L. Sci. 1A - Final Exam Review

Front 1

Why do we taste?

Back 1

Our taste receptors are chiral.

Front 2

Are trans fats good or bad?

Back 2

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

Front 3

What do detergents to?

Back 3

They coat hydrophobic particles with a hydrophobic coating.

Front 4

Henderson-Hasselbach

Back 4

pH = pKa + log [A-]/[HA]

Front 5

Is a deprotonated molecule more hydrophobic or more hydrophilic?

Back 5

Hydrophili

Front 6

What is the mathematical relation between Ka and pKa?

Back 6

pKa = -log [Ka]

Front 7

How does cholesterol influence fluidity?

Back 7

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

Front 8

Are unsaturated or saturated fats healthy?

Back 8

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)

Front 9

What could membranes do in response to cold to keept their membranes fluid?

Back 9

Decrease length of fatty acid tail

More unsaturated fatt acids

Front 10

What is the difference between necessary and sufficient.

Back 10

Necessary - taking away

Sufficient - adding

Front 11

Does Tat bind to TAR in RNA or DNA?

Back 11

RNA

Front 12

What does Rev need to export from t he nucleus once attached to RRE?

Back 12

Ran and Exportin

Front 13

What are characteristics of Rev?

Back 13

Stretch of arginines and nuclear localization

Front 14

How can cells have a positive ∆Gº and a negative ∆G?

Back 14

Cells might not be in standard state

Front 15

What is the mathematical equation relating ∆G, ∆Gº, and k?

Back 15

∆G = ∆Gº + RTlnK

R = 8.31
T is in Kelvin

Front 16

Why do we taste?

Back 16

Our taste receptors are chiral.

Front 17

Are trans fats good or bad?

Back 17

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

Front 18

What do detergents to?

Back 18

They coat hydrophobic particles with a hydrophobic coating.

Front 19

Henderson-Hasselbach

Back 19

pH = pKa + log [A-]/[HA]

Front 20

Is a deprotonated molecule more hydrophobic or more hydrophilic?

Back 20

Hydrophili

Front 21

What is the mathematical relation between Ka and pKa?

Back 21

pKa = -log [Ka]

Front 22

How does cholesterol influence fluidity?

Back 22

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

Front 23

Are unsaturated or saturated fats healthy?

Back 23

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)

Front 24

What could membranes do in response to cold to keept their membranes fluid?

Back 24

Decrease length of fatty acid tail

More unsaturated fatt acids

Front 25

What is the difference between necessary and sufficient.

Back 25

Necessary - taking away

Sufficient - adding

Front 26

Does Tat bind to TAR in RNA or DNA?

Back 26

RNA

Front 27

What does Rev need to export from t he nucleus once attached to RRE?

Back 27

Ran and Exportin

Front 28

What are characteristics of Rev?

Back 28

Stretch of arginines and nuclear localization

Front 29

How can cells have a positive ∆Gº and a negative ∆G?

Back 29

Cells might not be in standard state

Front 30

What is the mathematical equation relating ∆G, ∆Gº, and k?

Back 30

∆G = ∆Gº + RTlnK

R = 8.31
T is in Kelvin

Front 31

What is physiological temperature?

Back 31

310 K

Front 32

If calculating ∆G = ∆Gº + RTlnK for the forward reaction and you find that ∆G is positive, what does it mean?

Back 32

The reverse reaction is favored.

Front 33

For A-----B what is the rate constant equation?

Back 33

rate = k [A]

Front 34

Does Asp 25 or Asp 25' mediate base/acid catalysis?

Back 34

Asp 25' mediates acid catalysis
Asp 25 mediates base catalysis

Front 35

What does Ile 50 do in protease?

Back 35

It coordinates the water.

Front 36

What happens when molecules in a reaction are more cyclic?

Back 36

They are already less flexible, so there is less of an entropy penalty. It is a favorable thing.

Front 37

What are the steps of protease?

Back 37

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-

Front 38

What are three differences between a steady state and equilibrium?

