BICH 409 Final Exam Review

Kw equation

Kw = [H+][OH-]

Keq

[H+][OH-]/H2O

concentration of H+ and OH- in pure water

H+ = OH- = 10^-7M

pH = yo

-log[H+]

[H+] = 10^-pH

pOH =

-log[OH-]

[OH-] = 10^-pOH

as pOH increases, hydroxide ion concentration __________.

decreases

pKw =

-logKw = pH + pOH

pH + pOH = ?

14

strong electrolytes

NaCl, KCl, K2SO4, HCl, HNO3, H2SO4, NaOH, KOH

what is the difference between weak and strong electrolytes?

strong electrolytes completely dissociate in H2O, weak electrolytes partially ionize in water

which of the strong electrolytes are salts?

NaCl, KCl, K2SO4

which of the strong electrolytes are acids?

HCl, HNO3, H2SO4

which of the strong electrolytes are bases?

NaOH, KOH

Keq (equilibrium constant) =

products over reactants

Ka (acid dissociation constant) =

Keq * [H2O]

([55.5M])

what is the pH and pOH of a solution containing 0.014M NaOH?

pOH = -log[OH-] = 1.85

pH = 14 - pOH = 12.15

how do you convert 1mM to M?

1mM = 0.001M

how do you convert 1uM to M?

1uM = 10^-6M

The pOH of lye is 0.40, calculate the hydrogen ion and hydroxide ion concentrations.

pOH = -log[OH-]

[OH-] = 10^-pOH

[OH-] = 0.3979M

Kw = [H+][OH-]

10^-14M^2 = [H+][0.3979M]

[H+] = 2.51 x 10^-14M

Henderson-Hasselbach Equation

pH = pKa + log[CB/CA]

lactic acid has a pKa of 3.86. If the concentration of lactate is 2.42M and the concentration of lactic acid is 0.15M what is the pH of the solution?

pH = pKa + log[CB/CA]

pH = 5.07

calculate the ratio of the concentration of acetate and acetic acid required in a buffer system of pH 5.1. The pKa of acetic acid is 4.76.

pH = pKa + log[CB/CA]

pH - pKa = log[CB/CA]

5.1 - 4.76 = log[CB/CA]

0.34 = log[CB/CA]

[CB/CA] = 10^0.34

ratio = 2.19/1

a solution is buffered at a pH 6.5 by a weak acid and its conjugate base. the concentration of a weak acid is 0.332mM and the concentration of the conjugate base equals 1.667mM. what is the pKa of this weak acid?

pH = pKa + log[CB/CA]

pKa = pH - log[CB/CA]

pKa = 6.5 - log[0.01667M/0.00332M]

pKa = 5.8

which form is ionized in weak acids?

the protonated form is nonionized and the deprotonated form is ionized

which form is ionized in weak bases?

the protonated form is ionized and the deprotonated form is nonionized

acetic acid has a pKa of 4.76. at what pH is the acetic acid 3/4 ionized?

pH = pKa + log[CB/CA]

pH = 4.76 + log[.75/.25]

pH = 5.24

the pKa of the ammonium ion is 9.25. at what pH is ammonia 75% ionized?

pH = pKa + log[CB/CA]

pH = 9.25 + log[.25/.75]

pH = 8.77

calculate the pKa of a propionic acid solution, given that when the concentration of propionic acid is 0.10M and the propionate ion concentration is 0.43M, the pH is 5.50.

pKa = pH - log[CB/CA]

pKa = 5.5 - log[0.43/0.10]

pKa = 4.87

calculate the pKa of formic acid, given that when the concentration of formic acid is 0.1M and the formate ion concentration is 0.018M, the pH is 3.01.

pKa = pH - log[CB/CA]

pKa = 3.01 - log[0.018/0.01]

pKa = 3.75

water derives all its special properties from its:

a. small degree of ionization

b. high dielectric constant

c. high boiling and melting points

d. cohesiveness and adhesiveness

e. polarity and hydrogen-bonding capacity

e. polarity and hydrogen bonding capacity

which of the following statements about hydrogen bonds is true?

