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104 Cards in this Set

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Why do we taste?
Our taste receptors are chiral.
Are trans fats good or bad?
Bad, because their tails are straight, so they pack more tightly; cis fats are more disordered allowing for more movement

You WANT fluidity, just like unsaturated~kinks~more fluid~fish
What do detergents to?
They coat hydrophobic particles with a hydrophobic coating.
Henderson-Hasselbach
pH = pKa + log [A-]/[HA]
Is a deprotonated molecule more hydrophobic or more hydrophilic?
Hydrophili
What is the mathematical relation between Ka and pKa?
pKa = -log [Ka]
How does cholesterol influence fluidity?
At high temperatures, decrease fluidity because rigid 4-ring group interacts with the 1st few -CH2 groups on the fatty acid tail

At low temperatures, cholesterol increases membrane fluidity by disrupting structure
Are unsaturated or saturated fats healthy?
Unsaturated, because they have the double bonds, so the kinds decrease van der Waals forces, so they are more fluid at lower temperatures, (like fish are cold-blooded, so they need less fluidity at lower)
What could membranes do in response to cold to keept their membranes fluid?
Decrease length of fatty acid tail

More unsaturated fatt acids
What is the difference between necessary and sufficient.
Necessary - taking away

Sufficient - adding
Does Tat bind to TAR in RNA or DNA?
RNA
What does Rev need to export from t he nucleus once attached to RRE?
Ran and Exportin
What are characteristics of Rev?
Stretch of arginines and nuclear localization
How can cells have a positive ∆Gº and a negative ∆G?
Cells might not be in standard state
What is the mathematical equation relating ∆G, ∆Gº, and k?
∆G = ∆Gº + RTlnK

R = 8.31
T is in Kelvin
Why do we taste?
Our taste receptors are chiral.
Are trans fats good or bad?
Bad, because their tails are straight, so they pack more tightly; cis fats are more disordered allowing for more movement

You WANT fluidity, just like unsaturated~kinks~more fluid~fish
What do detergents to?
They coat hydrophobic particles with a hydrophobic coating.
Henderson-Hasselbach
pH = pKa + log [A-]/[HA]
Is a deprotonated molecule more hydrophobic or more hydrophilic?
Hydrophili
What is the mathematical relation between Ka and pKa?
pKa = -log [Ka]
How does cholesterol influence fluidity?
At high temperatures, decrease fluidity because rigid 4-ring group interacts with the 1st few -CH2 groups on the fatty acid tail

At low temperatures, cholesterol increases membrane fluidity by disrupting structure
Are unsaturated or saturated fats healthy?
Unsaturated, because they have the double bonds, so the kinds decrease van der Waals forces, so they are more fluid at lower temperatures, (like fish are cold-blooded, so they need less fluidity at lower)
What could membranes do in response to cold to keept their membranes fluid?
Decrease length of fatty acid tail

More unsaturated fatt acids
What is the difference between necessary and sufficient.
Necessary - taking away

Sufficient - adding
Does Tat bind to TAR in RNA or DNA?
RNA
What does Rev need to export from t he nucleus once attached to RRE?
Ran and Exportin
What are characteristics of Rev?
Stretch of arginines and nuclear localization
How can cells have a positive ∆Gº and a negative ∆G?
Cells might not be in standard state
What is the mathematical equation relating ∆G, ∆Gº, and k?
∆G = ∆Gº + RTlnK

R = 8.31
T is in Kelvin
What is physiological temperature?
310 K
If calculating ∆G = ∆Gº + RTlnK for the forward reaction and you find that ∆G is positive, what does it mean?
The reverse reaction is favored.
For A-----B what is the rate constant equation?
rate = k [A]
Does Asp 25 or Asp 25' mediate base/acid catalysis?
Asp 25' mediates acid catalysis
Asp 25 mediates base catalysis
What does Ile 50 do in protease?
It coordinates the water.
What happens when molecules in a reaction are more cyclic?
They are already less flexible, so there is less of an entropy penalty. It is a favorable thing.
What are the steps of protease?
1. Asp 25 on the right takes water's H, (base catalysis)

2. The now-deprotonated water attacks the amind backbone, (C=O), and joins it to break the double bond

3. Asp 25' on the left gives its H to the O, (in C=O), (acid catalysis)

--------------------------------
4. Asp 25' takes back its H, (base catalysis)

