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51 Cards in this Set

  • Front
  • Back
Why can cholesterol pass through lipid membranes?
It's amphipathic: HC NP group, OH polar group
Describe the shared structures of fatty acids.
Describe their interactions with other fatty acids and the IMF that comprise them.
Two alkyl chains, phosphate group, polar head group

Alkyl: VDW, HPhobic effect
Polar: H-bonds (solvated in water)
Describe the experiment that proved that lipid bilayers spontaneously form.
Glycine floating in water, phospholipids at bottom, sonicate, gel filtrate, found glycine trapped in vesicles
Why can't ions pass through membranes on their own?
Have interactions with water which would have to be broken in order to pass (wouldn't be replaced), unfavorable
How does chain length and number of double bonds influence Tm and why?
longer chain-->more dispersion of water molecules when HPhobic chains interact (favorable), more VDW forces between them

more double bonds-->lower Tm, more kinks, disrupts VDW with other FAs (packing)
Why are trans-fatty acids dangerous?
Enhance VDW, harder to break, lack enzymes to process them
How does cholesterol affect Tm and why?
Instead of sigmoidal shape, curve is flattened and fluidity has decreased dependency on temperature (can H-bond and VDW, but bulky, so disrupts other interactions)
How would you extract peripheral membrane proteins and why?
High salt concentration so ions compete with interactions holding them to hpilic head groups of integral membrane proteins.
How would you extract integral membrane proteins and why?
Organic solvent (detergent) is nonpolar, interacts with hydrophobic parts of membrane and removes them
Describe the molecular interactions that allow a-helices and b-sheets to traverse membranes.
a-helix isn't h-bonding to water, it's h-bonding to itself (1 a-helix can pass on its own), amphipathic, so can have HP side chains point into exterior

b-sheet: NH and CO interact in an interstrand fashion (needs more than 1 b-sheet to pass)
Why are b-barrels formed?
In order to prevent free h-bonds from sticking out, need a strand to loop around from the end and interact with beginning strand
How will amino acid groups be arranged in anti-parallel beta sheets?
Side chains alternate sides, so every other aa group will be hphobic for the most part
About how many amino acids are required to traverse a membrane? How is a hydropathy plot used to determine transmembrane sequences? How can they result in false positives?

Sums up hydrophibicity (delta G from NP to P env) for every amino acid in 20 residue window for entire protein sequence, if hydropathy index above 20 kcal, then that's probably where it passes the membrane

Beta strands fluctuate and won't go over 20, because they have no long hphobic strands (they alternate)
Describe how FRAP allows for the assessment of membrane dynamics.
Fluorescent probe attached to membrane protein, zap with laser

If it were static, there'd be very little recovery of fluorescence

If it had dynamic/fluid properties, surrounding regions would flow in and there'd be some recovery
For the equation:

Explain all variables
Explain what D is proportional to
Explain how t^1/2 relates with protein size
Explain how t^1/2 correlates to D
S is distance traveled
D is diffusion coefficient, proportional to how fast fluorescence is recovered
t^1/2 is the time taken to recover half the fluorescence lost
small t^1/2 means high D
Why is traverse diffusion so much slower than lateral diffusion? How might traverse diffusion be encouraged to occur?
In traverse diffusion, Polar head group must pass HP interior (unfavorable), if have high [PE] on one side of membrane, and low [PE] on other, concentration gradient will encourage transverse diffusion
Describe the fluid mosaic model membrane.
Protein islands floating in a sea of lipids
in terms of molecules, more lipid than protein
in terms of mass, varies
Describe the lipid raft model of membranes.
Proteins in raft have long trans-membrane domain; whole hunk of lipid moves as one piece (raft) in the sea held by many interacting proteins; constantly breaking and reforming; proteins in complexes; (if need respondse like a 2nd messenger this allows proteins involved in the response to be near each other)
Is diffusion driven by enthalpy, entropy, or both? Why?
Entropy: dispersion of matter from ordered to less ordered results in greater entropy (favorable)
If the concentration of glucose is 1.5 mM inside a cell and 5.5 mM outside, what is the gree energy change for transporting glucose out of the cell?
3.34 kJ/mol
What is the equation for efficiency?
Why would calculated efficiency of a protein differ in a biological setting?
Work Done/Energy Extended

Biological settings are more likely to have environments that would be more favorable for reaction to occur, so can achieve greater efficiency
What is the main mechanism utilized by pumps?
Transport coupled to ATP hydrolysis
What is the defining characteristic of P-type ATPases? Name 4 examples.
Self-phsophorylating ATPases