a. hydrogen bonds occur between nonpolar molecules

b. hydrogen bonds account for the high boiling point of water

c. a hydrogen bond can be as strong as a covalent bond

d. hydrogen bonds form between positively and negatively charged ions

e. water is a weak hydrogen bond donor, but a strong hydrogen bond acceptor

b. hydrogen bonds account for the high boiling point of water

you want to study an enzyme reaction at pH 4.0. which of the following weak acids would make the best buffer solution for this pH based on the given Ka values?

a. phosphoric acid, Ka = 7.3 x 10^-3

b. bicarbonate, Ka = 6.3 x 10^-11

c. H2PO4, Ka = 6.3 x 10^-8

d. acetic acid, Ka = 1.7 x 10^-5

e. lactic acid, Ka = 1.4 x 10^-4

e. lactic acid, Ka = 1.4 x 10^-4

what is the pH of 10^-4M HCl?

a. 11

b. 4

c. -4

d. 0.0001

e. none of these

b. 4

pH = -log(10^-4)

when the pH equals the pKa of a weak acid, then:

a. the weak acid becomes a strong acid

b. the concentrations of the weak acid and its conjugate base are equal

c. the weak acid is completely ionized

d. the weak acid is completely protonated

e. the net charge of the weak acid is zero

b. the concentrations of the weak acid and its conjugate base are equal

in a typical eukaryotic cell the pH is usually around 7.40. what is the hydrogen ion concentration in a typical eukaryotic cell?

[H+] = 10^-pH

[H+] = 10^-7.40

[H+] = 4 x 10^-8M

the extensive hydrogen-bonding network of liquid water molecules around a nonpolar molecule is called:

a. the rate at which nonpolar solutes intercalate into solution

b. a clathrate

c. an amphiphile

d. an amphiphilic molecule

e. a micelle

b. a clathrate

the large dipole moment of water is due to:

a. water's bent geometry

b. the electronegativity of the oxygen atom of water

c. the polarity of the O-H bond

d. all are correct

d. all are correct

what are the values for temperature, pressure, concentrations of the reactants and products, and the [H+] in the biochemist's standard state?

T = 25C = 298K

P = 1 atm

concentration of all reactants and products = 1M

water = 55.5M

[H+] = 1 x 10^-7M (pH 7.0)

what are the equations for Gibbs' free energy?

deltaG = deltaH - (T)(delta S)

what does the magnitude of the standard free energy change tell you?

- how far away from equilibrium you are under standard conditions

what does the magnitude of the free energy change tell you?

- how far away from equilibrium you are under the given conditions

- the maximum amount of energy that is available to do work

what is the sign(value) of deltaG when the reaction is exergonic under standard conditions and the reaction proceeds from reactants to products as written?

deltaG < 0

negative value

what is the sign(value) of deltaG when the reaction is endergonic under standard conditions and the reaction proceeds from products to reactants?

deltaG > 0

positive value

a protein going from the completely unfolded random state to its native folded state has the following thermodynamic parameters:

- deltaH = -125kJ/mol

- delta S = -0.77kJ/mol*K

based on the information given above, this folding process is:

a. endergonic

b. exergonic

c. exothermic

d. endothermic

e. enthalpically driven

f. entropically driven

g. enthalpically opposed

h. entropically opposed

i. at equilibrium

c. exothermic

e. enthalpically driven

h. entropically opposed

a protein going from the completely unfolded random state to its native folded state has the following thermodynamic parameters:

- deltaH = -125kJ/mol

- delta S = -0.77kJ/mol*K

at 25C, calculate the free energy change for the protein going from the completely unfolded random state to its native folded state.

deltaG = deltaH - (T)(deltaS)

deltaG = -125kJ/mol - (298.13K)(-0.77kJ/mol*K) = 104.56kJ/mol

a protein going from the completely unfolded random state to its native folded state has the following thermodynamic parameters:

- deltaH = -125kJ/mol

- delta S = -0.77kJ/mol*K

at what temperature does this process become exergonic?

