

What would an uncoupling drug to do respiration? A. decrease it *B. increase it*

What would happen if this process (H+ traveling down their gradient and creating ATP from ADP) were to run in reverse? A. ATP synthase would hydrolyze ATP to ADP + Pi B. A proton gradient would be generated *C. both* ----- running this in reverse would mean that the protons aren't moving down their gradient, and would be moving out (being pumped against their gradient) ... chemical energy allows for the spinning of the turbine ... V-type ATPase would be an example of something that runs in reverse

What would reverse the assembly (dissassociation) of anything that is recruited by a phosphoinositide? A. GAP B. GEF C. GDI D. a phosphoinositide phosphatase

What would reverse the assembly (dissassociation) of anything that is recruited by a phosphoinositide? A. GAP B. GEF C. GDI *D. a phosphoinositide phosphatase*

What would the proton ionopphore dinitrophenol (DNP) do to the pH of the lysosomal lumen? A. increase it B. decrease it C. no effect

What would the proton ionopphore dinitrophenol (DNP) do to the pH of the lysosomal lumen? *A. increase it* B. decrease it C. no effect

What's happening at the end of the curve that is seen (flat part) when ~preformed actin filament seeds~ are added? A. nucleation B. polymerization C. treadmilling

What's happening at the end of the curve that is seen (flat part) when ~preformed actin filament seeds~ are added? A. nucleation B. polymerization *C. treadmilling*

What's happening in the middle of the curve that is seen (steepest part) when ~no preformed actin filament seeds are added~? A. nucleation B. polymerization C. treadmilling

What's happening in the middle of the curve that is seen (steepest part) when ~no preformed actin filament seeds~ are added? A. nucleation *B. polymerization* C. treadmilling

What's required for actin movement in the sliding filament assay? A. Ca2+ B. ATP C. both

What's required for actin movement in the sliding filament assay? A. Ca2+ *B. ATP* C. both ----- this isn't a muscle so there is no Ca2+ involved ... it is just a naked actin filament ... no regulatory complex that makes it sensitive to Ca2+

What's required for actin-myosin cross bridge cycling in skeletal muscle sarcomeres? A. Ca2+ B. ATP C. both

What's required for actin-myosin cross bridge cycling in skeletal muscle sarcomeres? A. Ca2+ B. ATP *C. both* ----- now, the regulatory complex is on it, when you compare to the sliding filament assay (so you also need Ca2+)

What's retrieved to the ER? A. Membrane lipids B. Cargo receptors C. SNAREs D. All of the above and more

What's retrieved to the ER? A. Membrane lipids B. Cargo receptors C. SNAREs *D. All of the above and more*

What's the orientation of microtubules like in neurons? A. Microtubule plus ends are all toward the synapse in axons. B. In the dendrite, microtubules have two (antiparallel) orientations. C. both

What's the orientation of microtubules like in neurons? A. Microtubule plus ends are all toward the synapse in axons. B. In the dendrite, microtubules have two (antiparallel) orientations. *C. both*

When Ca2+ enters the cytosol of a skeletal muscle cell via voltage-gated channels, that causes ... A. Ca2+tastrophe B. Calcium-induced calcium release from the sarcoplasmic reticulum C. release of acetylcholine D. relaxation of skeletal muscle

When Ca2+ enters the cytosol of a skeletal muscle cell via voltage-gated channels, that causes ... A. Ca2+tastrophe *B. Calcium-induced calcium release from the sarcoplasmic reticulum* C. release of acetylcholine D. relaxation of skeletal muscle

When a GPCR binds its ligand, what does the α subunit of the heterotrimeric G protein do? A. release GDP B. bind GTP C. both

When a GPCR binds its ligand, what does the α subunit of the heterotrimeric G protein do? A. release GDP B. bind GTP *C. both*

When a cell secretes an extracellular signaling protein that acts through a receptor on the cell surface of the very same cell, that is ... A. autocrine signaling B. paracrine signaling C. endocrine signaling D. synaptic signaling

When a cell secretes an extracellular signaling protein that acts through a receptor on the cell surface of the very same cell, that is ... *A. autocrine signaling* B. paracrine signaling C. endocrine signaling D. synaptic signaling

When a portion of the endosomal membrane is endocytosed, this creates ... A. multivesicular body B. retrieval vesicle C. autophagosome

When a portion of the endosomal membrane is endocytosed, this creates ... *A. multivesicular body* B. retrieval vesicle C. autophagosome

When a survival factor receptor activates AKT kinase, what does AKT phosphorylate? A. IAPs B. Bcl2 C. a BH3-only protein D. p53 E. Rb

When a survival factor receptor activates AKT kinase, what does AKT phosphorylate? A. IAPs B. Bcl2 *C. a BH3-only protein* D. p53 E. Rb

When actin is polymerizing at the plus end at the same rate that it's depolymerizing at the minus end, that's A. treadmilling B. elongation C. shortening D. catastrophe 5, Which is lower? *A. Cc (T) B. Cc (D)

When actin is polymerizing at the plus end at the same rate that it's depolymerizing at the minus end, that's *A. treadmilling* B. elongation C. shortening D. catastrophe 5, Which is lower? *A. Cc (T) B. Cc (D) ----- no clue what the 5, thing is it was under the question when i went back to get the answer???

When active Rab5 is associated with the endosomal membrane, it activates phosphatidylinositol 3-kinase PI3K). PI3K creates a ______________ that recruits other proteins, including tethering proteins, to the endosomal cytosolic surface. A. phosphoinositide B. coated pit C. SNARE complex D. multivesicular body

When active Rab5 is associated with the endosomal membrane, it activates phosphatidylinositol 3-kinase PI3K). PI3K creates a ______________ that recruits other proteins, including tethering proteins, to the endosomal cytosolic surface. *A. phosphoinositide* B. coated pit C. SNARE complex D. multivesicular body

When an action potential in a neuron causes release of a signaling molecule that binds receptors on an adjacent target cell, this is ... A. autocrine signaling B. paracrine signaling C. endocrine signaling D. synaptic signaling

When do chromosomes reaggreggate with nuclear lamina? A. Prophase B. Prometaphase C. Metaphase D. Anaphase E. Telophase

When do chromosomes reaggreggate with nuclear lamina? A. Prophase B. Prometaphase C. Metaphase D. Anaphase *E. Telophase*

When does (small) saltatory oscillation of chromatids occur? A. Prophase B. Prometaphase C. Metaphase D. Anaphase E. Telophase

When does (small) saltatory oscillation of chromatids occur? A. Prophase B. Prometaphase *C. Metaphase* D. Anaphase E. Telophase

When does separation of sister chromatids occur in mitosis? A. Prophase B. Prometaphase C. Metaphase D. Anaphase E. Telophase

When does separation of sister chromatids occur in mitosis? A. Prophase B. Prometaphase C. Metaphase *D. Anaphase* E. Telophase

When does the nuclear envelope disintegrate? A. Prophase B. Prometaphase C. Metaphase D. Anaphase E. Telophase

When does the nuclear envelope disintegrate? A. Prophase *B. Prometaphase* C. Metaphase D. Anaphase E. Telophase

When does the spindle complex begins coming together around centrosomes? A. Prophase B. Prometaphase C. Metaphase D. Anaphase E. Telophase

When does the spindle complex begins coming together around centrosomes? *A. Prophase* B. Prometaphase C. Metaphase D. Anaphase E. Telophase

When microtubules polymerize from an organizing center, the push of growing microtubules on the cell periphery ... A. pulls the organizing center toward the plasma membrane B. results in central location of the organizing center

When microtubules polymerize from an organizing center, the push of growing microtubules on the cell periphery ... A. pulls the organizing center toward the plasma membrane *B. results in central location of the organizing center*

When one cell secretes a signaling molecule that acts on a nearby cell, that is ... A. autocrine signaling B. paracrine signaling C. endocrine signaling

When one cell secretes a signaling molecule that acts on a nearby cell, that is ... A. autocrine signaling *B. paracrine signaling* C. endocrine signaling

When seven γ tubulin small complexes (each containing two γ-tubulins) form a spiral so that one of the γ tubulins in the seventh small complex overlaps with one of the γ tubulins in the first small complexes, that creates ____ docking sites for α-β tubulin dimers. A. 1 B. 7 C. 13 D. 14

When the membrane of an intracellular vesicle fuses with the plasma membrane, this is ... A. endocytosis B. exocytosis C. both of the above

When the membrane of an intracellular vesicle fuses with the plasma membrane, this is: A. endocytosis *B. exocytosis* C. both of the above

When the microtubules of an axoneme are used to nucleate microtubule polymerization, polymerization occurs more rapidly at ... A. the plus end B. the minus end C. neither end

When the microtubules of an axoneme are used to nucleate microtubule polymerization, polymerization occurs more rapidly at ... *A. the plus end* B. the minus end C. neither end

When this is fluorescently tagged, it can be visualized as a "comet", riding along as a microtubule grows. Which is it? A. gamma-tubulin B. MTOC C. +TIP D. All of these

When this is fluorescently tagged, it can be visualized as a "comet", riding along as a microtubule grows. Which is it? A. gamma-tubulin B. MTOC *C. +TIP* D. All of these ----- - gamma-tubulin is at the minus end ... it has a role in nucleating the microtubule ... end that's associated with hit, that's polymerizing towards the plus end = the minus end ... wouldn't use gamma-tubulin to label the plus end! (same with MTOC) - MTOC is at minus end - +TIP is at plus end

When those three 6-carbon molecules are processed into 3-carbon molecules, how many 3 carbon molecules are there? A. 6 B. 3 C. 2

When those three 6-carbon molecules are processed into 3-carbon molecules, how many are there? *A. 6* B. 3 C. 2

Where are most mitochondrial proteins translated? A. in the cytosol B. in the matrix C. in the intermembrane space D. on ribosomes attached with the cytosolic face of the ER E. all of the above

Where are most mitochondrial proteins translated? *A. in the cytosol* B. in the matrix C. in the intermembrane space D. on ribosomes attached with the cytosolic face of the ER E. all of the above ------ 13 are translated in the matrix, but the rest (1,000+) are done in the cytosol! ... also it's not D because the only proteins that get to the ER are ones that have an ER signal sequence, and these mitochondrial proteins don't have that

Where are the most of the genes contained in the initial engulfed bacterium located today? A. in the mitochondria B. in the nucleus

Where are the most of the genes contained in the initial engulfed bacterium located today? A. in the mitochondria *B. in the nucleus* ----- most of the genes in the engulfed bacterium were shipped to the nuclear genome over time

Where is ATP produced by ATP synthase? A. stroma B. matrix C. thylakoid space D. intermembrane space E. A and B

Where is ATP produced by ATP synthase? A. stroma B. matrix C. thylakoid space D. intermembrane space *E. A and B*

Where is collagen produced? A. Basal lamina B. Connective tissue C. Epithelial cell layer

Where is collagen produced? A. Basal lamina *B. Connective tissue* C. Epithelial cell layer

Which actin growth curve would be more likely in the presence of active Arp 2/3 complexes? A. no preformed actin filament seeds B. preformed actin filament seeds

Which actin growth curve would be more likely in the presence of active Arp 2/3 complexes? A. no preformed actin filament seeds *B. preformed actin filament seeds*

Which anchors or reels in astral microtubules? A. dynein B. kinesin 5 C. kinesin 14 D. kinesins 4 or 10

Which anchors or reels in astral microtubules? *A. dynein* B. kinesin 5 C. kinesin 14 D. kinesins 4 or 10

Which animal has the highest percentage of unsaturated fatty acids in its membrane? A. Antarctic fish B. Desert iguana C. Human being D. Polar bear E. Thermophilic bacterium

Which animal has the highest percentage of unsaturated fatty acids in its membrane? *A. Antarctic fish* B. Desert iguana C. Human being D. Polar bear E. Thermophilic bacterium ----- unsaturated fatty acids stay fluid at a lower temperature so we need something that lives in the cold (warm-blooded animal) ... polar bear can regulate its own temperature so lipids don't worry as much, so it's the fish!

Which came last? A. formation of the oceans B. the first living cells C. photosynthetic cells D. formation of the earth E. eukaryotic photosynthetic cells

Which came last? A. formation of the oceans B. the first living cells C. photosynthetic cells D. formation of the earth *E. eukaryotic photosynthetic cells*

Which cytoskeletal element reorganizes in the course of mitosis? A. microtubules B. actin filaments C. intermediate filaments D. all of the above

Which cytoskeletal element reorganizes in the course of mitosis? A. microtubules B. actin filaments C. intermediate filaments *D. all of the above*

Which donates electrons that will reduce NADP+ to NADPH? A. photosystem I B. photosystem II C. both

Which donates electrons that will reduce NADP+ to NADPH? A. photosystem I B. photosystem II C. both ----- he never went back to this question ah ... i think it's B??? the electron initially comes from photosystem I so maybe C though?

