Please answer points a-e a. Which between A, B and C represent ϕ and ψ? b. Which between A, B and C is the bond that cannot freely rotate? c. Which information do we gather by knowing the values of ϕ and ψ? d. Which one is the peptide bond? e. Based on the numbers which label atoms, which atoms lie on the plane of the peptide bond?  

A generic protein can form a secondary structure with ϕ=−170∘ , ψ=150∘. From the Ramachandran plot, describe which structure would be.   

In Hemoglobin, explain why His E7 is essential (it is the one hanging on top of the heme) the importance of the quaternary structure in the binding with O2 there are 3 allosteric regulators (C02, H+ and BPG). List where they bind and which state (T or R) they stabilize.

Briefly explain why a protein folds making sure you talk about:  Which level of protein organization is the most responsible for final conformation of a protein- The thermodynamic driving force of the folding- make sure to distinguish between the surrounding (water) and the system (protein), go over the changes in ∆H and ∆S and how those would influence ∆G The types of interactions created in the tertiary structure

For the titration curve of this tripeptide (Glu-Cys-Arg- provided below in its fully protonated form), identify with the matching letters the first three max buffer regions, and the first three equivalence points. Then write the values of the pH for the max buffer regions and the value of the pI.    

How will the pka of Glu differ between ‘free’ tetrapeptide and tetrapeptide interacting with Lysine? Higher or lower than 4.2? Explain

Which of the following (A-C) represents a correct structure of the tripeptide Glu-Cys-Arg at pH=8.4 Reference table:

EXTRA POINTS: 10 Calculate the standard free-energy changes of the following metabolically important enzyme-catalyzed reaction at 25⁰C and pH 7.0 from the equilibrium constants given R = 8.314 J / mol·K and T= 25°C = 298K.   

Since enzymes are not rigid molecules but rather flexible proteins, which of the following may be attributed to this fact?   a.  active sites are able to conform to the shape of the substrate   b.  catalytic residues are oriented in such as way to aid in bond breakage and bond formation   c.  strain is placed upon the substrate while it binds to the enzyme   d.  near-attack conformations are achieved during formation of the transition state during an enzyme catalyzed reaction   e.  all of the above are correct

15. The catalytic mechanism below is an example of:   a.  covalent nucleophilic catalysis.   b.  covalent electrophilic catalysis.   c.  specific base catalysis.   d.  general base catalysis.   e.  low barrier hydrogen bond catalysis.