T = deltaH / deltaS

T < 162.33K

a protein going from the completely unfolded random state to its native folded state has the following thermodynamic parameters:

- deltaH = -125kJ/mol

- delta S = -0.77kJ/mol*K

at what temperature does this process become endergonic?

T > 162.33K

a protein going from the completely unfolded random state to its native folded state has the following thermodynamic parameters:

- deltaH = -125kJ/mol

- delta S = -0.77kJ/mol*K

at what temperature does this process at equilibrium?

T = 162.33K

thermodynamic equations to memorize

deltaG = deltaH - (T)(deltaS)

deltaG = deltaG' + RTlnQ where Q = [Pinitial]/[Rinitial]

deltaG' = -RTlnK'eq where Keq = [Pequilibrium] / [Requilibrium]

K'eq = e^(-deltaG'/RT)

K'eq = [P]eq / [R]eq = k1 / k2

which calculations don't require water or hydrogen ion concentrations?

K'eq = [products]eq / [reactants]eq

deltaG = deltaG' + RTln[products initial]/[reactants initial]

what is the gas constant (R)?

8.3145 J/mol*K

if deltaG' = -30.5 kJ/mol and T = 37C, what is K'eq?

K'eq = e^(-deltaG/RT)

K'eq = e^(30.5 kJ/mol / (310)(0.0083145)

K'eq = 137,749.85

ATP + H2O <--> ADP + Pi + H+

in the liver, T = 37C. the cellular concentrations are:

[ATP] = 2.25 mM

[ADP] = 0.05 mM

[Pi] = 1.65 mM

[H2O] = 55.6 M

[H+] = 10^-7 M

deltaG' = -30.5 kJ/mol

calculate deltaG

deltaG = deltaG' + RTln[ADP][Pi]/[ATP]

deltaG = -30.5 kJ/mol + (.0083145)(310)ln(.00005M*.00165M / .00225M)

deltaG = -56.83 kJ/mol

given:

- ADP + H2O --> AMP + Pi + H+ deltaG' = -35.7kJ/mol

- ATP + H2O --> ADP + Pi + H+ deltaG' = -30.5 kJ/mol

what is the deltaG' and K'eq for the following reaction (T = 37C, R = 0.0083145 J/molK)

- 2ADP --> AMP + ATP

flipping the reaction reverses the sign of deltaG'

deltaG' = -35.7 kJ/mol + 30.5 kJ/mol = -5.20 kJ/mol

K'eq = e^(-deltaG/RT)

K'eq = 7.519

- ATP + H2O --> ADP + Pi + H+ deltaG' = -30.5 kJ/mol

- glucose-6-phosphate + H2O --> glucose + Pi deltaG' = -13.8 kJ/mol

what is the standard free energy change and equilibrium constant at 310K for the following net reaction?

- ATP + glucose --> glucose-6-phoshpate + ADP + H+

deltaG' = -30.5 kJ/mol + 13.8 kJ/mol = -16.70 kJ/mol

K'eq = e^(-deltaG/RT)

K'eq = e^(-16.7 / (.0083145*310)

K'eq = 651.42

consider the following reaction catalyzed by phosphoglucoisomerase at 37C.

- glucose-6-phosphate --> fructose-6-phosphate

at equilibrium, the ratio of fructose-6-phosphate/glucose-6-phosphate = 0.41. calculate K'eq and deltaG'.

K'eq = 0.41

deltaG' = -RTlnKeq

deltaG' = (.0083145)(310)ln(0.41)

deltaG' = 2.3 kJ/mol

consider the following reaction catalyzed by phosphoglucoisomerase at 37C.

- glucose-6-phosphate --> fructose-6-phosphate

would the previous reaction proceed as written under standard conditions?

no, it would proceed from fructose-6-phosphate towards glucose-6-phosphate

consider the following reaction catalyzed by phosphoglucoisomerase at 37C.