Which donates electrons to an "electron transport chain" that generates a proton gradient? A. photosystem I B. photosystem II C. both

Which donates electrons to an "electron transport chain" that generates a proton gradient? A. photosystem I B. photosystem II C. both ----- he never exlicitly answered this one but i'm pretty sure it's PS II bc it drives the p+ pump that happens before the electron goes to PS I

Which end of the microtubule starts at the gamma-tubulin ring complex? A. minus end B. plus end C. both

Which end of the microtubule starts at the gamma-tubulin ring complex? (it's the bottom part of the last picture thingy) *A. minus end* B. plus end C. both

Which filament is more stable? A. capped at both ends B. free plus end C. capped only at minus end D. capped only at the plus end

Which filament is more stable? *A. capped at both ends* B. free plus end C. capped only at minus end D. capped only at the plus end

Which happened last? A. engulfment of the photosynthetic bacterium B. origin of the nucleus C. engulfment of the protomitochondrion

Which happened last? *A. engulfment of the photosynthetic bacterium* B. origin of the nucleus C. engulfment of the protomitochondrion

Which has a region of homology to a monomeric G protein? A. a G protein coupled receptor (GPCR) B. a G-α subunit C. a G-β/γ complex

Which has a region of homology to a monomeric G protein? A. a G protein coupled receptor (GPCR) *B. a G-α subunit* C. a G-β/γ complex

Which is NOT a known function of basal lamina? A. Creates a barrier to restrict location of specific cells. B. Forms a semi-permeable boundary that filters soluble molecules. C. Scaffolds layers of cells and fixes them in place. D. Retains deposited molecules to aid in regeneration after cell damage. E. All of the above are functions of basal lamina.

Which is NOT an advantage of small molecule therapeutics? A. Reduced side effects vs chemo/radiation B. Maximize efficacy/targeting against a specific type of cancer C. May be combined with other treatment modalities D. "Arms race" between tumor cells and drug function

Which is NOT an advantage of small molecule therapeutics? A. Reduced side effects vs chemo/radiation B. Maximize efficacy/targeting against a specific type of cancer C. May be combined with other treatment modalities *D. "Arms race" between tumor cells and drug function*

Which is NOT true of laminin? A. Major component of basal lamina B. Forms a trimer with three distinct chains C. Organizes into long fibrillar bundles D. Has multiple binding sites for other laminin proteins

Which is NOT true of laminin? A. Major component of basal lamina B. Forms a trimer with three distinct chains *C. Organizes into long fibrillar bundles* D. Has multiple binding sites for other laminin proteins ----- not C bc it's a sheet structure!!! D is yes bc that's what makes it into a sheet!!! hehehe

Which is a second messenger molecule? A. cAMP B. Ca2+ C. diacylglycerol (DAG) D. inositol trisphosphate (IP3) E. all of the above

Which is a second messenger molecule? A. cAMP B. Ca2+ C. diacylglycerol (DAG) D. inositol trisphosphate (IP3) *E. all of the above*

Which is a spring-like protein that anchors the myosin thick filament bundle? A. tropomodulin B. titin C. myosin D. nebulin E. CapZ

Which is a spring-like protein that anchors the myosin thick filament bundle? A. tropomodulin *B. titin* C. myosin D. nebulin E. CapZ

Which is an example of energy? A. Sunlight B. Potential energy of an electron donor C. A transmembrane electrical, chemical, or electrochemical gradient D. Chemical energy of oxidative substrates (e.g. fats, carbohydrates, etc.) E. Chemical energy in the phosphoester or phosphoanhydride bonds of ATP F. All of the above

Which is more likely to be bound to ADP? A. actin at the plus end B. actin toward the minus end

Which is more likely to be bound to ADP? A. actin at the plus end *B. actin toward the minus end*

Which is most accurate? A. the enzymes in the cis, medial, and trans Golgi compartments are all the same B. there is a gradient of enzyme localization such that some are more enriched in some compartments than others C. enzymes are strictly confined to one part of the Golgi

Which is most accurate? A. the enzymes in the cis, medial, and trans Golgi compartments are all the same *B. there is a gradient of enzyme localization such that some are more enriched in some compartments than others* C. enzymes are strictly confined to one part of the Golgi

Which is the "tension sensing" kinase that plays a role in preventing full kinetochore capture until biorientation has been achieved? A. Akt B. RTK C. PKA D. Aurora B E. PKC

Which is the "tension sensing" kinase that plays a role in preventing full kinetochore capture until biorientation has been achieved? A. Akt B. RTK C. PKA *D. Aurora B* E. PKC

Which is true? A. 3 carbons from CO2 are fixed in the first reaction of the Calvin cycle B. the Calvin cycle produces a 3 carbon sugar C. both

Which is true? A. 3 carbons from CO2 are fixed in the first reaction of the Calvin cycle B. the Calvin cycle produces a 3 carbon sugar *C. both*

Which kinase seems likely to be involved in regulation of melanosome movement? A. PKA B. PKB C. PKC D. PKG

Which kinase seems likely to be involved in regulation of melanosome movement? *A. PKA* B. PKB C. PKC D. PKG ----- - PKA mediates effects of Galpha-s ... activates adenylyl cyclase ... makes cAMP ... activates PKA - phosphodiesterase decreases cAMP

Which kinesin can "walk" on two different microtubules at one time? A. kinesin-1 B. kinesin-5 C. kinesin-13 D. kinesin-14

Which kinesin can "walk" on two different microtubules at one time? A. kinesin-1 *B. kinesin-5* C. kinesin-13 D. kinesin-14 ----- it moves each microtubule towards its plus end and can make them slide past each other/produce some tension

Which kinesin can "walk" on two microtubules at once, sliding the microtubules past each other? A. kinesin-1 B. kinesin-5 C. kinesin-13 D. kinesin-14

Which kinesin can "walk" on two microtubules at once, sliding the microtubules past each other? A. kinesin-1 *B. kinesin-5* C. kinesin-13 D. kinesin-14

Which kinesin is a microtubule "catastrophe factor"? A. kinesin-1 B. kinesin-5 C. kinesin-13 D. kinesin-14

Which kinesin is a microtubule "catastrophe factor"? A. kinesin-1 B. kinesin-5 *C. kinesin-13* D. kinesin-14

Which kinesin is minus-end directed? A. kinesin-1 B. kinesin-5 C. kinesin-13 D. kinesin-14

Which kinesin is minus-end directed? A. kinesin-1 B. kinesin-5 C. kinesin-13 *D. kinesin-14*

Which link the hemidesmosomes and desmosomes together, creating mechanical stability of cells? A. actin filaments B. microtubules C. intermediate filaments

Which link the hemidesmosomes and desmosomes together, creating mechanical stability of cells? A. actin filaments B. microtubules *C. intermediate filaments*

Which microtubule end is at the centrosome? A. minus B. plus C. both

Which microtubule end is at the centrosome? *A. minus* B. plus C. both

Which motor protein is needed for cytokinesis? A. Dynein B. Myosin II C. Kinesin-4 D. Kinesin-14 E. Ncd80

Which motor protein is needed for cytokinesis? A. Dynein *B. Myosin II* C. Kinesin-4 D. Kinesin-14 E. Ncd80

Which mutation outcome would NOT contribute to cancer's origin, malignancy, or growth? A. Oncogene GOF (gain of function) B. Increased cell-cell adhesion C. Tumor suppressor LOF (loss of function) D. Moderate genetic instability E. Masking of abnormal surface proteins from immune cell detection

Which mutation outcome would NOT contribute to cancer's origin, malignancy, or growth? A. Oncogene GOF (gain of function) B. Increased cell-cell adhesion C. Tumor suppressor LOF (loss of function) D. Moderate genetic instability *E. Masking of abnormal surface proteins from immune cell detection*

Which of molecule causes the cell to undergo DNA replication and division? A. Mitogen B. Growth factor C. Survival factor

Which of molecule causes the cell to undergo DNA replication and division? *A. Mitogen* B. Growth factor C. Survival factor

Which of molecule induce G1- and S-cyclins? A. Mitogen B. Growth factor C. Survival factor

Which of molecule induce G1- and S-cyclins? *A. Mitogen* B. Growth factor C. Survival factor

Which of molecule prevents apoptosis? A. Mitogen B. Growth factor C. Survival factor

Which of molecule prevents apoptosis? A. Mitogen B. Growth factor *C. Survival factor*

Which of the following are roles of ECM? A. Cell signaling B. Providing compression resistance in a tissue C. Linking cells together into a tissue D. Providing binding sites for ligands for cell surface receptors. E. All of the above

Which of the following does a PTB domain bind? A. motifs containing phosphotyrosine B. proline-rich motifs C. a specific phosphoinositide D. motifs containing phosphoserine or phosphothreonine

Which of the following does a PTB domain bind? *A. motifs containing phosphotyrosine* B. proline-rich motifs C. a specific phosphoinositide D. motifs containing phosphoserine or phosphothreonine

Which of the following does a Src homology 2 (SH2) domain bind? A. motifs containing phosphotyrosine B. proline-rich motifs C. a specific phosphoinositide D. motifs containing phosphoserine or phosphothreonine

Which of the following does a Src homology 2 (SH2) domain bind? *A. motifs containing phosphotyrosine* B. proline-rich motifs C. a specific phosphoinositide D. motifs containing phosphoserine or phosphothreonine

Which of the following does a pleckstrin homology (PH) domain bind? A. motifs containing phosphotyrosine B. proline-rich motifs C. a specific phosphoinositide D. motifs containing phosphoserine or phosphothreonine

Which of the following does a pleckstrin homology (PH) domain bind? A. motifs containing phosphotyrosine B. proline-rich motifs *C. a specific phosphoinositide* D. motifs containing phosphoserine or phosphothreonine

Which of the following has a sugar binding domain? A. selectins B. lectins C. NCAMs D. ICAMs E. Ig Superfamily proteins

Which of the following has a sugar binding domain? A. selectins *B. lectins* C. NCAMs D. ICAMs E. Ig Superfamily proteins ----- lectin = domain on the tip of the selectin that actually binds to the oligosaccharide

Which of the following have their own DNA? A. mitochondria B. chloroplasts C. peroxisome D. A and B E. all of the above

Which of the following have their own DNA? A. mitochondria B. chloroplasts C. peroxisome *D. A and B* E. all of the above

Which of the following interact via immunoglobulin-like domains? A. selectins B. lectins C. NCAMs D. ICAMs E. Ig Superfamily proteins

Which of the following interact via immunoglobulin-like domains? A. selectins B. lectins C. NCAMs D. ICAMs *E. Ig Superfamily proteins*

Which of the following is FALSE regarding PCD? A. A subset of PCD is apoptosis. B. PCD can be used during development to sculpt tissues. C. A subset of PCD is necrosis. D. PCD generally avoids inflammation of surrounding tissues. E. PCD can be used to destroy cells with irreparable DNA damage.

Which of the following is FALSE regarding PCD? A. A subset of PCD is apoptosis. B. PCD can be used during development to sculpt tissues. *C. A subset of PCD is necrosis.* D. PCD generally avoids inflammation of surrounding tissues. E. PCD can be used to destroy cells with irreparable DNA damage.

Which of the following is NOT true of nucleoporin protein complexes? A. They mediate passive transport of some molecules. B. They are complexes of proteins that pass through 2 lipid bilayers. *C. They covalently bind nuclear localization sequences.* D. They change conformation to allow passage of large proteins. E. There are thousands of them in each nuclear membrane. ----- A. true ... contain H2O filled channel so some things can passively transport through there B. true ... inner and outer nuclear envelope C. false! interaction has to be temporary so they can dissociate and reassociate over and over again D. true ... we don't know for sure, but we suspect this is happening E. true

Which of the following is a shared feature of anaphase promoting complex/cyclosome (APC/C) and SCF? A. They target cyclins for degradation. B. They target CKI proteins for degradation. *C. They are polyubiquitin ligases.* D. They require an F-box adapter protein to bind their target molecules. ----- APC/C and SCF are both responsible for proteolysis of cell cycle components, but they regulate different aspects. APC/C ubiquitylates cyclins, holding the cell cycle in check, while SCF ubiquitylates CKIs that can bind and inhibit activated cyclin-Cdk complexes, releasing the complexes to promote the cell cycle. F-box is a substrate-binding subunit that guides SCF targeting.

