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Biochemistry > Condensed Overalls > Flashcards

Condensed Overalls Flashcards

1
Q

What are the essential fatty acids?

A

Linoleic acid 18:2 (9,12) aka 9,12-OctadecaDIENoic acid.
Alpha linoleni acid 18:3 (9,12,15) aka 9,12,15-OctaTRIENoic acid.
Arachidonic acid (not strictly cuz synthesized from linoleic)

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2
Q

Main storage energy medium for body?

A

Triglycerides.

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3
Q

What is a phospholipid?

What linkage bond?

A

(Glycerolphospholipids)
Glycerol backbone, with FA’s on SN1+2, SN3 has phosphodiester linkage with highly polar or charged group.
X=H, choline, ethanolamine, inositol.

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4
Q

What are the PL’s and what are their charges?

Where are they located?

A 
PC ZWIT outer leaf
PE ZWIT inner leaf
PS (-) inner leaf (can be flipped to outside of cell in RBC’s during coags)
PI (linositol) (-) inner leaf
PG (glycerol) (-) inner leaf
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5
Q

What is PAF platelet activating factor?

And what type of linkage does it have on it’s glycerol chain

A

PAF is released from basophils, stimulates platelet aggregation+serotonin (vasoconstrictor) release.

Ether linked chain that can be sat/unsat.

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6
Q

What are glycolipids?

A

Spingolipid with sphingo backbone, fa, and sugar moiety (aka monosaccharide).

Cerebroside.

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7
Q

What are the significance of Glycoproteins?

A

Can be O linked or N linked.

O linked outside S/T hydroxyl chain, N linked asn N amino group.

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8
Q

Micelles are?

A

Monolayer lipids
Hydrophobic core
Hydrophilic heads (cross head bigger than side chain)

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9
Q

Vesicles are?

A

Cross sect heads equal to tails.
Lipid bilayer
Hydrophilic core, membrane interior hydrophilic.
Liposomes, they are good for drug delivery.

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10
Q

What interactions stabilize lipid bilayers?

A

Noncovalent hydrophobic.
H bonds (polar heads+h20)
Ionics (between PL heads or PL head+protein)
Van der waals (close fatty acyl chain packing)

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11
Q

TNBS
FDNB
Purpose? Function?

A 
FDNB (full) permeant out and in
TNBS (out) impermeant
Identify cellular location of PL’s by measure absorbance.
FDNB total lipid everywhere.
TNBS total lipid outside.
Do math. And find amt intracellularly.
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12
Q

Where are GPI linked proteins located?

Tell me their profile.

A

Extracellularly.
Amphitrophic, attached to protein via PI
Can remove with pH change.

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13
Q

Give me integral protein profiles detective.

A

Spans membrane bilayer, typically domains are alpha helices which helps minimize the hydrophilic nature of the peptide bond, hydrophobic hydrocarbon core. Polar residues interact with the polar heads of the PL’s. can form micelles w/ proteins.
Hard to remove, gotta use detergents like Trition 100 or octylglycoside, SDS, or non ionic detergents too.

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14
Q

Peripheral proteins detective?

A

Loosely attached to plasma membrane by H bond/electrostatics
Can be removed by changing pH
removal of calcium via chelaters
or urea which breaks the Hbond.

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15
Q

Amphitropic proteins have an attachment to membrane with lipids via what interaction?
How to release?

A

Covalent or noncovalent to lipids such as PI glycan anchor.

Released by PLC or PLD.

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16
Q

EA
IEA
WHAT ARE THESE FOR?

A

EA permeant both, can label all proteins
IEA only outside impermeant, can only label GPI linked proteins.
Protein identification

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17
Q

Hydropathy plot question 101

How many Transmembrane domains are found in this protein?

A

Solvent dont matter.
Top of graph is hydrophobic
Bottom is hydrophilic.
Number of hills above x axis is # of transmembrane domains in the protein.

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18
Q

Give me some of them cholesterol stats.

A

Buffer-like
Increase temp, cholesterol lowers fluidity which stabilizes
Decrease temp, cholesterol increases fluidity
Broadens phase transition temp.

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19
Q

Frap? Fluorescence recovery after photobleaching?

A

Measures speed at which blue returns to field of vision.
Measures how quickly PL’s move within membrane.
Mostly lateral movement = fast

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20
Q

How can I accomplish transbilayer movement?

A

Flips, flops, scrams (only scram doesnt need ATP).

PROTEINS DO NOT ROTATE ACROSS THE BILAYER.

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21
Q

How can I tether proteins to the membrane?

A

Lipidmodifications

Fatty acids, prenyl groups, complex GPI glycosylphosphatidylinositol linkages.

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22
Q

What do inverse agonist do? And antagonist?

A 
Inverse= decrease receptor activity below basal level.
Antagonist = keeps receptor activity at basal level.
23
Q

Example of endocrine signal

A

Glandular tissue
Pancreas
Carry via blood.

24
Q

What are some types of protein modifications?

What is it for?

A

Plasma membrane localization (typically localizes to lipid rafts).
Rafts and caveolae are enriched in cholesterol and glycosphingolipids. Presumed functions endocytosis, membrane trafficking, signal transduction.
Myristoltion (irreversible amide bond)
Palmitoylation (reversible thioester bond)
Prenylation (irreversible farn/geran)

25
Q

Myristoylation?

A

Protein modification

Add 14C FA to Gly residues (irreversible bc AMIDE BOND)

26
Q

Palmitoylation

A

Protein modification.
Add 16C fatty acid to Cys residues (reversible) bc Thioester bond.
Increases affinity for cholesterol rich lipid rafts in membranes.
Thioesterases can remove palmitate.