- glucose-6-phosphate --> fructose-6-phosphate

the physiological concentration of glucose-6-phosphate is 2.0mM and the physiological concentration of fructose-6-phosphate is 0.5mM.

calculate deltaG.

deltaG = deltaG' + RTln([products]/[reactants]

deltaG = -1.27 kJ/mol

consider the following reaction catalyzed by phosphoglucoisomerase at 37C.

- glucose-6-phosphate --> fructose-6-phosphate

would the previous reaction proceed as written under physiological conditions?

yes it would proceed as written

aconitase catalyzes the isomerization of citrate to isocitrate. deltaG' = 5 kJ/mol, T = 25C.

calculate K'eq for this reaction.

K'eq = e^(-deltaG / RT)

K'eq = e^(-5/(.0083145*298)

K'eq = 0.1329

aconitase catalyzes the isomerization of citrate to isocitrate. deltaG' = 5 kJ/mol, T = 25C.

if you started with 1M citrate and 1M isocitrate, calculate the equilibrium concentrations of citrate and isocitrate?

- [citrate] = 1.7654

- [isocitrate] = 0.2346

??? find out how to solve

aconitase catalyzes the isomerization of citrate to isocitrate. deltaG' = 5 kJ/mol, T = 25C.

what is the preferred direction of this reaction under standard conditions?

isocitrate --> citrate

phosphoenolpyruvate + ADP --> ATP + pyruvate + H+

- deltaH' = 31.02kJ/mol

- deltaS' = 0.1863 kJ/mol*K

based on the information given above, which of the following statements regarding this folding process are correct?

a. endergonic

b. exergonic

c. exothermic

d. endothermic

e. enthalpically driven

f. entropically driven

g. enthalpically opposed

h. entropically opposed

i. at equilibrium

j. exergonic at all temperatures

k. endergonic at all temperatures

l. none of the choices are correct

d. endothermic

f. entropically driven

g. enthalpically opposed

ATP + fructose-6-phosphate --> fructose 1,6-bisphosphate + ADP

- deltaH' = -83.39 kJ/mol

- deltaS' = -0.2008 kJ/molK

based on the information given above, which of the following statements regarding this folding process are correct?

a. endergonic

b. exergonic

c. exothermic

d. endothermic

e. enthalpically driven

f. entropically driven

g. enthalpically opposed

h. etropically opposed

i. at equilibrium

j. exergonic at all temperaturews

k. endergonic at all temperaturews

l. none of the above choices are correct

c. exothermic

e. enthalpically driven

h. entropically opposed

what is the pH and pOH of a solution containing 0.425mM KOH?

pOH = -log(0.000425M)

pOH = 3.372

pH = 14-pOH

pH = 14-3.372

pH = 10.63

what is the pH and pOH of a solution containing 276.23uM HCl?

pH = -log(275.23*10^-6M)

pH = 3.559

pOH = 14 - pH

pOH = 10.44

what is the pH and pOH of a solution containing 7.45*10^-5M NaOH?

pOH = -log(7.45*10^-5)

pOH = 4.128

pH = 14 - 4.128

pH = 9.872

what is the pH and pOH of a solution containing 4.65 x 10^-4M HCl?

pH = -log(4.56x10^-4M)

pH = 3.333

pOH = 14 - pH

pOH = 10.667

the pOH of window cleaner is 2.4. calculate the hydrogen ion and hydroxide ion concentrations.

[OH-] = 10^-pOH

[OH] = 10^-2.4

[OH-] = 3.98 x 10^-3M

[H+] = 10^-pH

[H+] = 10^-11.6

[H+] = 2.512

the pH of gastric juice is around 0.80. calculate the hydrogen ion and hydroxide ion concentrations.

[H+] = 10^-pH

[H+] = 10^-0.80

[H+] = 0.158

[OH-] = 10^-pOH

[OH-] = 10^-13.2

[OH-] = 6.310 x 10^-14

H2PO4- has a pKa of 6.86. if the concentration of H2PO4- is 0.622 mM and the concentration of H1PO4^2- is 0.038 mM what is the pH of the solution?

pH = pKa + log([]/[])

pH = 6.86 + log (0.038/0.622)

pH = 5.646

calculate the pH resulting from mixing 100mL of 0.25M pyruvic acid with 200mL of 0.35M sodium pyruvate. the pKa of pyruvic acid is 2.50.