Which of the following is a transmembrane adhesion protein that allows WBC to roll along the interior surface of a vessel? A. selectins B. lectins C. NCAMs D. ICAMs E. Ig Superfamily proteins

Which of the following is a transmembrane adhesion protein that allows WBC to roll along the interior surface of a vessel? *A. selectins* B. lectins C. NCAMs D. ICAMs E. Ig Superfamily proteins ----- WBC has oligosaccharide, vessel has selectins ... transient binding and unbinding as it travels along

Which of the following is degraded every time a cell cycle occurs? A. S-Cdk B. M-Cdk C. G1/S-Cdk D. M-cyclin E. None of the above

Which of the following is degraded every time a cell cycle occurs? A. S-Cdk B. M-Cdk C. G1/S-Cdk *D. M-cyclin* E. None of the above

Which of the following is electrogenic? A. V-type p+ pump B. Bacteriorhodopsin C. Na+/glucose symporter D. Na+/K+ pump E. All of the above.

Which of the following is electrogenic? A. V-type p+ pump B. Bacteriorhodopsin C. Na+/glucose symporter D. Na+/K+ pump *E. All of the above.*

Which of the following is expressed on the surface of endothelial cells and binds to oligosaccharides? A. selectins B. lectins C. NCAMs D. ICAMs E. Ig Superfamily proteins

Which of the following is expressed on the surface of endothelial cells and binds to oligosaccharides? *A. selectins* B. lectins C. NCAMs D. ICAMs E. Ig Superfamily proteins

Which of the following is not an example of a carcinoma? A. Myeloma B. Breast cancer C. Colorectal cancer D. Lung cancer

Which of the following is not an example of a carcinoma? *A. Myeloma* B. Breast cancer C. Colorectal cancer D. Lung cancer ----- It is not surprising that many cancers are derived from epithelial cells (i.e. are carcinomas) as these cells are more proliferative and also more exposed to the environment.

Which of the following is true of Cdc25 protein? A. It is a protein kinase. B. It inactivates M-Cdk complexes. C. Its loss in fission yeast results in small cell size. D. It is activated by M-Cdk complexes.

Which of the following is true of Cdc25 protein? A. It is a protein kinase. B. It inactivates M-Cdk complexes. C. Its loss in fission yeast results in small cell size. *D. It is activated by M-Cdk complexes.* ----- Cdc25 phosphatase will dephosphorylate and activate cyclin-Cdk complexes. In a positive feedback loop at the onset of mitosis, M-Cdk inactivates its inactivator, Wee1, and activates its activator, a Cdc25.

Which of the following is true of Wee1 protein? A. It activates M-Cdk complexes. B. It is activated by M-Cdk complexes. C. Its loss in fission yeast results in small cell size. D. It is a protein phosphatase.

Which of the following is true of Wee1 protein? A. It activates M-Cdk complexes. B. It is activated by M-Cdk complexes. *C. Its loss in fission yeast results in small cell size.* D. It is a protein phosphatase. ----- Wee1 kinase will phosphorylate and inactivate cyclin-Cdk complexes. In a positive feedback loop at the onset of mitosis, M-Cdk inactivates its inactivator, Wee1, and activates its activator, a Cdc25. The small cell size in wee mutants can result from Wee1 depletion.

Which of the following microtubule types is NOT located between the centromeres, but radiates outward from the poles? A. astral B. kinetochore C. interpolar

Which of the following microtubule types is NOT located between the centromeres, but radiates outward from the poles? *A. astral* B. kinetochore C. interpolar

Which of the following morphological changes is NOT typically seen in a cell that is undergoing apoptosis? A. Large cells break up into membrane-enclosed fragments. B. The cell swells. C. The cell rounds up. D. The nuclear chromatin breaks into fragments. E. The nuclear envelope disassembles.

Which of the following morphological changes is NOT typically seen in a cell that is undergoing apoptosis? A. Large cells break up into membrane-enclosed fragments. *B. The cell swells.* C. The cell rounds up. D. The nuclear chromatin breaks into fragments. E. The nuclear envelope disassembles. ----- While cells undergoing necrosis normally swell and burst, apoptotic cells shrink and condense.

Which of the following mutations is pro-apoptotic? A. Mutations in the pro-apoptotic effector Bcl2 family proteins Bax and Bak that prevent their association with the outer mitochondrial membrane. *B. A mutation in the BIR domain of the IAP protein DIAP1 that prevents binding to either caspases or anti-IAP proteins.* C. A mutation in the anti-IAP protein Reaper that prevents its binding to the IAP proteins. D. A mutation in the CARD domain of caspase-9 that prevents its binding to Apaf1. ----- Association of Bax and Bak with the mitochondrial membrane is necessary (although not sufficient) for the activation of the intrinsic pathway of apoptosis, so those mutations are anti-apoptotic. The same is true for the association of procaspase-9 with Apaf1 in apoptosomes. Interfering with the binding of IAPs to the caspases promotes apoptosis, while interfering with the binding of IAPs to anti-IAPs represses apoptosis.

Which of the following plays the smallest role in cell junctions? A. Actin B. Intermediate filaments C. Microtubules D. Transmembrane proteins E. Plasma membrane

Which of the following plays the smallest role in cell junctions? A. Actin B. Intermediate filaments *C. Microtubules* D. Transmembrane proteins E. Plasma membrane

Which of the following proteins activates the mitochondrial pathway of apoptosis? A. The tumor suppressor protein p53, when activated in response to extensive DNA damage. B. All of these are mechanisms for inducing mitochondrial apoptosis. C. The BH3-only protein Bid, when cleaved by the initiator caspase-8 (from the extrinsic pathway). D. The BH3-only protein Bad, when activated by dephosphorylation. E. The anti-IAP protein Omi, when activated by dephosphorylation.

Which of the following proteins activates the mitochondrial pathway of apoptosis? A. The tumor suppressor protein p53, when activated in response to extensive DNA damage. *B. All of these are mechanisms for inducing mitochondrial apoptosis.* C. The BH3-only protein Bid, when cleaved by the initiator caspase-8 (from the extrinsic pathway). D. The BH3-only protein Bad, when activated by dephosphorylation E. The anti-IAP protein Omi, when activated by dephosphorylation. ----- Activated BH3-only proteins or anti-IAP proteins can result in the activation of the intrinsic pathway of apoptosis. In response to DNA damage that cannot be repaired, the tumor suppressor protein p53 activates the expression of genes encoding BH3-only proteins (such as Puma).

Which of the following proteins is NOT encoded by a proto-oncogene? A. E-cadherin B. Src C. EGF receptor D. Myc E. Ras

Which of the following proteins is NOT encoded by a proto-oncogene? *A. E-cadherin* B. Src C. EGF receptor D. Myc E. Ras ----- Loss-of-function mutations in the tumor suppressor E-cadherin promote the epithelial-mesenchymal transition and local invasiveness.

Which of the following statements are true about fibronectin? A. Fibronectin molecules can assemble into fibrils without proximity to cells. B. Fibronectin often forms homodimers by cross-linking through covalent attachment of lysine residues. *C. Fibronectin carries asparagine-linked oligosaccharides.* D. Fibronectin binds to integrins, collagens, and glycosaminoglycans through its type III repeats. ----- Fibronectin is a matrix multidomain glycoprotein and can form fibronectin fibrils on the surface of cells. This assembly is regulated by the tension exerted by the cells via surface proteins such as integrins. Type III fibronectin repeats are responsible for integrin binding, whereas binding to collagen and heparin is mediated by type I and type II repeats. Fibronectin heterodimers are held together by C-terminal disulfide bonds.

Which of the following statements describe fibrillar extracellular matrix (ECM) proteins? A. They are found in proteoglycans. B. They form hydrated gels and occupy large volumes. C. They include hyaluronan. *D. They include collagens.* E. They are a special category of glycoproteins found in the ECM. ----- Glycosaminoglycan (GAG) chains, such as hyaluronan or those covalently linked to core proteins in proteoglycans, occupy large amounts of space and form hydrated gels that resist compression. Fibrous proteins, primarily collagens, constitute a significant fraction of the total protein mass in the extracellular matrix. Some fibrillar ECM proteins, such as fibronectin and laminin, carry conventional N-linked oligosaccharides and are classic glycoproteins; however they are not covalently linked to GAGs and thus are not considered to belong to the specialized class of proteoglycans.

Which of these acts in a similar fashion as stathmin? A. nocodazole B. taxol C. colchicine

Which of these acts in a similar fashion as stathmin? *A. nocodazole* B. taxol C. colchicine

Which of these could act via binding an intracellular receptor? A. a hydrophobic molecule such as a steroid hormone B. a large polar and/or charged molecule C. both

Which of these could act via binding an intracellular receptor? *A. a hydrophobic molecule such as a steroid hormone* B. a large polar and/or charged molecule C. both

Which of these has a function similar to thymosin? A. latrunculin B. cytochalasin B C. phalloidin

Which of these has a function similar to thymosin? *A. latrunculin* B. cytochalasin B C. phalloidin ----- thymosin = binds up free actin and sequesters it, preventing it from polymerization

Which of these molecules stabilizes microtubules? A. nocodazole B. taxol C. colchicine

Which of these molecules stabilizes microtubules? A. nocodazole *B. taxol* C. colchicine

Which of these would be more likely to cause formation of the contractile ring? A. nucleation of straight actin filaments, parallel bundling of the actin filaments, and phosphorylation of myosin light chain kinases that stimulate myosin cross bridge cycling B. inhibition of myosin activity, stimulation of Arp2/3 nucleation of branched actin organization, and involvement of filament in cross-linking actin branches

Which of these would be more likely to cause formation of the contractile ring? *A. nucleation of straight actin filaments, parallel bundling of the actin filaments, and phosphorylation of myosin light chain kinases that stimulate myosin cross bridge cycling* B. inhibition of myosin activity, stimulation of Arp2/3 nucleation of branched actin organization, and involvement of filament in cross-linking actin branches

Which time point represents the restriction point in the mammalian cell cycle? A. between M and G1 B. right before G1 ends and S begins (almost between G1 and S) C. between G2 and M D.after G2 (in M) E. M

Which time point represents the restriction point in the mammalian cell cycle? A. between M and G1 *B. right before G1 ends and S begins (almost between G1 and S)* C. between G2 and M D.after G2 (in M) E. M ----- Under favorable conditions and in the presence of signals to grow and divide, cells in early G1 (or G0) progress through a commitment point near the end of G1 known as Start (in yeasts) or the restriction point (in mammalian cells).

Which type of ATPase would be found in lysosomal membranes? A. vacuolar, or V-type B. phosphorylation Factor, or F-type C. L-type

Which type of ATPase would be found in lysosomal membranes? *A. vacuolar, or V-type* B. phosphorylation Factor, or F-type C. L-type

Which type of G-α subunit activates phospholipase C-β, which generates IP3 (which stimulates Ca2+ release from the ER) and DAG (which contributes to activation of protein kinase C)? A. Gs B. Gi C. Gq D. Gt

Which type of filament plays a role in the mechanics of mitosis? A. actin (in the contractile ring at cytokinesis) B. microtubules in the mitotic spindle C. intermediate filaments (the lamins of the nuclear lamina) D. All of the above

Which, when coupled to a fluorescent tag, allows visualization of actin filaments in fixed (proteins stabilized before microscopy) cells? A. latrunculin B. cytochalasin B C. phalloidin

Which, when coupled to a fluorescent tag, allows visualization of actin filaments in fixed (proteins stabilized before microscopy) cells? A. latrunculin B. cytochalasin B *C. phalloidin* ----- - fixed = all proteins are cross-linked and won't change their position

Will Dr. Fisher's sons pass their mom's mtDNA to their kids if they have kids? A. nope (it's destroyed soon after fertilization) B. yes (they inherited their mtDNA from their mom)

Will Dr. Fisher's sons pass their mom's mtDNA to their kids if they have kids? *A. nope (it's destroyed soon after fertilization)* B. yes (they inherited their mtDNA from their mom)

What is a monomeric G protein?

a G protein with only one peptide chain

What keeps the pH of the lysosome low?

a V-type ATPase that uses ATP hydrolysis to pump H+ into the lysosome and acidify the lumen

What is the size of a typical prokaryote cell?

a few microns ... 2 microns/2 micrometers (μm)

How do multipass transmembrane proteins with some polar AAs create a channel for the passage of ions?

a few polar AAs end up oriented away from the surface/actual nonpolar membrane of the lipid bilayer

What is a site of nucleation for microtubules to grow out toward the cell periphery?

a pair of centrosomes with its triplet microtubules

What does the serine/threonine kinase/TGF(β)/Smad signaling pathway rely on the formation of?

a transcriptional regulatory complex (much like the JAK-STAT pathway!)