Na-K ATPase (AP recovery)
Ca-ATPase (relax muscles, Ca out)
H-K ATPase (H+ into stomach)
Flipase (maintains membrane assymetry)
Describe the general mechanism of P-type ATPases using Ca2+-ATPase.
E1 state: open to cytosol, high Ca++ affinity, Asp isn't phosphorylated

ATP(binds N)& Ca bind (Active conformaation)

P transferred from ATP to ASP
EVERSION to E2 (favored when Asp phosphorylated)

E2: Open to extracellular space, low affinity for Ca, release Ca++

Hydrolyze Pi with H2O (makes process irreversible): EVERSION
What do transporters do?
Difference between antiporter and symporter.
2 species crossing membrane, one goes with gradient, other against it

Antiporter:opposing directions
Symporter: same
How do concentration gradients affect transporter speed? Give examples.
Smaller gradient-->fast transport (Na-Ca transporter)

Bigger gradient (harder to overcome), slower transport (Ca ATPase)
Why doesn't Cl- pass through Na+ receptors? Why can Li+ pass through Na+ receptors?
Charged residues along channel are negative, so repels Cl

Li is smaller than Na so it can move through
Describe the mechanism of specificity for sodium channels.
Relies on ion size when water molecules are associated; thus anything same size or smaller than Na and its associated water size will fit and pass thorugh channel.
Describe the mechanism of specificity for potassium channels.
Because of potassium's charge density the distance at which it associated with water optimally will be greater than saodium's distance of optimal association. The channel lines itself with carbonyl groups that are this same optimal distance from K, such that when water molecules are shedded by K+, their interactions lost through solvation will be compensated by interactions with the carbonyls. This carbonyl distance is too big for Na+ so its water associationg will not be compensated by resolvation.
How do cell-attached, whole-cell, and excised-path modes differ in patch clamp experiments?
Cell-attached (gigaohm seal): Suction placed on membrane with pipette, can measure ion channel activity in response to drugs, etc.

Whole-cell mode: increased suction on gigaohm busts open membrane, and can measure interior whatever

Excised-path mode: (inside out), detach portion of membrane by pulling, and now have exposed intracellular side of membrane channels and can manipulate their environment
Describe the stochastic nature of channels and how average traces would differ from individual traces.
Individual ion channels don't stay open for the same amount of time, more likely to be open under certain conditions than others, the amount of time open can't be predicted.

Average of individual traces shows that there are times when channels are more likely to be open (and are open) and a time range when they begin to close.
Describe ACh receptor permeability to ions. Which get through and why? What kind of ion channel is the Ach receptor?
Equally permeable to both Na and K, but concentration gradient drives Na

Ligand: receptor has to bind small molecules before opening
Describe changes in ACh receptor structure when ACh binds.
When closed, HP leucine residues face inside of channel, when ACh binds, subunits rotate CCW so serines face interior.
What is required for conformational change of Na and K channels? How do they revert? How can reversion time be altered?

When closed, the outside of the receptor membrane is negative, and the inside is positive, along with a ball and chain that is also positively charged.

Depol-->Conf change-->Receptor open

Now inside is negative (ball still positive) and outside positive.

Positive charge on nugget interacts with negative charge of channel and plugs it. Once original potential reached, will conf change again.

Making chain on ball longer increases open time.
Explain how a repellent induces tumbling in chemotaxis.
Repellent binds MCP receptor, activates CheA(phosphorylated his, +N isn't stable), phosphate given to CheY on Asp (unstable, hydrolyzed spont), CheY is phosphorylated, binds flagellum and induces CCW rotation (tumble)

CheY can hydrolyze phosphate off itself, but too slow, so CheZ speeds up its termination
Explain how chemotaxis is able to detect gradients of attractants.
If attractant binds MCP, CheA is inactive, CheR is able to methylate MCP, reducing attractant effects. Now more attractant will be required to maintain walking. This makes CheA more likely to be active to get tumbling.

If repellant binds, CheA gets activated, phosphate from its his given to both CheB and Che Y; CheB will then demethylate MCP and make it more sensitive to attractant, thus reducing the probability of maintained tumbling. So more repellent will need to bind to continue tumbling.
CheB can remove phosphate from itself on its own.
Describe how lipid soluble signals differ from hydrophilic signals in transduction of their message?
Lipid soluble signals can interact with hydrophobic portion of membrane and can pass through easily and bind intracellular receptors, whereas hydrophilic signals can't pass; they bind extracellular receptors, and use G-protein systems.
Describe what happens when light hits retinol in rhodopsin.
Helices undergo conformational change, changing the structure of cytoplasmic loops and giving them new activity.
Describe the three subunits that comprise G-proteins.
Alpha: has covalently attached FA interacting with membrane; has GDP

Beta: always interacts with gamma

Gamma: FA chain interacting with membrane
Describe the sequence of events that occurs when epinephrine binds its receptor. Identify points of amplification.