Back 38

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

Front 39

WHat does Azt lack?

Back 39

3' -OH

Front 40

What does cyclin need to bind to in order to active and start the cell cycle?

Back 40

CDK1

Front 41

At which end do microtubues grow, (negative end or positive end)?

Back 41

Positive

Front 42

What is Kd mathematically equal to?

Back 42

Kd = [koff]/[kon] = [A][B]/[AB]

Front 43

What t1/2 in relation to koff and kon?

Back 43

t1/2 = ln2 / [koff]

Front 44

If the hydrolysis of ATP is favorable, why doesn't it happen more often?

Back 44

High activation energy ~ kinase lowers that

Front 45

Is a higher kd more favorable or unfavorable?

Back 45

Unfavorable

Front 46

Is Ras-GTP active or inactive?

Back 46

Active

Front 47

Why is ATP so stable?

Back 47

High concentration of negative charge, which shields it from nucleophiles that are necessary to attach to the electrophilic phosphate atom to break it.

Front 48

What purpose does base catalysis serve in kinase phosphorylation?

Back 48

Activates the tyrosine nuclephile

Front 49

Do enzymes affects thermodynamics?

Back 49

No enzyme affects thermodynamics

Front 50

What amino acids could serve as substrates for phosphorylation?

Back 50

Any amino acid with -OH on its R-group

Front 51

Does Gleevec affect all cells?

Back 51

No, only problem-cells

Front 52

How does Fuzeon work?

Back 52

Corresponds to the C-terminus of gp41 and binds to the N-terminal end of gp41 in the pre-hairpin structure.

Front 53

What is the relation between koff[A][B] and kon[AB]?

Back 53

koff[A][B] = kon[AB]

Front 54

Do Tat and Rev bind to the DNA sequence or the RNA sequence?

Back 54

RNA

Front 55

What is one of the proteins that Rev allows out?

Back 55

Gag

Front 56

What is the purpose of the TATA box in eukaryotes?

Back 56

Allows additional transcription factors to bind.

Front 57

Is the TATA box found in eukaryotes or prokaryotes?

Back 57

Eukaryotes

Front 58

Is the N-terminus at the 5' or 3' end?

Back 58

5', (so codes from N-terminus to C-terminus)

Front 59

What do SNARES do?

Back 59

Allow for fusion of vesicles along the secretory pathway

Front 60

Are saturated or unsaturated fats healthy?

Back 60

Unsaturated, because double bonds provide kinks that make it more fluid, which is desirable

Front 61

What is protelytic processing?

Back 61

Part of the protein is cleaved off directly after translation.

Front 62

How does transcription work in prokaryotes?

Back 62

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

Front 63

How is the template formed for DNA?

Back 63

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

Front 64

What is the purpose of the 5' cap?

Back 64

Recognized by translation mutation factors

Front 65

What do coat proteins do?

Back 65

Aid in vesicle formation

Front 66

How does TAT work?

Back 66

Binds at the 5' end and recruits CyclinT and Cdk9 to phosphylate RNA polymerase

Front 67

How does tRNA edit?

Back 67

1. Size
2. Flip to chamber where not direct matches enter and are degraded
3. EF-TU GTP to EF-TU GDP

Front 68

What are the most common electrophiles?

Back 68

C=O
C-N
P=O

Front 69

If the pKa of a conjugate acid is higher, will it be more acidic or basic?

Back 69

Basic, because it will not want to give away its extra H.

Front 70

For doubly-bonded atoms, what does accepting the electron allow?

Back 70

It allows the double bond to break by placing the extra electron on the O

Front 71

How do Saquiavir and Ritonavir inhibit HIV protease?

Back 71

By inhibit HIV protease by binding to its active site, copmetiting with the substrate.

Front 72

What are 3 strategies to block HIV?

Back 72

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

Front 73

What is the mathematical expression for Keq?

Back 73

Keq = Kfor/Krev

Front 74

What evidence is there that RNA came first?