Electrons from the photoreaction center of photosystem I are eventually accepted by what general electron carrier that has a role in dark reactions?

acceptor = NADP+ --> NADPH

What does photosystem II do/how does it work?

accepts light energy and donates an electron to the ETC

What is happening to actin at the leading edge that is super important for protrusion to occur?

actin anchoring to the sub-stratum/ECM by integrins - this keeps the actin from being pushed backward

What is involved in cytokinesis?

actin and myosin

What mediates cell motility?

actin cytoskeletal rearrangement

What is happening at the trailing end of the lamellipodium?

actin is interacting with myosins

What is happening during treadmilling?

actin is polymerizing at the plus end at the same rate that it is depolymerizing at the minus end

What are formin dimers?

actin-nucleating factors that accelerate polymerization and generate straight filaments

What does ~Gq~ do?

activates PLC-β (... generates DAG and IP3 ... IP3 can activate Ca2+ channels on the ER and increase intracellular Ca2+ levels ... DAG and Ca2+ can activate PKC)

What does G α-q do?

activates phospholipase C, which activates IP3 and DAG

is p16 active or inactive in a non-proliferating cell?

active! - it sequesters G1-Cdk and prevents G1-cyclin from binding - Rb stays active and keeps E2F turned off ---> expression of S phase genes is inhibited

When a GTP binding protein is bound to GTP it is _____.

active/on

what is a benign tumor coming from a gland called?

adenoma

What is an effector protein for Gs-α?

adenylyl cyclase

What anchoring proteins have actin filaments as intracellular cytoskeletal attachments?

adherens junction and actin-linked cell-matrix junction

At what point does actin become capped?

after it's assembled

When are signaling complexes more commonly assembled? (before or after the signaling molecule)

after the hormone/signaling molecule binds to the receptor

in order for a cell to move on from metaphase what must happen?

all kinetochores must attach to MTs!!! this is the third checkpoint ... "metaphase to anaphase transition"

What is gated transport?

allows for diffusion of small molecules and active transport of specific larger molecules

What would happen if during assembly, a G-protein was turned off?

allows for dissociation of the coat

Where does a mitochondrial targeting sequence direct a protein to?

allows it to be directed to a receptor in the TOM complex (and to later be moved through TIM23 complex and brought into matrix)

What is the purpose of the hinge on the SRP?

allows the arm to swing into place

What does spectrin do in RBCs?

allows them to be deformed as they move through capillaries

How do vesicles move in a cell?

along microtubule tracks

What does acetylcholine cause in skeletal muscle cells?

an action potential and contraction

What replaces the electron that is lost in photosystem I?

an electron that comes from photosystem II!

What is transcytosis?

antibody going from one side of the cell to another (ex: from the intestine to the side of the cell that is near the bloodstream)

Why is the TOM complex so important?

any protein that is coming from the cytosol to any part of the mitochondria is translocated through it

differences between apoptosis and necrosis

apoptosis = - strict cellular control mechanism - cell shrinkage - no release of intercellular contents necrosis - not regulated (not PCD) ... death in response to tissue damage/trauma - cell swelling - release of intracellular contents into surroundings

What are some examples of non-gated channel proteins?

aquaporins and K+ leak channels

According to the endosymbiotic hypothesis of mitochondrial origin, what was the origin of the first proto-mitochondrion?

archaeal cell could have obtained a nucleus and then engulfed and aerobic bacterium OR it could have engulfed the aerobic bacterium and then obtained a nucleus

According to the endosymbiotic hypothesis of chloroplast origin, what was the origin of the first proto-chloroplast?

archael cell with a nucleus and an aerobic bacterium in it engulged a photosynthetic bacterium

where is the Ndc80 complex found?

at + end of a kinteochore MT

Where can PI be phosphorylated (at what positions)?

at the 3, 4, and 5 positions of the ring

How is phospholipid membrane asymmetry established?

at the plasma membrane, flippases flip specific phospholipids to the correct side of the membrane (PS, PE, PI to cytoplasmic and PC and SM to exoplasmic)

What end do microtubules polymerize more rapidly at?

at the plus end

Where are FtsZ proteins used/seen?

bacteria and chloroplasts

What does mitochondrial DNA look like/resemble?

bacterial DNA rather than nuclear DNA (due to endosymbiotic hypothesis stuff)

What is an example of a light-fueled ATP pump?

bacteriorhodopsin

What is another name for the plus end of actin?

barbed end

Why does myosin II does have that name?

because it has two heads

Why is NSF required for the process of homotypic membrane fusion?

because it would not normally spontaneously happen

Why doesn't the actin filament slide back after being released by the myosin head?

because there are many other myosin heads holding it under tension

Why did membrane bound organelles develop?

because there wasn't enough space! they allow for increased surface area and compartments to give more area for work to be done between environments A and B

Why is it important that there is a tight seal between the Sec61 complex and the polypeptides that are being forced through it?

because you want to keep the Ca2+ in the ER (you don't want it to leave the cell)

What structure does filamin take on?

becomes a filamin dimer ... this structure allows for assembly of gel-like networks

Where are cadherins found?

between cells

What do the lumenal subunits of a nuclear pore do?

bind the pore itself into the membrane and allow the membrane to have a tight bend/hairpin angle

How do fibronectin and laminin fix cells in place?

bind to integrins

What do hsp70 chaperones do?

bind to mitochondrial protein and prevent it from folding in the cytosol

How does the Na+/glucose symporter work?

binding is cooperative (binding of Na+ increases the affinity of the carrier for glucose) ... when Na+ is released inside the cell, glucose also releases the gradient is set up using ATP ("secondary active transport"

What causes a GTP binding protein to activate?

binding of GTP ... the switch helix is electrostatically attracted to the negative charges on the last P of the GTP

How come KDEL receptor proteins can escape the ER membrane but then can be trafficked back?

binding of a protein with a KDEL sequence to a KDEL receptor causes a conformational change in the KDEL receptor that allows its packaging into retrieval vesicle. When the KDEL receptor releases its cargo in the ER lumen, the protein returns to its unbound conformation.

What's a proton ionophore?

binds a proton one side of the membrane and move it down its gradient to the other side of the membrane

How does ~phalloidin~ work?

binds along filaments and stabilizes them

How does taxol (paclitaxel) work?

binds along microtubule filaments

How does ~latrunculin~ work?

binds free actin and prevents it from polymerizing (binds actin subunits)

tell me about plectin pls

binds the microtubules to intermediate filaments

What do GDIs do?

binds to G-protein GDP and sequesters it and prevents it from interacting with a GEF

How does nacodazole work?

binds tubulin subunits

When does a M6P receptor bind? When does it dissociate?

binds with high pH (basic) and releases with low pH (acidic) [binds in golgi and releases in lysosome]

Gleevec

blocks the oncogenic kinase by sitting in the ATP binding pocket and not allowing it to be activated

What is the cause of myasthenia gravis and associated unilateral ptosis?

body makes antibodies against the Ach receptors in muscle ... even when Ach is released, it can't activate the muscle properly

Intrinsic or extrinsic apoptosis pathway or both?: executioner caspases

both

Intrinsic or extrinsic apoptosis pathway or both?: initiator caspases

both

What is the relationship between transporter-mediate diffusion and [solute]? What is the relationship between simple diffusion and channel-mediated transport and [solute]?

both vary with [solute]

How is mRNA transported through nuclear pores?

bound to RNA export factors (recognize when an mRNA is completely mature)

What does calnexin do? Where is it found?

bound to interior face of lumen, so it can't leave the ER ... it prevents proteins from being taken out of the ER

How does cofilin break up the D-ends of filaments?

by binding along the outside and making them brittle, so they're more likely to break under stress ... breaking creates a new minus end that could depolymerize

how can Rb and p53 be blocked? what happens if this occurs?

by virus proteins! this leads to overproliferation of cells and cancer ex: papillomaviruses sequestering Rb and p53 via E6 and E7

Cadherins or integrins?: Contain a single-strand chain of repeated motifs.

cadherins

Cadherins or integrins?: Control tissue patterning in development by homophilic interactions

cadherins

Cadherins or integrins?: Requires extracellular Ca2+ to maintain rigidity.

cadherins

Cadherins or integrins?: Interact with myosin via actin to cause lateral contraction of epithelia.

cadherins adhesion belt is carrying out this contraction

What is the transmembrane adhesion protein that cell-cell junctions use?

cadherins (classical for adherens junctions and nonclassical for desmosomes)

Cells that express the same cadherins like to be in the same place because _____.

cadherins are homophilic and like to be in the same place together

cadherin domain motifs

cadherins have cadherin domain motifs on their extracelullar face

What is apolipoprotein B?

can be bound as cargo to a receptor on the surface of a cell ... this clears LDL out of the bloodstream (it basically just wraps around the LDL particles and moves them around)

tell me about MAP2 pls

can form a lattice of microtubules (can bundles them together)

radiation therapy

cancer cells are more susceptible to ionizing radiation radiation because they often lack the ability to halt their cell cycle and repair the cell cycle

How does colchicine work?

caps filament ends and also binds tubulin subunits

When recruited to the membrane, what can adaptin bind?

cargo receptor (and then cargo) and clathrin

What is autophagy?

carrying of parts of intracellular organelles

what do mitogens do?

cause the cell to undergo DNA replication and division (make G1- and S-cyclins and enter S phase)

What does colchicine do to microtubules?

causes depolymerization

What does nocodazole do to microtubules?

causes depolymerization

How does cholera impact CFTR?

causes severe diarrhea by over-activating CFTR, causing it to release excess Cl- ... this causes water to be drawn out of cells

What effect does ~phalloidin~ have on filaments?

causes stabilization

What is ~autocrine~ signaling?

cell secretes a substance that acts on receptors on that very same cell

What is ~contact-dependent~ signaling?

cell surface proteins on 2 different cells that directly interact with each other and cause signaling in one cell/in both

integrins are involved with _____.

cell-matrix anchoring junctions (actin-linked cell-matrix junctions and hemidesmosomes)

What is the key MTOC?

centrosome

What is required for there to be zero potential difference across a membrane?

charges have to be equal on both sides! concentrations don't necessarily have to be equal

What directly fuels the dark reactions of photosynthesis?

chemical of ATP and NADPH

cytokinesis requires formation of a _____ by a contractile ring of actin and myosin.

cleavage furrow

What does Endo-H do?

cleaves high-mannose and precursors of complex oligosaccharides until they have been pared to the core region; it is an endoglycosidase

What happens when dynamin severs the vesicle from the donor membrane?

coat disassembles, vesicle is naked and can fuse with target compartment (uncoating)

COPI coats are recruited by a G protein named ARF. What happens when an ARF GAP acts on ARF after coat recruitment?

coat dissociates

How are lysosomes acidified?

combination of v-class ATPases and movement of Cl- ions into the lysosome

What is deconvolution?

computer-based method for subtracting out of focus light from a serious of fluorescent micrographs (look at where the light is more random and then the computer finds where the real light is) to yield a sharper 3D picture

~Cell-surface proteins of one cell directly interact with cell-surface proteins of another cell, initiating intracellular signaling in one or both cells.~ What kind of signaling is this?

contact-dependent signaling

What do you supposed the role of the sugar-nucleotide (UDP-Gal, UDP-GlcNac, CMP-NANA) in the sugar transfer is? (i.e. why can't a free sugar be transferred?)

coupling to the exothermic reaction of the breaking of the phosphodiester bond allows the normally unfavorable reaction to occur

Where are most GAGs found?

covalently attached to protein backbones to create proteoglycans

What is the normal function of a v-type ATPase?

create H+ gradient (pumping protons to acidify compartments)

On a graph of rate of transport vs concentration of transported molecule, what does the line of transporter-mediated diffusion/passive transport look like?

curved

What activates the JAK-STAT signaling pathway?

cytokine receptors

Where do these SNAREs interact? (cytosolic face or lumenal face)?

cytosolic face

What side of the membrane is phosphoinositide found?

cytosolic side

What triggers muscle contraction?

depolarization on a pre-synpatic neuron and release of Ach which then binds to its receptor (a Na+ channle) on the post-synaptic neuron and causes Na+ to go into the next cell and a VG Ca2+ channel to be activated (and Ca2+ to be released)

How does LTP work when a NMDA channel is activated?

