Calculate the pH of $1.0L$$1.0\ L$ of water to which the following was added. Note calculate each separately

• a. $30mL$$30\ mL$ of $1.0M$$1.0\ M$ HCl

  $$30mL\ast \frac{1L}{1000mL}\ast \frac{1.0moles}{1Liter}=0.03molesHCl$$
  $$pH=-lo{g}_{10}([0.03])=1.5228787452803376$$

• b. $50mL$$50\ mL$ of $1.0M$$1.0\ M$ NaOH

  $$50mL\ast \frac{1L}{1000mL}\ast \frac{1.0moles}{1Liter}=0.05molesNaOH$$
  $$pOH=-lo{g}_{10}([0.05])=1.3010299956639813$$
  $$pH=14-1.3010299956639813=12.698970004336019$$

If the equilibrium constant for a reaction is $2.22\ast {10}^{5}M$$2.22 * 10^5\ M$ , calculate the standard free-energy change ( $\mathrm{\Delta }{G}^{\circ }$$\Delta G^{\circ}$ ) for the reaction.

For the peptide : Gly-His-Arg-Gly-Gly-Ala-Trp-Ala

• a. Calculate the pI

  • N-Gly = 9.6 , amine

  • His = 6.0 , amine

  • Arg = 12.48 , amine

  • C-Ala = 2.34 , carboxylic acid

  • 2.34 , 6.0 , 9.6 , 12.48

  • pH = 10 :

    • 10 < 2.34 = False = Deprotonated Carboxylic Acid = -1
    • 10 < 6.0 = False = Deprotonated Amine = 0
    • 10 < 9.6 = False = Deprotonated Amine = 0
    • 10 < 12.48 = True = Protonated Amine = +1
  $$pI=\frac{9.6+12.48}{2}=11.04$$

• b. What is the overall charge on this peptide at pH 4 , 7 , and 9

  • pH = 4 :

    • 4 < 2.34 = False = Deprotonated Carboxylic Acid = -1
    • 4 < 6.0 = True = Protonated Amine = +1
    • 4 < 9.6 = True = Protonated Amine = +1
    • 4 < 12.48 = True = Protonated Amine = +1
    • Net-Charge = -1 + 1 + 1 + 1 = 2

  • pH = 7 :

    • 7 < 2.34 = False = Deprotonated Carboxylic Acid = -1
    • 7 < 6.0 = False = Deprotonated Amine = 0
    • 7 < 9.6 = True = Protonated Amine = +1
    • 7 < 12.48 = True = Protonated Amine = +1
    • Net-Charge = -1 + 0 + 1 + 1 = 1

  • pH = 9 :

    • 9 < 2.34 = False = Deprotonated Carboxylic Acid = -1
    • 9 < 6.0 = False = Deprotonated Amine = 0
    • 9 < 9.6 = True = Protonated Amine = +1
    • 9 < 12.48 = True = Protonated Amine = +1
    • Net-Charge = -1 + 0 + 1 + 1 = 1

If a protein were chemically synthesized in hexane ( non-polar ) instead of water ( polar ) , would it retain the same structure?

• The protein would be "inside-out" , with hydrophobic regions on the outside , and hydrophilic regions on the inside.

Of the levels of structure discussed ( primary , secondary , etc ) , which would be the most likely to be affected? Why?

• Primary structure would remain unchanged
• Secondary and Tertiary Structure would be affected.
• The protein would fold differently as now the side chains are responding to differences in polarity that has now flipped.

Sickle cell anemia is a genetic disease resulting from a single amino acid substitution ( glutamate to valine ) in the sixth position in the hemoglobin β chain. This mutation causes hemoglobin to polymerize into strands in the deoxygenated state , but not in the oxygenated state. How does this observation help support other evidence that hemoglobin undergoes a shift in its 3-D structure?

• Its further proof that folding is dependent upon the amino acid sequence.
• Glutamate is negatively charged.
• Valine is non-polar , aliphatic
• Valine sticks and different hemoglobin molecules with their protruding valines agglutinate / polymerize

Sequencing of an unknown polypeptide has yielded the following information:

• a. Val, Ile, Tyr, and Phe are in a 2:1:1:1 molar ratio
• b. Treatment with 1-fluoro-2,4-dinitrobenzene ( FDNB ) yielded complete hydrolysis and 2,4-dinitrophenyl phenylalanine and no free phenylalanine
• c. Digestion with chymotrypsin yielded free phenylalanine and isoleucine, and a tripeptide of Tyr and Val

What is the sequence of the polypeptide? To make sure you receive all points possible please tell me what each piece of information is telling you , and provide the cleavage points ( from part c ) in your final answer.

• a = tells us the sequence is 5 amino acids in length , and includes the following amino acids : Val , Val , Ile , Tyr , Phe

• b = tells us phenylalanine must be the first amino acid in the sequence

• 1	2	3	4	5
  Phe

  c = chymotrypsin cleaves at the C-terminal side of Phe , Trp , or Tyr

  • Product-1 = Phe
  • Product-2 = IIe
  • Product-3 = Val , Val , Tyr

• There are 2 potential ways to for chymotrypsin to generate the products described

  • Val-Val-Tyr || Phe || IIe
  • Phe || IIe || Val-Val-Tyr

• But only one has Phenylalanine in the first position

• Therefore the sequence is : Phe-IIe-Val-Val-Tyr

Describe the mechanism of how 2,3-BPG affects oxygen binding to hemoglobin.

• 2,3-BPG is a small negatively charged molecule

• It binds to the positively charged central cavity of Hemoglobin

  • This binding stabilizes the T state

Is BPG necessary for effective oxygen transport? Why?

• its necessary to stabilize the T state
• this is needed to offload oxygen to the tissues

A graduate student is trying to purify a protein from a sample that contains the desired protein and an unwanted protein. Some details of each protein are given below.

• a. Desired protein: high percentage of Val, Ile, Phe, and Ala
• b. Unwanted protein: high percentage of Ser, Thr, and Gln

Which chromatography method should she use and why?

• The desired protein is non-polar
• Therefore , you should use standard normal-phase chromatography with a non-polar mobile phase to isolate the desired protein and leave the unwanted protein trapped in the stationary phase.

Describe both the lock and key model and the induced fit model of protein binding to a ligand.

• Ligand and receptor shapes are tightly evolved to match.
• In the induced fit model , the ligand initially transiently binds , causing a a change in the shape of the receptor. Only after this change can further reactions be catalyzed.

Which of these models is the preferred model of binding and why?

• It might depend on the final target.
• Induced fit model adds a regulatory step. ??? idk