Back 74

Can splice out its own introns and RNA was selected for its catalytic functions.

Front 75

What part of RNA gives it its special catalytic properties?

Back 75

Sugar 2' OH

Front 76

How does cyclin attach to Cdk1?

Back 76

Through isopeptide bond between glycin and lysine

Front 77

What does APC do?

Back 77

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

Front 78

What are cyclin-dependent kinase inhibitors?

Back 78

Cell cycle roadblocks that inhibit cells from entering the G1 phase in the standard cell cycle

Front 79

What does the Cdk1-Cyclin B complex do to mitosis?

Back 79

Converts nuclear membranes into tiny vesicles; compacts the DNA through the phosphorylation of condensins

Front 80

What is the centromere made up of?

Back 80

Microtubules

Front 81

What is cytokinesis?

Back 81

Pinching apart of the cell at the end of division.

Front 82

What is the growth rate of microtubules?

What is the shrinkage rate of microtubules?

What is the rate expression at equilibrium?

Back 82

Growth rate = kon[monomer][polymer_ends]

Shrinkage rate = koff[polymer_ends]

Equilibrium: kon[monomer][polymer_ends] = koff[polymer_ends]

Front 83

What does Campostar do?

Back 83

Blocks DNA replication

Front 84

What does Taxol do?

Back 84

Blocks mitosis

Front 85

What does an operator do?

Back 85

Binds to a repressor site, so the sigma factor cannot bind over it to the transcription site, (it halts transcription)

Front 86

Describe B-Galactosidase.

Back 86

ONly recognizes the galactose part of the lactose, so it will hydrolyze any molecule containing galactose attached to something else.

Front 87

What does lacZ do?

Back 87

Codes for B-Galactosidase.

Front 88

What does lacI do?

Back 88

Turns off B-Galactosidase control by overlapping the RNA polymerase binding site for lacZ

Front 89

How does transcription function in prokaryotes vs. eukaryotes?

Back 89

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

Front 90

What does the lysine on the kinase do?

Back 90

Acid catalysis on the ATP

Front 91

What does Asp 166 on the kinase do?

Back 91

Base catalysis on the substrate, making the substrate, (threonine), a much better nucleophile so it can attach the phosphate of ATP, accelerating the reaciton

Front 92

What is the overall effect on the ∆H and ∆S by the kinase?

Back 92

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.

Front 93

What is the equilibrium expression for koff and kon of Ras-GDP?

Back 93

koff[Ras-GDP] = kon[Ras][GDP]

Front 94

What is kd of Ras-GDP?

Back 94

kd = [Ras][GDP]/[Ras-GDP] = koff/kon

Front 95

What is the philadelphia chromosome?

Back 95

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

Front 96

What is different about Bcr-Abl?

Back 96

It has unregulated Abl activity.

Front 97

What does the unphosphorlated threonine do?

Back 97

Keeps the kinase closed and inactivated. When the threonine is phosphorylated, the kinase is activated and opens up so it can phosphorylate

Front 98

What do Lys, Ser, and Glu do in the kinase?

Back 98

Hold the ATP in place

(Lysine helps stabilize the additional negaitve charge that builds up in the transition state)

Front 99

What do Asp 184 and Asn 171 do in the kinase?

Back 99

Hold the magnesium in place.

Front 100

What holds ATP in place in kinase?

Back 100

Lys, ser, and glu.

Front 101

Describe the 6-step process growth factor binding?

Back 101

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

Front 102

Describe the process for kinase phosphorylation?

Back 102

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

Front 103

What is the basic process for activating a kinase?

Back 103

1. Unlatch
2. Unclamp when SH2 or SH3 ligands join
3. Switch by phospohtyrlating Tyr

Front 104

What is the difference between Abl and Src?

Back 104

Src unlatches by dephosphorylation of Tyr 522, whereas Abl unlatches by dephosphorylation of myristoyl group; switch has to phosphotyrlate two Tyr in Abl