depolarization removes the Mg2+ blocking the NMDA channel, which with glutamate bound, allows Ca2+ to enter into the post synaptic cell ... this induces the postsynaptic cell to insert AMPA receptors into the plasma membrane, which increases the cell's sensitivity to glutamate this process makes it easier for the post-synaptic cell to reach threshold voltage and fire an AP ... the individual synapse becomes more sensitive to stimulation

What does cofilin do in a branched actin filament network?

depolymerizes old actin at the end of the network

What is a signal patch?

derived from AAs at several points along the protein (they are closely held together when the protein is folded into its 3D structure)

What anchoring proteins have intermediate filaments as intracellular cytoskeletal attachments?

desmosome and hemidesmosome

what makes the cell cycle unidirectional?

destruction of key proteins as a phase ends

Different phosphoinositides on different membranes recruit ...

different proteins and contribute to compartment identity

How do hydrophobic molecules (O2, CO2, N2, steroids, hormones, etc.) get across the lipid bilayer?

diffuse freely

How do things smaller than 5,000 daltons get into the nucleus?

diffuse freely through the nuclear pore

Where does IP3 go?

diffuses to ER and binds ligand-gated Ca2+ channel and allows release of Ca2+ from the ER

How do scientists study the ER?

disrupt the cell and shake it up a lot and then the cell will break up into microscomes (little mini baby ERs awwww so cute) ... SRPs and Sec61 reassociate with ribosomes in solution

What allows for fusion of the vesicle with the plasma membrane?

dissociation of complexin due to high Ca2+ levels

What are carbohydrates originally bound to in the ER membrane?

dolichol (a lipid in the ER membrane)

What is important for mitochondrial fission?

dynamin

What do RTKs do once they are activated?

each receptor phosphorylates the other (trans-autophosphorylation activates kinase domains)

Where does endocytosis eventually lead to/where does the engulfed material end up?

early endosome

How do electron microscopes work?

electron beam used instead of light because electrons have a much shorter wavelength!

What does multi-ubiquitination tag the protein to do?

endocytosis

What is necessary for a protein to move from the stroma to the thylakoid space?

energy of some sort

Is a low affinity donor to a high affinity acceptor an energy releasing or an energy requiring process?

energy releasing process

What is phagocytosis?

engulfing a large particle (ex: bacterium)

What is macropinocytosis?

engulfing a large portion of the extracellular fluid

How was the mitochondria formed in eukaryotes?

engulfment of an aerobic bacterium (this is why the mitochondria has an extra membrane)

What is the nuclear lamina?

equivalent of cytoskeleton, but in the nucleus

what is the rate determining step of metastasis?

escape from parent tissue (this requires mutations)

why is it evolutionarily beneficial for cells to stop expressing telomerase?

every cycle of replication can increase the mutation load!!

How does bacteriorhodopsin work?

every time a photon of light hits it, it isomerizes and switches from right to left handed isomer of retinal ... p+ then hop from one binding and move from the cytosol to the extracellular space (step by step)

What does the process of laminar disassembly during cellular division look like?

everything gets phosphorylated and falls apart and basically just becomes a soup and then after that, the nuclear envelope starts reassembling (Er membrane wraps around groups of chromosomes and keeps fusing) ... phosphatases dephosphorylate and then you have 2 cells yay omg

What does light energy do in photosynthesis?

excites electrons

How can the plasma membrane be englarged?

exocytosis events

O-linked glycosylation leads to formation of _____.

extremely large carbohydrate groups

Intrinsic or extrinsic apoptosis pathway or both?: DISC

extrinsic

Where are t-SNAREs located in an intralumenal vesicle?

facing the inside of the vesicle (not the cytosol)

True or false?: Tight junctions are made of two connexon hemichannels each comprising six connexin subunits.

false GAP junctions!

True or false?: Gap junctions weave along the surface of the cell in interlacing sealing strands with gaps between the strands.

false this is talking about tight junctions

True or false: Hyaluronan consists of a protein backbone with hundreds of covalently-linked GAG chains.

false! no protein ... it's a simple GAG chain! can assemble a bunch of aggrecans along its length that do contain proteins but the hyaluronan contains no proteins whatsoever.

True or false: Integrins are cell-cell transmembrane adhesion proteins.

false! they do cell-matrix

True or false: Hemidesmosomes use actin filaments.

false! they use intermediate filaments

Mircrotubules are rigid and stable. True or false?

false!! they are very dynamic and constantly growing and shrinking depending on the conditions

What is a source of carbon atoms in CO2 produced by mitochondria?

fats and carbohydrates

Is elastin a GAG or a fibrous protein?

fibrous protein

How does a protein get into the intermembrane space?

first is inserted into the inner membrane, and then is cleaved free by a peptidase/protease OR (for a protein with many thiol groups) an intermembrane protein with thiol groups on it can ratchet the cytosolic protein through the translocator into the intermembrane space OR a cytosolic protein can enter into the intermembrane space through TOM and then be inserted into the inner membrane by TIM22

What catalyzes the flipping of phospholipid molecules to the correct side of the plasma membrane?

flippases

What is synaptogenesis?

formation of new synapses

What do the ring subunits of a nuclear pore do?

found on both cytoplasmic and nuclear face ... have fibrils

What nucleates microtubules?

gamma-tubulin ring complexes

How is actin arranged in the cell cortex?

gel-like network

M-Cdk

has to be taken down/destroyed at metaphase-anaphase transition

anaphase B

has to do with astral and interpolar MTs being pulled apart

anaphase A

has to do with shotening of kinetochore microtubules which causes dragging of the chromatids apart

How do selectivity filters in Cl- and K+ channels work?

helix dipoles of the selectivity filter have their + ends (for Cl- channel)/- ends (for K+ channel) facing towards the inside of the channel so only - charged (for Cl- channel)/+ charged (for K+ channel) ions can pass through

Why does an integral membrane disappear when it undergoes a salt wash?

helix is inserted into the membrane or it has a covalently bound lipid that attaches it to the membrane

where do leukemias originate?

hematopoietic cells (blood)

Is the temperature of phase transition higher or lower for saturated than for unsaturated tails?

higher

what does overactivation of both Ras and Myc cause?

higher rates of tumorigenesis than either of them alone

ratio of nucleus:cytoplasm in cancer cells

higher than in regular cells

What does mono-ubiquitination tag the protein to do (?)?

histone regulation

How does hsp70 machinery help a protein fold?

holds the protein in place and then after ADP on the protein is replaced with ATP, it dissociates rom the protein along with the hsp70 machinery

ok so here there's a few slides about hypertonic/hypotonic stuff

honestly sis if u don't know it by know idk what to tell ya big rip

How does a P-type pump work?

hydrolyzes ATP and uses the energy from that to become phosphorylated itself (accepts the *P*)

What do phosphatases do?

hydrolyzes a phosphoester bond to remove a phosphate group (takes Ps off)

What is simple diffusion?

hydrophobic molecules moving across membranes from areas of high to low concentration

What do chaperon proteins bind to?

hydrophobic regions of proteins that aren't normally exposed

What is homotypic membrane fusion?

identical v-SNAREs and t-SNAREs on separate vesicles coming together to form a conjoined vesicle which will later fuse into one vesicle

Why are Cl- ions necessary when H+s are entering a lysosome?

if H+ alone was entering the lysosome, the positive electrical potential inside the membrane would quickly eliminate positively charged ions from the lysosome surface ... with Cl- going at the same time, the electrical potential is eliminated and enough H+ ions can enter to acidify the organelles without charging the membrane

at the start checkpoint, when would cells exit to G0?

if they are not receiving mitogen signals

Why is PI important on the inside of the cell?

important docking sites for intracellular signaling proteins 1. extracellular signal activates external receptor protein 2. activated PI 3-kinase phosphorylates PI hanging around in the membrane 3. intracellular signaling protein binds to PI 4. signaling cascade inside of the cell

Where are Rabs found?

in many different locations/membrane and associated with many different compartments

Where is cholesterol found?

in some animal membranes (not in bacteria/plants) ... it intercalates between hydrocarbon tails and points polar head group and protrudes those toward the phospholipid head group

Where are the mitochondrially-encoded proteins synthesized?

in the mitochondrial matrix

When a GTP binding protein is bound to GDP it is _____.

inactive/off

What happens with tension on the actin/cadherin structure?

increased overall strength because more actin is being recruited when alpha-catenin is extended/unfolded and vinculin binding site is exposed

How does inactivation of signaling protein work?

inhibition of an intermediate protein by a downstream signal

How does receptor inactivation work?

inhibition of the receptor by its own downstream signal

What does ~Gi~ do?

inhibits adenylyl cyclase (... doesn't produce cAMP ... doesn't activate PKA)

What does G α-i do?

inhibits adenylyl cyclase which decreases cAMP

What does Gi do to adenylate cyclase?

inhibits it

Are GPI-anchored proteins soluble/transmembrane proteins? Single pass or multi-pass?

initially single-pass transmembrane proteins

Cadherins or integrins?: Are found in actin-linked cell-matrix junctions.

integrins

What does the final conformation of a transmembrane protein depend on?

interaction between (few) polar AAs in the helices

What helps the protein fold correctly once its in the membrane?

interactions between polar side chains

Where do H+ accumulate in the mitochondrion? Where are they pumped from?

intermembrane space (they are pumped from the matrix into the intermembrane space)

when does centriole replication occur?

interphase

In a Na+ leak channel, what direction does the Na+ leak?

into the cell

Intrinsic or extrinsic apoptosis pathway or both?: Apaf1

intrinsic

Intrinsic or extrinsic apoptosis pathway or both?: Bcl2-family proteins

intrinsic

Intrinsic or extrinsic apoptosis pathway or both?: apoptosome

intrinsic

Intrinsic or extrinsic apoptosis pathway or both?: cytochrome c

intrinsic

How was the nucleus (and surrounding ER) formed in eukaryotes?

invagination of the plasma membrane

What are transverse (T) tubules formed from?

invagination of the plasma membrane

How is actin reorganized during mitosis?

involved in formation of the contractile ring

How does LDL get brought into a cell?

it attaches to an LDL receptor on the membrane and then the receptor binds to adaptin which is bound to clathrin ... membrane begins to curve, vesicle is pinched off, uncoated intracellular vesicle released and can fuse internally with the endosome ... hydrolytic enzymes in the lysosome cleave cholesterol esters and cholesterol can now be incorporated into membranes

What is something that is special about cholesterol?

it can flip-flop between the 2 sides of the membrane

What does spectrin do for a plasma membrane?

it can give real strength and resilience to a plasma membrane

tell me about tropomodulin pls

it caps actin at the minus end in a sarcomere

tell me about CapZ pls

it caps actin at the plus in a sarcomere

What does the input of light energy do/cause during photosynthesis?

it contributes to the redox potential of the reduced products (drives generation of high redox potential products) - provides enough energy to an electron that when it's captured, the reduced product has a very high reduction potential (high PE) and when it donates to an acceptor, this releases enough energy to pump p+ (which causes generation of ATP) - causes reduced product to have a very high redox potential, which allows electrons to be transferred to NADP+ to create NADPH

What happens when both ends of an actin filament are capped?

it creates a stable filament (unlikely to change in size) ... depolymerization COULD occur at the minus end

How is confocal fluorescence microscopy better than conventional fluorescence microscopy?

it cuts back on the fuzziness and gives you a clear picture at the level you're looking at

What does PI3K activity do to the rate of IP3 production?

it decreases it because it decreases the amount of PIP2 present, which decreases IP3 production

How do uncoupling proteins work? What is an example of one?

it essentially functions as a proton pore that dissipates the gradient by letting H+ ions flow freely down their gradient example = brown fat

How does DNP work?

it functions as a chemical uncoupler, masking the charge of an H+ and carrying it across the membrane (dissipates the gradient)

How does brown fat work?

it has a lot of mitochondria ... UCP dissipates the gradient causing increased metabolism/respiration and increasing the amount of heat produced

What does it mean when something has high redox potential?

it has a lot of potential energy

What do the microtubules look like in the axoneme?

it has a series of doublet microtubules

What is ~STAT 1/2~?

it has an SH2 domain and it gets phosphorylated by JAK and dimerizes

Why is the lumen of the golgi more acidic (lower pH) than the ER?

it has proton pumps that are acidifying it

what has to happen to APC in order for it to bind to cdc20?

it has to be phosphorylated

What is the purpose of a carrier protein?

it helps a hydrophobic signal molecule be soluble in the aqueous environment outside the cell

What is a mannose 6-phosphate tag?

it is a sugar tag for lysosomal targeting and retention on a N-linked oligosaccharide attached to a lysosomal hydrolyase

What makes photosystem II special?

it is a very powerful oxidant and takes electrons from things (particularly water)

What does the actin in a dendritic network look like?

it is branched! Arp 2/3 nucleation of new filaments is mediating this

What is special about the microtubule cap?

it is more stable than the GDP-bound microtubule

what happens when CAK (Cdk-activating kinase) acts on a partly active Cdk?

it phosphorylates on the T loop and change it into its fully active form

What does the 19S core do in a proteasome?

it pulls stuff lol ... every time an ATP is hydrolyzes, it tugs the protein down more and pulls of the ubiquitin chain

What does the PI-3-Kinase-Akt signaling pathway stimulate?

it stimulates animal cells to survive and grow!!!