27
Q

How can you remove palmitate

A

Thioesterases.

28
Q

Prenylation?

A

Add isoprene units.
Farynesylation (used to make cholesterol), statins block farnesyl by inhibiting HMG COA REDUCTASE (which is upstream of farnesylation and required for normal signaling). thats why statins have side effects.
Gernaylgeranylation 20C

29
Q

How to make cholesterol?

A

Prenylation farnesylation 15C.

30
Q

What enzyme is needed for normal cell signaling?

A

HMG COA REDUCTASE

31
Q

How can I stop normal cell signaling?

A

Block HMG COA REDUCTASE (upstream of farnesylation)
Which blocks farnesylation.
Statins block farnesylation

32
Q

A-subunit of heterotrimeric G proteins

A

N terminal myristoylation Gly residues (irreversible amide bond) or palmitoylation Cyc residues (reversible thioester) for membrane anchoring.

33
Q

By-subunit (dimer) of heterotrimeric G protein

A

Y subunit farn/gern for membrn anchoring.

34
Q

Activates adenylate cyclase (effector enzyme)

Toxin sensitivity?

A

Ga(s)

Cholera toxin

35
Q

Inhibits adenylate cyclase (effector enzyme)

Toxin sensitivity?

A

Ga(i)

Pertussis toxin

36
Q

Activates phospholipase C (beta isomer) (effector enzyme)

A

Ga(q)

37
Q

Ga(12)

A

Effector enzyme: numerous

Including activating the monomerics like RhoGEF, Rho

38
Q

Tell me about the cycle of monomeric G proteins

A

Turned on by GEF aka SOS
Turned off by GAP/RGS (GTPase accelerating/activating proteins) which stimulates the intrinsic ATPase activity of monomeric protein.
GDI binds the monomeric protein to keep it inactive.
GDI for Ras (binds to ras+GDP keeping it inactive), for Rho (envelopes RhoGDP’s post-translationally attached lipophilic group, pulls it off the membrane so that GEF cannot start the process over).

39
Q

Growth differentiation, regulation of gene expression, cell survival?
Which monomeric G protein fam

A

Ras

40
Q

Integrin activity, actin cytoskelton (regultion of cytoskeltal organization), NADPH oxidase, movement, cell-cell and cell-matrix interactions.

A

Rho

41
Q

Which proteins control GDP binding?

A

GEF, GDS, GDI

42
Q

Where are the GPCRs bound?

A

G protein is bound to the last TM domain, near the C terminus of the receptor (interacts with the THIRD intraecullar loop C3, and carboxyl terminus of the receptor).
Phosphorylation at these sites uncouple the receptor from the G protein.

43
Q

Why are bas1ic residues important for bidning PI?

A

Because they are binding to the negatively charged phospholipids
Therefore it is logical that I have alot of ARG and Lys for that ionic interaction.

44
Q

What does the phosphorylation of S/T do?

A

Prevents further interaction with the G proteins because it drops the G proteins off after phosphorylation.

45
Q

Activation of AC

A

CONVERTS atp to cAMP.

All of them are activated by a(s).

46
Q

PKC active form likes to phosphorylate everything it sees.

A

So keep it inactive until you need it.

Kept inactive by the regultory subunits, which get activated when you get 4 cAMPs.

47
Q

What are 2 ways to keep PKA inactive?

A

Dont supply it with the 4 cAMPs that are neccessary to activate catayltic subunits.
Or keep it in a particular subcellular location. With AKAPs (A Kinase Anchoring Proteins). akap binds to the regulatory subunits, keeping the PKA in a location (that is specified) so when cAMPs are available and activate it, the PKA will phosphorylate things in the target location. Aka localized stimulation.

48
Q

What are the sites for toxin modification?

A

Alpha subunits linked to the regulation of adenylate cyclase.

49
Q

Cholera toxin

A

Likes to colonize on the brush border or SI (diarrhea).
GTPase unable to turn off, forever active. ribosylates the ARG in that binding site a(s). (GTP is there but cant hydrozlyze).
Increased AC, cAMP, PKA, EFFLUX Cl-, water +electroyltes follow = dehydration.
Treatment is glucose+electroyltes.

50
Q

Bordetella pertussis

A

Targets epithelial cells of resp tract. ADP ribosylates the GDP alpaha (i) Beta gamma.
Inhibitory receptor cannot activate the G alpha i which is supposed to inhibit the AC.
Increased cAMP. AC ACTIVE.
Cant clear pulm secretions, neuro probs cuz decreased O2, tx erythromycin.

51
Q

What can dissociate camp to form 5’ AMP?

A

PDE: phosphodiesterase.

52
Q

Where does arrestin like to bind?

What does arrestin do?

A

On the phosphorylated domains of GPCR (after G proteins have been released and activated).

Prevents rebinding of G(a) and G(by) with the receptor.
And the phosphorylated G proteins are sequestered into CCP and endocytosed until they are recycled to continue again or degraded.

53
Q

What are the Grk’s

A

Ser/Thr kinases.
Prenylation
Palmitoylation
Direct phosphorylation of receptor and PH domains, which bind PIP2.

54
Q

Signaling domains may regul1te what?

A

Recruitment and scaffolding
Specificity. (Bring to substrate preventing indiscriminate reactions)
Enzyme activity
Temporal control of signaling pathways.

Biochemistry (4 decks)

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