5. C-N breaks to gives an H from the N back to Asp 25, which the breaks off of Asp 25 and joins H-N-H-
What are three differences between a steady state and equilibrium?
1. In steady state, ∆G < 0, whereas in equilibrium, ∆G = 0
2. Forward and reverse reactions are different
3. Energy is required to keep steady state going
WHat does Azt lack?
3' -OH
What does cyclin need to bind to in order to active and start the cell cycle?
CDK1
At which end do microtubues grow, (negative end or positive end)?
Positive
What is Kd mathematically equal to?
Kd = [koff]/[kon] = [A][B]/[AB]
What t1/2 in relation to koff and kon?
t1/2 = ln2 / [koff]
If the hydrolysis of ATP is favorable, why doesn't it happen more often?
High activation energy ~ kinase lowers that
Is a higher kd more favorable or unfavorable?
Unfavorable
Is Ras-GTP active or inactive?
Active
Why is ATP so stable?
High concentration of negative charge, which shields it from nucleophiles that are necessary to attach to the electrophilic phosphate atom to break it.
What purpose does base catalysis serve in kinase phosphorylation?
Activates the tyrosine nuclephile
Do enzymes affects thermodynamics?
No enzyme affects thermodynamics
What amino acids could serve as substrates for phosphorylation?
Any amino acid with -OH on its R-group
Does Gleevec affect all cells?
No, only problem-cells
How does Fuzeon work?
Corresponds to the C-terminus of gp41 and binds to the N-terminal end of gp41 in the pre-hairpin structure.
What is the relation between koff[A][B] and kon[AB]?
koff[A][B] = kon[AB]
Do Tat and Rev bind to the DNA sequence or the RNA sequence?
RNA
What is one of the proteins that Rev allows out?
Gag
What is the purpose of the TATA box in eukaryotes?
Allows additional transcription factors to bind.
Is the TATA box found in eukaryotes or prokaryotes?
Eukaryotes
Is the N-terminus at the 5' or 3' end?
5', (so codes from N-terminus to C-terminus)
What do SNARES do?
Allow for fusion of vesicles along the secretory pathway
Are saturated or unsaturated fats healthy?
Unsaturated, because double bonds provide kinks that make it more fluid, which is desirable
What is protelytic processing?
Part of the protein is cleaved off directly after translation.
How does transcription work in prokaryotes?
A sigma factor binds at the -35/-10, which creates conformational changes so proceeds to start transcription at +1 and stops when reaches two complimentary strands and a stretch of T's and A's
How is the template formed for DNA?
RNA recruits a poly-A template and d-TTP, (while the original RNA degrades), leaving this template to which d-ATP is supposed to bind
What is the purpose of the 5' cap?
Recognized by translation mutation factors
What do coat proteins do?
Aid in vesicle formation
How does TAT work?
Binds at the 5' end and recruits CyclinT and Cdk9 to phosphylate RNA polymerase
How does tRNA edit?
1. Size
2. Flip to chamber where not direct matches enter and are degraded
3. EF-TU GTP to EF-TU GDP
What are the most common electrophiles?
C=O
C-N
P=O
If the pKa of a conjugate acid is higher, will it be more acidic or basic?
Basic, because it will not want to give away its extra H.
For doubly-bonded atoms, what does accepting the electron allow?
It allows the double bond to break by placing the extra electron on the O
How do Saquiavir and Ritonavir inhibit HIV protease?
By inhibit HIV protease by binding to its active site, copmetiting with the substrate.
What are 3 strategies to block HIV?
1. Fill hydrophobic pockets with hydrophobically-interacting drug.
2. Drug could mimic the hydrogen bond donors and acceptors, enhancing the favorable negative ∆H(Drug-Protein)
3. Pre-regidifying the enzyme, reducing the entropy lost during binding
4. Water-liberating inhibitors - decreases the favorable entropy due to water
What is the mathematical expression for Keq?
Keq = Kfor/Krev
What evidence is there that RNA came first?
Can splice out its own introns and RNA was selected for its catalytic functions.
What part of RNA gives it its special catalytic properties?
Sugar 2' OH
How does cyclin attach to Cdk1?
Through isopeptide bond between glycin and lysine
What does APC do?
Adds Us to athe Cyclin/Cdk1 complex, targeting it to a proteasome, so cyclin is destroyed and cdk1 is released, where cyclin is destroyed and Cdk1 is released
What are cyclin-dependent kinase inhibitors?
Cell cycle roadblocks that inhibit cells from entering the G1 phase in the standard cell cycle
What does the Cdk1-Cyclin B complex do to mitosis?
Converts nuclear membranes into tiny vesicles; compacts the DNA through the phosphorylation of condensins
What is the centromere made up of?
Microtubules
What is cytokinesis?
Pinching apart of the cell at the end of division.
What is the growth rate of microtubules?