What happens if you put a bunch of G-actin (bound to ATP) in a test tube?

it will spontaneously associate and dissociate until there is enough of an aggregation that allows polymerization of a new filament

If a protein that normally would have a KDEL sequences is mutated so that its sequence is LSEL, what is the likely consequence?

it would get secreted eventually

ok ya i drew out the SRP stuff so heehee

it's beautiful and i am proud

listen ok i wish i could attach pics of the gorgeous diagram of the Ran cycle I just spent 45 minutes making but like I can't bc i'm not paying for Quizlet Pro so ......

just text me if u want the pics they're FIREEEEEE

What is the name of a microtubule-severing protein?

katonin

What is the purpose of the Na+/K+ pump in cells?

keeps the Na+ that is coming into the cell from building up

What kinesins are minus-end directed (move towards the minus end)?

kinesin-14

What is requires for NMDA receptors to be activated?

large depolarization and glutamate in the synapse

What effect does ~cytochalasin B~ have on filaments?

leads to depolymerization

phosphorylation of nuclear lamins by M-cyclin/Cdk

leads to disintegration of the nuclear envelope during prometaphase

What source of energy drives release of an electron by a chlorophyll in a special pair of photosystem II?

light energy

How does staining work? (incident white light)

light of different wavelengths that is not that color bounces off and doesn't get transmitted through (only some wavelengths pass through stained samples, and we see these as colors)

What directly fuels the light reactions of photosynthesis?

light!

What is the benefit of "super-resolved fluorescence microscopy"?

limit of resolution is better than .2 μm (200nm) like it is in a regular light microscope

What anchors Gs-α at the plasma membrane?

lipid tail/lipid anchor

What triggers assembly and contraction of the contractile ring?

local activation of RhoA

What is ~paracrine~ signaling?

local signaling (one cell secretes a signaling molecule that acts on nearby cells)

what can mutations in Rb cause?

loss of cyclin/Cdk control ... allows cells to S phase in the absence of cyclin/Cdk activation

What is thought to cause autism?

loss of normal pruning ... this is very overstimulating as it causes there to be too many competing signals in the brain

What is synaptic pruning?

loss of synapses that aren't being heavily used

Where might a v-type ATPAse be found?

lysosome, endosome, or vacuole

mRNA for a typical cytosolic protein is ... A. translated by ribosomes in the cytosol B. translated by ribosomes attached to SER C. translated by ribosomes attached to RER D. translated in ER lumen and transported back into cytosol E. translated in nucleus and exported to cytosol

mRNA for a typical cytosolic protein is ... *A. translated by ribosomes in the cytosol* B. translated by ribosomes attached to SER C. translated by ribosomes attached to RER D. translated in ER lumen and transported back into cytosol E. translated in nucleus and exported to cytosol

What is occurring if the microtubule is polymerizing quickly?

many dimers at the plus end are bound to GTP ("GTP cap" of microtubule ... more likely to occur at the plus end because polymerization is more rapid there)

Where is ATP made in the mitochondrion?

matrix

What is the charge of the mitochondrial matrix? What is the charge of the intermembrane space?

matrix is positive and the intermembrane space is negative

What is Vmax?

maximum rate of transport of the carrier (point where the transporter is saturated)

What is Km?

measure of affinity of the carrier for the molecule it is transporting 1/2 Vmax = Km

What do cadherins do inside the cell?

mediate attachment to the cytoskeleton

What are motile cilia and flagella built from?

microtubles and dyneins

What forms the structure of flagella and motile cilia?

microtubules

What is involved in the formation of the mitotic spindle?

microtubules

When mitochondria move around, what "tracks" are they carried on?

microtubules

What ensures maternal inheritance of mitochondria in mammals?

mitochondria of the sperm are tagged with ubiquitin ... mitochondria is destroyed due to this tag after fertilization

What organelles are proteins not trafficked in vesicles to?

mitochondria, choloroplasts, peroxisomes

Where might an F-type ATPase be found?

mitochondria/chloroplast

What binds mitochondrial targeting sequences and aligns proteins with a translocator of the outer mitochondrial membrane?

mitochondrial import receptor proteins

What do detergents in water exist as at low concentrations?

monomers

What is co-translational translocation?

most proteins cross to the ER lumen as they are translated

Name a nucleotide switch protein that is NOT a G protein.

motor protein on the microtubule (kinesin/dynein/myosin)

What is an antenna complex?

multitude of pigments including chlorophylls that transfer light energy from one chlorophyll to another until the eventual transfer of energy to chlorophylls in the special pair which will give up an electron

What myosin(s) can carry cargo?

myosin 5 and myosin 6

What was the first myosin that was discovered?

myosin II

What form do myosin II units associate into?

myosin II units associate by their tail regions into thick bundles

Is ~production of inhibitory protein~ an example of positive or negative feedback?

negative feedback ... leads to suppression of the very same signal that started the signaling cascade

Is ~receptor sequestration~ an example of positive or negative feedback?

negative feedback ... leads to suppression of the very same signal that started the signaling cascade

Can you use a hydropathy plot to analyze an amphipathic alpha-helix?

no ... AAs are alternating between polar and nonpolar every 2/3 and protein isn't long enough due to helix length

Are the Rabs on different membranes around the intracellular membranes the same?

no way!

In cystic fibrosis, what does the deletion of F508 cause to happen?

not only is the protein made non-functional, it makes CFTR be recognized as a misfolded protein (so it never gets trafficked from the ER to the plasma membrane)

Where is most of the genetic material in chloroplasts located?

nuclear genome

How are large proteins transported through nuclear pores?

nuclear import proteins (importins) and nuclear export proteins (exportins)

What do gamma-tubulin ring complexes do?

nucleate the formation of all of these microtubules

Oncogeneor Tumor Supressor?: myc

oncogene

how many copies of DNA in G1?

one copy

How do voltage-gated channels work?

open when membrane potential changes and exceeds threshold ex: voltage-gated Na+ channels

What triggers fusion of synaptic vesicles with the membrane?

opening of voltage-sensitive Ca2+ channels ... this increases cytosolic Ca2+ NT is only released when an AP fires and Ca2+ is released

What does an excitatory NT do?

opens channels that depolarize the membrane (ex: Na+) ex: Ach-gated cation channels, gluatemate-gated Ca2+ channels, serotonin-gated cation channels

What does an inhibitory NT do?

opens channels that hyperpolarize the membrane (ex: Cl-) ex: GABA-gated Cl- channels, glycine

saltatory behavior

oscillations towards/away from the poles/equator

In a Cl- leak channel, what direction does the Cl- leak?

out of the cell

In a K+ leak channel, what direction does the K+ leak?

out of the cell

Where is [Ca2+] high?

outside the cell

Where is [Cl-] higher?

outside the cell

Where is [K+] higher?

outside the cell

Where is [Na+] high?

outside the cell

What is the source of the carbon atoms in CO2 produced by mitochondria?

oxidative fuels (fats/carbohydrates/proteins)

What is the final electron acceptor?

oxygen (has a very high affinity for electrons)

what stimulates Puma and Noxa?

p53 accumulation

p53 and Rb are alike in what way? A. When mutated, both allow over-proliferation of cells. B. Both ultimately reduce activity of Cdks. C. Both are classified as tumor suppressors. D. Both are regulated through phosphorylation. E. All of the above.

p53 does NOT ... A. Induce BH3-only protein expression (Puma/Noxa) B. Become polyubiquitylated and targeted for degradation by Mdm2 C. Induce expression of p21, a CKI D. Become phosphorylated by MAP kinase

p53 does NOT ... A. Induce BH3-only protein expression (Puma/Noxa) B. Become polyubiquitylated and targeted for degradation by Mdm2 C. Induce expression of p21, a CKI *D. Become phosphorylated by MAP kinase* ----- D is describing myc

What allows for binding of a protein in different compartments and release of a protein in the ER lumen (binding/release of receptor/cargo)?

pH differences

What is the basis for binding of cargo in one compartment and release in another?

pH differences

A macrophage secretes a cytokine that acts on a neighboring cell. What kind of signaling is this?

paracrine

~An adipocyte secretes an "adipokine" that acts locally on muscle cells.~ What kind of signaling is this?

paracrine signaling

What is maternal inheritance?

passing of a gene from mother to offspring and from daughters of that mother to their offspring

Are channel proteins active or passive transporters?

passive transporter ... transport is done down an electrochemical gradient

What recruits adaptin AP2 to a site for vesicle formation? Draw it.

phosphoinositide

What does PI-3 kinase do?

phosphorylates phosphoinositol to create a phosphoinositide (--> further recruitment of Rab-GEF and other tethering proteins)

What happens when MLCs are phosphorylated in smooth muscle?

phosphorylation of MLCs causes change in the tail conformation of the myosin II and that allows those thick bundles to form ...

what causes dissociation of the nuclear envelope?

phosphorylation of nuclear lamins

What kind of modification is indicated by the circled P (there's a picture on the other side of this hehehe)?

phosphotyrosine

Where is energy from sunlight absorbed?

photoreaction center in a chloroplast

How can photosynthesis and respiration be linked?

photosynthesis can produce sugars that can be used to fuel respiration

Where is oxygen produced during phototsynthesis (which photosystem)?

photosystem II (only here! not in photosystem I) ... made when H2O is used to get an electron

How do mechanically-gated channels work?

physical force pulls open channel (ex: stress-activated) ex: channels in the hair cells in the cochlea

What is the role of ATP in the transfer of ADP into the mitochondrial matrix? What facilitates this action?

plays a role in facilitating ADP movement into the matrix in exchange for the increased negatively charged ATP movement toward the build up of positive charges (H+) in the intermembrane space ADP/ATP carrier protein helps this all happen

What end of actin is added to?

plus end

What end are myosins moved towards?

plus end (idk if this is of the actin filament or what??)

What end of the microtubule does the kinetochore bind to?

plus end of the microtubule

What end does myosin move towards when it moves?

plus ends ... it pulls the Z discs towards the center

What is a mitochondrial targeting protein that still has its targeting sequence called?

precursor protein

What is a characteristic of the signal sequence that signals for import into the nucleus?

presence of a stretch of multiple positively charged AAs

What would mutations in the enzymes that affect the transfer of GlcNac-phosphate onto the mannose residue (GlcNac phosphotransferase) or remove GlcNac to expose M6P (GlcNacase) cause?

prevention of the formation of the M6P tag

What happens without a thylakoid signal sequence?

protein enters through TOC and then through TIC and then stays in the stroma

What is the function of the rough ER?

protein synthesis (transmembrane proteins and soluble proteins destined to organelle lumens or to be secreted out into the extracellular space)

What is a transmembrane protein?

protein whose polypeptide chain passes completely through the lipid bilayer; exposed to both faces of the membrane

What is a glycoprotein?

protein with sugars attached to it ... if branching = glycoprotein

What is the ECM composed of?

proteins and polysaccharides that are secreted by local cells

What do microtubule-binding proteins do?

proteins that can organize microtubules

What is perlecan?

proteoglycan

What is generated by the electron transport chain?

proton gradient

What is another name for chemiosmosis?

proton motive force

What's an uncoupling protein?

proton pore that allows protons to move down a concentration gradient and dissipates any proton gradient that may have existed

What does water put into the photosynthesis cycle? Where do these things go?

protons (go to create the H+ gradient) and electrons (go to oxygen)

What is flippase?

pump that flips phospholipids whose head groups contain free amino acids (PS, PE, PI) using ATP ... flips them back to the inside so they're always facing the inside

What does the Ca2+ ATPase do?

pumps Ca2+ into the ER and sarcoplasmic reticulum of muscle cells keeps [Ca2+] super low in the cytoplasm

Can membranes flip-flop?

rarely! this is only something that cholesterol can do phosphlipids within the membrane can laterally diffuse as well as rotate, and their fatty acid tails can flex