0.25M x 100mL = 25mmoles

0.35M x 200mL = 70mmoles

pH = pKa + log[salt]/[acid]

pH = 2.50 + log(70/25)

pH = 2.947

calculate the ratio of the concentration of formate to formic acid required in a buffer system of pH 4.25. The pKa of formic acid is 3.75. ratio = ?

pH = pKa + log[CB]/[CA]

[CB]/[CA] = 10^pH-pKa

[CB]/[CA] = 10^4.25-3.75

[CB]/[CA] = 10^0.5

ratio = 3.162

a solution is buffered at a pH of 4.75 by a weak acid and its conjugate base. the concentration of a weak acid is 0.732mM and the concentration of the conjugate base equals 0.267mM. what is the pKa of this weak acid?

pH = pKa + log([CB]/[CA])

pKa = pH - log[CB]/[CA]

pKa = 4.75 - log([0.267]/[0.732])

pKa = 5.188

the pKa of a phenol shown below is 10.00. at what what pH is phenol 35% ionized?

protonated phenol <--> deprotonated phenol

CB = deprotonated = 0.35

CA = protonated = 0.65

pH = pKa + log([CB]/[CA])

pH = 10.00 + log(0.35/0.65)

pH = 9.731

the pKa of a methylammonium is 10.62. at what pH is methylammonium 2/5 ionized?

CB = deprotonated = 0.60

CA = protonated = 0.40

pH = pKa + log[CB]/[CA]

pH = 10.62 + log(0.6/0.4)

pH = 10.796

what is the 3-letter and 1-letter abbreviation for glycine?

gly, G

what is the 3-letter and 1-letter abbreviation for alanine?

ala, A

what is the 3-letter and 1-letter abbreviation for valine?

val, V

what is the 3-letter and 1-letter abbreviation for leucine?

leu, L

what is the 3-letter and 1-letter abbreviation for isoleucine?

ile, I

what is the 3-letter and 1-letter abbreviation for proline?

pro, P

what is the 3-letter and 1-letter abbreviation for methionine?

met, M

what is the 3-letter and 1-letter abbreviation for phenylalanine?

phe, F

what is the 3-letter and 1-letter abbreviation for tyrosine?

tyr, Y

what is the 3-letter and 1-letter abbreviation for tryptophan?

trp, W

what is the 3-letter and 1-letter abbreviation for lysine?

lys, K

what is the 3-letter and 1-letter abbreviation for arginine?

arg, R

what is the 3-letter and 1-letter abbreviation for histidine?

his, H

what is the 3-letter and 1-letter abbreviation for aspartate?

asp, D

what is the 3-letter and 1-letter abbreviation for glutamate?

glu, E

what is the 3-letter and 1-letter abbreviation for asparagine?

asn, N

what is the 3-letter and 1-letter abbreviation for glutamine?

gln, Q

what is the 3-letter and 1-letter abbreviation for serine?

ser, S

what is the 3-letter and 1-letter abbreviation for threonine?

thr, T

what is the 3-letter and 1-letter abbreviation for cysteine?

cys, C

what is the isoelectric point (pI)?

the pH at which the amino acid has no net charge

what is the formula for pI?

pI = 1/2(pK1 + pK2)

for any amino acid with a neutral side chain, at any pH below the pI of the amino acid, the amino acid will:

a. have a net negative charge

b. have 0 net charge

c. have a net positive charge

d. be neutral without any net charge

e. have an equal number of positive and negative charges

c. have a net positive charge

at what pH is the side chain of cysteine 75% ionized?

a. 7.7

b. none of these

c. 8.8

d. 8.2

e. 7.8

c. 8.8

pH = pKa + log([base]/[acid])

pH = 8.3 + log(.75/.25)

pH = 8.78