What is the shrinkage rate of microtubules?

What is the rate expression at equilibrium?
Growth rate = kon[monomer][polymer_ends]

Shrinkage rate = koff[polymer_ends]

Equilibrium: kon[monomer][polymer_ends] = koff[polymer_ends]
What does Campostar do?
Blocks DNA replication
What does Taxol do?
Blocks mitosis
What does an operator do?
Binds to a repressor site, so the sigma factor cannot bind over it to the transcription site, (it halts transcription)
Describe B-Galactosidase.
ONly recognizes the galactose part of the lactose, so it will hydrolyze any molecule containing galactose attached to something else.
What does lacZ do?
Codes for B-Galactosidase.
What does lacI do?
Turns off B-Galactosidase control by overlapping the RNA polymerase binding site for lacZ
How does transcription function in prokaryotes vs. eukaryotes?
In prokaryotes, sigma factor binds at -35 and -10 and then starts transcription at +1; stops at a hairpin formed by two sets of complimentary areas and a string of T's and A's.

In Eukaryotes, transcription factors bind and change conformation by the TATA box; transcription starts at +1 and the ending is more complex

For both, translation stops at UAG, UGA, or UAA
What does the lysine on the kinase do?
Acid catalysis on the ATP
What does Asp 166 on the kinase do?
Base catalysis on the substrate, making the substrate, (threonine), a much better nucleophile so it can attach the phosphate of ATP, accelerating the reaciton
What is the overall effect on the ∆H and ∆S by the kinase?
Proximity and orientation decrease the ∆S penalty, while acid and base catalysis make the ∆H term more favorable.

The overall effect is to stabilize the transition state of the reaction, provide a pathway with lower ∆G , and accelerate the rate at which the reaction proceeds.
What is the equilibrium expression for koff and kon of Ras-GDP?
koff[Ras-GDP] = kon[Ras][GDP]
What is kd of Ras-GDP?
kd = [Ras][GDP]/[Ras-GDP] = koff/kon
What is the philadelphia chromosome?
bottom part of the 9 chromosome is exchanged with the bottom prat of the 22 chromosome, making 9 longer than normal and 22 shorter than normal that codes for Bcr-Abl
What is different about Bcr-Abl?
It has unregulated Abl activity.
What does the unphosphorlated threonine do?
Keeps the kinase closed and inactivated. When the threonine is phosphorylated, the kinase is activated and opens up so it can phosphorylate
What do Lys, Ser, and Glu do in the kinase?
Hold the ATP in place

(Lysine helps stabilize the additional negaitve charge that builds up in the transition state)
What do Asp 184 and Asn 171 do in the kinase?
Hold the magnesium in place.
What holds ATP in place in kinase?
Lys, ser, and glu.
Describe the 6-step process growth factor binding?
1. Growth factors bind
2. Ligands combine and autophosphorylate with their own kinases
3. Attracts adaptor protein
4. Recruits RasGef
5. Ras-GEF activates Ras by converting GDP to GTP
6. Ras-GTP activates kinase cascade in which MPKKK phosphorylates MAPKK which phosphorylates MAPK, which relays relays the message intonucleus to phosphorylate a transcription factor
Describe the process for kinase phosphorylation?
1. Thr 197 becomes phosphorylated, which activates the kinase
2. Lysine pulls the third hposphate off ATP by adding H, (acid catalysis); third phosphate group goes to the stabilizing MG+2
3. Aspartic acid pulls the H off of the substrate (tyrosine), by base catalysis, so the phosphate can be added on
What is the basic process for activating a kinase?
1. Unlatch
2. Unclamp when SH2 or SH3 ligands join
3. Switch by phospohtyrlating Tyr
What is the difference between Abl and Src?
Src unlatches by dephosphorylation of Tyr 522, whereas Abl unlatches by dephosphorylation of myristoyl group; switch has to phosphotyrlate two Tyr in Abl