What is required in order for phagocytosis to occur?

rearrangement of the actin cytoskeleton

What catalyzes the flipping of phospholipid molecules to the lumenal side of the ER membrane?

scramblases

What does acetylcholine cause in salivary gland cells?

secretion of digestive enzymes

what does E7 do?

sequesters Rb

Does the ~TGF-β receptor pathway~ involve tyrosine kinase or serine/threonine kinase?

serine/threonine kinase - only receptor we know that's an enzyme that's not an RTK

Does the ~Akt, PKA, and PKC pathway~ involve tyrosine kinase or serine/threonine kinase?

serine/threonine kinase - phosphorylates Bad ... this allows a 14-3-3 protein to bind those phosphoserines/phosphothreonines

What regulates actin filament depolymerization?

severing proteins (gelsolin and cofilin)

What does an uncoupler do to chloroplast ATP synthesis?

shuts it down (no ATP made)

What does an uncoupler do to mitochondrial ATP synthesis?

shuts it down (no ATP made)

What is the structure of spectrin like? What does this help it do?

spectrin has a long structure that gives it its stretchability and resistance to tensile force

Where is ATP made in the cholorplast?

stroma

An α-motorneuron sends a signal from the spinal cord that results in secretion of acetylcholine that acts on a skeletal muscle cell that is adjacent to the nerve terminal. What kind of signaling is this?

synaptic

How does a F-type ATP synthase work?

synthesizes ATP in reverse (in mitochondria)

How do bacteria survive if their electron transport chain isn't working?

the ATP synthase works in the opposite direction, using ATP to form a proton gradient

In regard to the MAP-kinase pathway, ~what happens if a mutant Ras lacks GTPase activity~?

the Ras would always be on ... the output would always be on and stimulating gene expression ... this could be a cause of cancer! (there are several Ras mutants that cause tumorigenesis)

What is retrograde flow?

the actin cytoskeleton isn't anchored, so when it growing instead of protruding, it pushes the whole network backwards

Tropomyosin wraps around _____.

the actin filament

What makes sure that an AP is unidirectional?

the ball and chain VG channels that become inactivated once the inside of the membrane becomes positive ... even if Na+ were to drift towards channels that were just used, they will be inactivated so they won't respond! ---> these channels will remain inactivated until the cell is repolarized completely

Why is 16% of the membrane in a liver hepatocyte smooth ER membrane?

the liver makes cholesterol and lipid particles that need to be packaged and sent out (this is done in the SER)

Where does the unequal charge distribution on the helix cause the positive charges to be attracted to?

the matrix

Is the pH lower in the golgi or in the ER?

the pH is a little bit lower in the golgi (more acidic)

What determines the variations in severity of mitochondrial conditions?

the percentage of mutated DNA that was passed on

What end do actin filaments tend to polymerize more rapidly at?

the plus end

What accounts for the phenomenon of "sorting out"?

the self-recognition and anchoring by cadherins - can aggregate into groups of E-cadherin and N-cadherin - can aggregate to have cells expressing a high level of E-cadherin to bind the tighest and segregate towards the middle, while cells expressing a low level of E-cadherin are found towards the outside

What would happen if clathrin couldn't bind to its adaptor protein?

there couldn't be formation of a clathrin coat so there couldn't be clathrin coat and vesicles

What happens with Gt in the dark?

there is a high [cGMP] ... rhodopsin is inactive ... cGMP binds cation channels and opens them, causing Na+ and Ca2+ to rush in and depolarize the cell ... high rate of NT release

What happens every time a neuron fires?

there's an increase of Ca2+ and secretion from a secretory vesicle

Why is 60% of the membrane in a pancreatic exocrine cell rough ER membrane?

these cells release secreted proteins

What happens when two waves are in phase?

they add together, creating a wave with higher amplitude and a brighter light

When the α subunit binds GTP, it dissociates from the β-γ pair and from the receptor. α and β-γ diffuse away, but are confined to the plasma membrane. Why?

they are anchored in the plasma membrane by lipid tails

What are glycophosphatidylinositol (GPI) anchors?

they are basically just glycosylated PIs

what happens to cyclins during the cell cycle?

they are broken down at the end of each phase to regulate progression through the phases by ubiquitination and proteolylsis

What is special about tight parallel bundles?

they are close together ... there is no space for myosins here, so these have a different function than contractile bundles

what happens to centrioles during M?

they are fully duplicated and begin to move even further apart ... start nucleating MTs

How do motor proteins work?

they are tethered to microtubule tracks that they move along carrying either a vesicle/vesicular tubular cluster

What happens to the 5 glyceraldehyde 3-phosphate molecules that are produced in the Calvin cycle?

they are used to regenerate the starting compound

What is the difference between the AMPA and NMDA receptor?

they both bind glutamate, but NMDA receptor is blocked by Mg2+

What does a lipid anchor do?

they can diffuse around the plasma membrane, but can't be free in the cytosol ... they keep the α and β/γ domains sequestered to the plasma membrane

What happens if M6P receptors exit to the plasma membrane?

they can retrieve proteins from the extracellular space

What happens when two waves are out of phase?

they cancel each other out, creating a wave with lower amplitude and a dimmer light

What happens to two RTKS when a signal protein ligand binds?

they dimerize!

How do things larger than 60,000 daltons get into the nucleus?

they don't heheeh (they don't diffuse ... need some kind of directed transport)

How do ions (H+, Na+, HCO3-, K+, Ca2+, Cl-, Mg2+, etc.) get across the lipid bilayer?

they don't! heehehhe trick question

How do collagen bundles organize in mammalian skin?

they run in 90 degree directions to each other and weave in an out like wicker-work ... provide for a lot of good tensile strength in the skin

What is the problem with the formation of bilayers in water?

they still have a free edge (energetically unfavorable) ... they spontaneously form spheres (liposomes)

How do proton ionophores work? What is an example of one?

they work as chemicals that mask the charge of protons and allow them across the membrane example = DNP

What would happen if mitochondrial protein wasn't associated with chaperone proteins?

they wouldn't fit through the translocator if they were folded

If a protein is synthesized in the mitochondria and is inserted into the inner membrane what is its root?

through OXA into inner membrane

How does glucose get into a cell?

through a facilitative glucose transporter that allows glucose to diffuse through the transporter down its concentration gradient (in most cells, moving from the outside of the cell to the inside)

How are carbohydrates linked?

through the NH2 domain of the asparagine side chain (*N*-linked glycosylation

Photosystem II pumps protons into what space?

thylakoid space

Where do protons accumulate during photosynthesis?

thylakoid space

Where do H+ accumulate in the chloroplast? Where are they pumped from?

thylakoid space (they are pumped from the stroma to the thylakoid space)

what keeps glucose inside the endothelial cells lining the gut?

tight junctions

What can restrict protein diffusion?

tight junctions (or other barriers) tight junctions act as an actual physical barrier ... there are different proteins on either side of the tight junctions, but the domains will never meet!

How is actin arranged in filopodium?

tight parallel bundles

Where is myosin anchored?

to the sub-stratum

What is thought to cause schizophrenia?

too much synaptic pruning

In what direction does a "reverse" ATPase work?

toward the pumping of protons

In what direction does a "forward" ATPase work?

towards the production of ATP

What are two ways that polar and charged molecules can be moved across membranes?

transporters and channel proteins

What is the normal function of CFTR?

transporting Cl- from inside the cell to the extracellular space

What does an uniport carrier do?

transports a single molecule/single class of molecule at a time

True or false?: Tight junctions prevent solutes from flowing from apical to basolateral compartments of the extracellular space.

true

True or false: Adherens junction use actin filaments.

true!

True or false: Hemidesmosomes and desmosomes use intermediate filaments.

true!

True or false: Proteoglycans are a type of glycoprotein.

true! proteoglycans are a special class of glycoproteins

Intermediate filaments are resistant to breaking under tensile stress. True or false?

true! they are stretchy and hard to break!

Oncogeneor Tumor Supressor?: p53

tumor supressor

how many copies of DNA in G2/M phase?

two copies

what does centriole replication during interphase give rise to?

two separate centrosomes during mitosis

each chromosome consists of:

two sister chromatids attached at centromeres and at many points along the arms by cohesin complexes

What is symport?

two solutes move in same direction ex: Na+/glucose symport

What is antiport?

two solutes moving in opposite directions ex: HCO3-/Cl-

Does the ~JAK pathway~ involve tyrosine kinase or serine/threonine kinase?

tyrosine kinase - STATs interact through SH2 domains, binding phosphotyrosines

What part of a RTK is the catalytic domain?

tyrosine kinase domain (it phosphorylates tyrosines)

What stimulates mitophagy?

ubiquitination of proteins on the cytosolic face of the outer mitochondrial membrane

What kind of protein is GLUT1?

uniport carrier

What are membranes more fluid: when they consist of chains with unsaturated or saturated hydrocarbon chains?

unsaturated

Looking at a string of AAs, how would you be able to determine that a helix is an amphipathic alpha-helix?

use FAMILY VW and look for 2/3 polar and nonpolar alternating AAs (?)

How are secretory vesicles in neurons able to be partially docked with the plasma membrane so that they can very rapidly fuse with the plasma membrane upon receipt of the signals?

using SNARE-like proteins, complexin, and Ca2+ thing

What is the partial zipper SNARE complex composed of?

v-SNARE of the synaptic vesicle (full of neurotransmitters) and SNARE-like proteins on the presynaptic plasma membrane interacting to form the partially assembled SNARE bundle

What protein acidifies intracellular compartments?

v-type ATPase or a proton pump

How do preformed signaling complexes on a scaffold protein work?

when an signal molecule binds to the receptor and activates it, the already localized/attached intracellular signaling proteins are activated and cause downstream signals

When does the treadmilling range occur?

when both Cc(T) and Cc(D) = 0

What happens once you have end capture on both ends of a chromosome?

when everything is captured, that crosses a signaling checkpoint that allows anaphase to begin

Why are the cytoplasmic and exoplasmic/lumenal sides of membranes similar in plasma membrane and intracellular organelles?

when making an organelle, the membrane is turned inside out from the way it is in the plasma membrane

What activates Rho proteins? A. GEF B. GDI C. GAP

What activates Rho proteins? *A. GEF* B. GDI C. GAP

What form are the actin monomers coming in in?

T form

Where dynein found in a mitotic spindle?

at the plus end of an astral microtubule (near the plasma membrane)

What do angstroms (A) measure?

atomic distance/measurement (down to the level of individual atoms)

What do integrins do?

attachment to the ECM

A tumor cell secretes a growth factor that binds to receptors on its own cell surface. What kind of signaling is this?

autocrine

~A cell secretes a signaling molecule that acts on receptors of the same cell.~ What kind of signaling is this?

autocrine signaling

Where does autophagy eventually lead to/where does the engulfed material end up?

autophagosome that fuses with the late endosome (eventually goes to lysosome)

What is a switch protein?

helix that switches back and forth (depending on whether or not it is bound to GTP/GDP)

How do voltage-gated channels sense membrane voltage?

helix with arginines (+) on it slides from one side of the protein to another when the voltage changes, moving closer to the negative side of the cell and opening and closing the channel

What is the cytosolic pH relative to the lysosomal pH?

higher than lysosomal (cytosolic = 7.2, lysosomal = 5.0)

What influences cellular mechanical properties and signaling?

higher-order actin filament arrays

What are some characteristics of dark-field microscopy?

highlights things that are reflective

Where are binding sites for Ca2+ found on cadherins?

hinge region between cadherin domains

Where are memories stored in the brain?

hippocampus

Telomeres preserve DNA's ________ from shortening during replication. A. Leading strand B. Okazaki fragments C. Parental strand D. Lagging strand

Telomeres preserve DNA's ________ from shortening during replication. A. Leading strand B. Okazaki fragments C. Parental strand *D. Lagging strand*

What does a glycosidase do?

hydrolyzes glycosyl units from a carbohydrate (CHO); removes sugars

What kind of molecules do ABC transporters bind?

hydrophobic molecules

Where are the nuclearly-encoded mitochondrial proteins synthesized?

in the cytosol

Where does the processing of carbohydrates (connected to proteins) occur?

in the golgi as the protein passes cis --> medial --> trans

Where do disulfide bonds form during post-translational modification (I'm gonna call it PTM from now on deal w it) of a protein?

in the lumen of the ER ... where disulfide isomerase is found

Where are proteins encoded by mitochondrial DNA transcribed?

in the matrix

What effect does ~latrunculin~ have on filaments?

leads to depolymerization

phosphorylation of MAPs and catastrophins by M-cyclin/Cdk

leads to destabilization of Mts in mitotic spindles (shortening events)

hemidesmosomes

- anchor cellular IFs to the ECM via integrin proteins - using integrins

Inherited mitochondrial conditions can be ...