How is this cascade terminated? What would happen if epinephrine were to get stuck to the receptor?
Epi binds b-adrinergic receptor, receptor change conformation, catalyzes exchange of GDP for GTP in alpha unit (receptor can do many times--amplification); alpha-GTP binds adenylate cyclase, who'll convert ATP into cAMP, 2 cAMP molecules then bind PKA regulatory subunits, releasing active subunits who will phosphorylate stuff (many times! AMPLIFICATION)

cAMP PDE hydrolyzes cAMP to AMP, dissociating them from regulatory PKAs and letting them bind PKAs.

ALpha subunit has inherent GTPase activity, but it's slow (acts as a timer), conversion to GDP means dissociation from adenylate cyclase and haulting cAMP production.

If epi concentration decreases, B-A receptor disactivated.

Beta-adrinergic receptor kinase recognizes b-A receptor that's been active too long, ad will phosphorylate it. B-arrestin recognizes this and will prevent receptor from activting anymore G-proteins, and target it for breakdown.
What are 4 characteristics of second messengers?
Small molecule/ion
Produced early in PW
Point of amplification
Bind targets
Describe the sequence of events that occurs when vasopressin binds its receptor.
Vasopressin binds vaso receptor, alph subunit exchanges GDP for GTP, dissociates, binds PLC
In PLC what is the function of the following domains:
Pleckstrin homology
Catalytic domain
PH & C2: bind polar head groups in membrane
EF: connect PH and catalytic domain
Catalytic domain: you're a shithead if you don't know
What does PLC catalyze and what are the effects of the reaction? Identify all second messengers. Describe how the reaction is terminated.
Breaks down PIP2 into IP3 and DAG (helps activate PKC)

IP3 binds Ca++ chanels in ER and release Ca++ into cell to bind calmodulin, PKC, etc to change their conformation and thus activate them.

Calcium is a second messenger!
So is IP3!

IP3 hydrolyzed to inositol, or can be phosphorylated until it's broken down into inositol (can't bind Ca channels)
Describe the process by which PKC is activated.

What is the effect of DAG on Ca++ concentration?
Pseudosubstrate connected to C1A/B domains of PKC is bound at active site, making it inactive.

DAG binds C1A/B domains and C2 will bind polar head group of membrane is Ca is around, inducing conformational changes which expel pseudosubstrate inhibitor from active site.

DAG increases Ca++ concentration.
Describe the sequence of events that occurs when calcium binds calmodulin.
4 calciums bind calmodulin resulting in change in structure that can now interact with positively charged a-helices, it now activates CaM kinases. Second conformational change allows for autophosphorylation, permiting CaM kinases to stay active after decreases in Ca++ concentrations.
Describe the sequence of events that occurs when HGH binds its receptor.
Binds JAK recepors with associated tyrosine kinases; binding induces dimerization of JAKs and they phosphorylate each other.

JAK then phosphorylates STAT proteins which have SH2 domains with tyrosine residues. JAK phosphorylates these tyrosines and one SH2 will interact with tyr-P on other SH2 to form dimer. STAT can now bind DNA to interact with genes and cause cell proliferation.
Describe the sequence of events that occurs when EGF binds its receptor. Identify amplification points.
EGF binds EGF receptor, receptor dimerizes and phosphorylates one another. Grb-2 is then phosphorylated, who interacts with Sos, who then exchanges GTP for GDP in associated Ras, making it active and dissociate. Has its own intrinsic GTPase activity.
Sos activates many Ras=AMP
Describe the pathway that Ras takes once activated and its effects.
Ras phosphorylates MAPKKK who phosphorylates MAPKK who phosphorylates MAPK who phosphorylates mNK (MAP Kinase-interacting kinase)
When MAPK (ERK), ERK goes into nucleus and phosphorylates Elk-1 which is a trx factor that manipulates gene expression.
How could Ras be a cause for cancer?
Mutate RAS and obliterate GTPase activity. Makes it constitutively active.
Give three examples of how cancer can result from unregulated kinase activity.
1)c-Src: normally inactive, Kinase domain bound to regulatory domain w/P-tyr that interacts with SH2 who's attached to SH3, stretching kinase and deforming it into active state.

If SH2/3 is displaced (get something else to bind them) or tyr dephosphorylated, kinase is active.

2) Translocation between bcr and abl genes such that Abl (highly regulated tyr kinase) has its promoter attached to Bcr (highly expressed, little regulation) kinase, leading to Abl activity and bcr expression (uncontrolled cell grwoth)

3) Mutation that aused disulfide bridge in EGF receptor, wouldn't need EGF for activation, there'd be constant expression of Ras.