- X-linked - autosomal - from inheritance of mutant mitochondria

If a plasma membrane is 3.5 nm wide, how many amino acids does it take to get from one side of the membrane to the other?

1 turn = 3.5 AA = .54 nm 3.5 nm/.54 nm = 6.5 turns 6.5 turns * 3.5 AAs/turn = *23 AAs*

steps of mitosis

1. prophase 2. prometaphase 3. metaphase 4. anaphase 5. telophase

How many gamma-tubulins are in a gamma-tubulin small complex (gamma-TuSc)?

what happens to centrioles during G1?

2 centrioles start to separate from each other

What is a special pair?

2 chlorophylls that are positioned by a protein that puts them in proper orientation

What is phosphatidic acid composed of?

2 fatty acids, a phosphate, and a glycerol backbone

How many heads does myosin II have?

2 heads

A nuclearly-encoded mitochondrial matrix protein must be translocated through ... A. a translocator of the outer membrane B. a translocator of the inner membrane C. both

A nuclearly-encoded mitochondrial matrix protein must be translocated through ... A. a translocator of the outer membrane B. a translocator of the inner membrane *C. both*

A mitochondrial inner membrane protein that is encoded by the mitochondrial genome must be translocated through ... A. a translocator of the outer membrane B. a translocator of the inner membrane *C. neither of the above* ----- i think this is wrong .... i'm pretty sure if the protein is made in the mitochondria, it comes into the inner membrane through OXA which is a translocator of the inner membrane!!!

Activation of a GPCR might lead to sequestration of that receptor by an arrestin protein. This is an example of ... A. receptor desensitization B. positive feedback C. signal amplification

Activation of a GPCR might lead to sequestration of that receptor by an arrestin protein. This is an example of ... *A. receptor desensitization* B. positive feedback C. signal amplification

Is collagen a GAG or a fibrous protein?

fibrous protein

After Sar1 recruits the inner COPII coat proteins, the inner coat proteins can be bound to ... A. COPII outer coat proteins B. transmembrane cargo receptors C. both of the above

After Sar1 recruits the inner COPII coat proteins, the inner coat proteins can be bound to ... A. COPII outer coat proteins B. transmembrane cargo receptors *C. both of the above*

Is fibronectin a GAG or a fibrous protein?

fibrous protein

Cdc6 is involved in the _____ checkpoint, while Cdc25 regulates the _____ checkpoint. A. metaphase-anaphase, start B. start, G2-M C. G2-M, start D. start, metaphase-anaphase

Cdc6 is involved in the _____ checkpoint, while Cdc25 regulates the _____ checkpoint. A. metaphase-anaphase, start *B. start, G2-M* C. G2-M, start D. start, metaphase-anaphase

Is laminin a GAG or a fibrous protein?

fibrous protein

are gain of function or loss of function mutations more common?

loss of function mutations

Caffeine is a phosphodiesterase inhibitor. This would tend to ... A. increase activation of PKA B. decrease activation of PKA C. have no effect

Caffeine is a phosphodiesterase inhibitor. This would tend to ... *A. increase activation of PKA* B. decrease activation of PKA C. have no effect

how can an inactive phosphorylated Cdk be activated?

Cdc25 phosphatase removes the inhibitory phosphate

Conversion of a PI(4)P to a PI indicates the action of a ... A. Kinase B. Phosphatase C. Both

Conversion of a PI(4)P to a PI indicates the action of a ... A. Kinase *B. Phosphatase* C. Both ----- phosphatase removes Ps

How many triply-phosphorylated PI forms are there? A. 1 B. 2 C. 3

How many triply-phosphorylated PI forms are there? *A. 1* B. 2 C. 3

In what order to these events occur? 1. cargo receptor binds cargo 2. vesicle begins to form 3. adaptin binds clathrin 4. cargo receptor binds adaptin A. 1, 4, 3, 2 B. 1, 2, 3, 4 C. 2, 4, 1, 3 D. 3, 1, 4, 2

In what order to these events occur? 1. cargo receptor binds cargo 2. vesicle begins to form 3. adaptin binds clathrin 4. cargo receptor binds adaptin *A. 1, 4, 3, 2* B. 1, 2, 3, 4 C. 2, 4, 1, 3 D. 3, 1, 4, 2

question(s) asked at G1-S (start transition) checkpoint

Is the environment favorable?

What kinase does the second messenger that is produced by an effector protein for Gs-α activated?

PKA (cAMP-dependent protein kinase)

when is Cdc6 degraded?

S phase when S-cdks phosphorylate it

Sos is a guanine nucleotide exchange protein (GEF) for a monomeric G protein. What effect will Sos have on its target G protein? A. activate B. deactivate C. both

Sos is a guanine nucleotide exchange protein (GEF) for a monomeric G protein. What effect will Sos have on its target G protein? *A. activate* B. deactivate C. both

Stathmin can tie up free tubulin dimers. What does this do to microtubule polymerization rate? A. increases B. decreases

Stathmin can tie up free tubulin dimers. What does this do to microtubule polymerization rate? A. increases *B. decreases*

The Rab effector PI3K. What does it produce? A. a phosphoinositide B. Rab GTP C. Rab GDP

The Rab effector PI3K. What does it produce? *A. a phosphoinositide* B. Rab GTP C. Rab GDP

The bacterial cytoplasm is topologically equivalent to: A. the cytosol of a eukaryotic cell B. the mitochondrial intermembrane space C. the mitochondrial matrix

The bacterial cytoplasm is topologically equivalent to: A. the cytosol of a eukaryotic cell B. the mitochondrial intermembrane space *C. the mitochondrial matrix*

The photosystem I photoreaction center absorbs light that is ... A. ultraviolet B. visible C. infrared

The photosystem I photoreaction center absorbs light that is ... A. ultraviolet *B. visible* C. infrared

True or False: A single mutation is NOT enough to turn a normal cell into a cancer cell. A. True B. False

True or False: A single mutation is NOT enough to turn a normal cell into a cancer cell. *A. True* B. False ----- A single mutation is not enough to change a normal cell into a cancer cell: most cancers develop gradually from a single aberrant cell by the accumulation of a number of genetic and epigenetic changes over time.

What do ESCRTs do?

mediate membrane curvature (in opposite direction of what we're used to) and form intralumenal vesicles

Sar1 is a G protein. When its GEF acts on it, what happens regarding its amphiphilic helix?

WROSHOOH and amphiphilic helix inserts into membrane

What is a sarcomere?

a contractile unit

What is KDEL?

amino acids that compose an ER retention/retrieval signal

How does a M6P tag work?

an M6P receptor will bind to the M6P tag ... this causes packaging of those proteins into vesicles that end up in the endosome (and later the lysosome) ... the protein is released in the lysosome and the phosphate will be removed from the M6P tag, "turning it off", and the M6P receptor will leave the lysosome in a vesicle and head back to the trans golgi network (or exit to the plasma membrane)

In a non-photosynthetic plant cell, how is ATP produced?

catabolism of sugars exported from photosynthetic cells

What does adenyl/adenylate cyclase do?

catalyzes production of cAMP from ATP (takes 2 Ps away from ATP and forms a phosphodiester bond)

What does cAMP do?

causes its effects until it is degraded by cAMP phosphodiesterase

What would happen if the adaptin could no longer bind the LDL receptor?

cholesterol uptake would go down/be prevented

What side of the golgi is the ER on (cis/trans?)

cis golgi

Where do vesicles that bud off from the ER go?

cis golgi

AP2 is recruited by a phosphoinositide. What happens when an phosphoinositide phosphatase acts on that phosphoinositide?

de-recruits AP2 (it no longer has its binding site)

What happens to paternal mtDNA after fertilization in mammals?

degraded!!!

True or false?: Gap junctions are always fully open.

false you can put tracers in retinal cells ... light can modify the extent to which they travel

True or false: GAG chains carry a net positive charge.

false! net negative charge (sulfur and hydroxyl groups)

True or false: Hemidesmosomes are cell-cell anchoring junctions.

false! they are cell-matrix anchoring junctions

What happens when two waves are completely out of phase?

flat line ... no light is seen

How do cells commit suicide?

flip PS to the extracellular leaflet of the plasma membrane, triggering phagocytosis by other cells - PS propagates on external surface of the cell very rapidly - scramblase flips phospholipids randomly from one side to another

what happens when cyclin binds to Cdk?

it becomes partly active and the T loop partially unfolds

What does the presence of both CapZ and tropomodulin do for an actin filament?

it makes the filament stable ... it won't polymerize/depolymerize at either end!

What does the 20S core do in a proteasome?

it serves as the central hollow core

What's the pattern of inheritance of mitochondrial DNA for plants and animals?

maternal!!

congress

move to the equator

How does chemiosmosis work?

movement of protons down their gradient causes mechanical energy due to the turning of the ATP synthase and this results in production of ATP from ADP (potential energy in the form of chemical energy); coupling of the proton gradient to the driving of ATP synthesis

What is depolarization?

movement towards more (+) number

What is repolarization/hyperpolarization?

movement towards more (-) number

What does GLUT1 do?

moves glucose from areas of high concentration (ex: outside the cell) to areas of low concentration (ex: inside the cell) [concentration drives direction of movement]

What is active transport?

moving a solute against its concentration gradient, using an input of energy

How are channels opened/closed?

multiple sliding helices that open/close the inner pore

where do sarcomas originate?

muscle/connective tissues

What is a function of the COPII coat?

promote membrane curvature

How were investigators first really able to understand that myosins could move actins?

sliding filament assay

What does Gs do to adenylate cyclase?

stimualtes it

On a graph of rate of transport vs concentration of transported molecule, what does the line of simple diffusion and channel-mediated transport look like?

straight line

What is a signal sequence?

strand along the protein whose sequence can be identified

During photosynthesis, where is ATP made?

stroma

chemotherapy

taxol stabilized MTs, preventing mitosis and apopotosis in rapidly dividing cells

What prevents microtubules from sliding in cilia/flagella?

tethering/linking proteins

How does LTP work when an AMPA channel is activated?

the AMPA channel opens, which allows Na+ influx into the postsynaptic neuron (which depolarizes it)

What happens to the ATP bound to the individual monomers that come in over time?

the ATP in the filament hydrolyzes

What is resolution?

the ability to discriminate 2 objects as 2 separate objects

What is the set of genes that is encoded in the chloroplast similar to?

the genes that are found in photosynthetic bacteria

How is the helical structure of an alpha-helix formed?

the oxygen in the carboxyl group hydrogen bonds to the hydrogen in the amino group of another amino acid in the chain 4 amino acids down the chain

Why are ~the signal proteins of the TGF(β) superfamily acting through receptor serine/threonine kinases and Smads~ special?

this pathway is the only one that we know that function via a serine/threonine kinase

When electrons are stripped from water and O2 is formed, in what space do the protons end up?

thylakoid space

All anchoring junctions use _____.

transmembrane proteins and intracellular adaptors

What binds COPII inner coat proteins?

transmembrane proteins with exit signals on their cytosolic domains

What allows for rapid reloading of cargo (ex: NT)?

transport proteins in the vesicle

How do ribosomes get into the nucleus?

transported as individual subunits

What kinds of microtubules do centrosomes have?

triplet microtubules

How do chromosomes attach to microtubules?

via kinetochores

What do aquaporins allow to pass?

water molecules (but not H+s!!!)

How do nucleotide switch proteins work? (i.e. why are they in different conformation when bound to NTP or NDP?)

when GTP is bound, there is an electrostatic interaction that pulls the switch helix in ... when NTP is hydrolyzed to NDP, the attraction is no longer there and it bounces back!

When is mTOR active?

when nutrients are available ... it suppresses autophagy

Lysosomal hydrolases are functional under what condition?

when pH is low (~5)

Can ~RTK~ create binding sites for proteins with SH2 or PTB domains?

yes ... tyrosine kinase!!!

Can ~Src~ create binding sites for proteins with SH2 or PTB domains?

yes ... tyrosine kinase!!!

Does the SR CA2+ ATPase require ATP to function (pump Ca2+ from the cytosol into the SR lumen)?

yes! it is ATP dependent

Can proteins diffuse within the membrane?

yes! they have a certain kind of fluidity (just like lipids), but they move much more slowly because they are 50x as big

MCB 2 FINAL

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