1. Use the dihedral angles depicted in the image. Which pairs of dihedral angles could represent: a. Phi and Psi for a residue in an alpha helix? b. Phi and Psi for a residue in a beta sheet? GG (a) (b) (c) (d) (e) (f) **Hint: you can look up an image of the Ramachandran plot to help.

2

Please give me correct solution for both questions c and d.

(True or False) 1.) Fatty acids can be found in ceramides and TAGs. 2.) The adenine base can easily form hydrogen bonds with thymine with the least energy requirement. 3.) The 3'end of nucleic acids structurally has a free OH group bonded to the 3' carbon of the sugar. 4.) Naturally occurring RNA molecules are always single stranded in the cell 5.) The Watson and Crick double stranded DNA structure is always antiparallel.

You are performing an enzymatic reaction to digest DNA and nothing is working.The working solution for the digestion buffer should contain 400 mM Tris, pH 8.0 and 125 mM MgCl2. Mixed are: 0.2 ml of 2M Tris, pH 8.0 stock solution 0.25 ml of 5M MgCl2 stock solution *Solution completed with 0.55 ml water to make a final volume of 1ml. a) Before checking the calculation, what important question do you have to ask first for this specific solution? (not a generic question about all solutions)   b) You are satisfied with the answer to a) and you believe he made a dilution error. You use the equation that applies to dilutions to check his calculations. Aha! you find the problem. What is it and how did you find out?

Consider the following protein mixture: Protein A B C D Molecular Weight (kDa) 50 150 200 350 Affinity to Metal ion === Zn²+ === 1. Using hydrophobic interaction chromatography, the protein that will be eluted last is [Select] 2. Using affinity chromatography, the protein that will be eluted last in a Zn²+-containing column is 3. The protein with the fastest migration towards the anode in SDS-PAGE is [Select] IpH value 7 3 9 5 [Select] [Select] 4. Using a buffer solution with a pH of 4, the protein that will bind to an anion exchanger is 5. The protein that will be eluted last in a gel filtration column is [Select] 6. Using isoelectric focusing, the protein that will have a protein band nearest to the cathode (negative electrode) is [Select] % Hydrophobicity 20 45 75 55

Answer each of the following with a word, phrase, or numeral (4 points each = 16 points). Please label your answers as (a), (b), (c) and (d). (a) Among (i) hydrophobic effect, (ii) van der Waals interactions, (iii) hydrogen bonds and (iv) conformational entropy, the force disfavoring duplex B-DNA formation from single strands. (b) Reason why salt bridges at the surfaces of cytosolic proteins are weak. (c) Type of nucleic acid duplex that forms when all glycosidic bonds are anti, chains are antiparallel, and all sugar puckers are C3' endo. (d) Amino acid that is most commonly found in the cis configuration in proteins.

Consider the proteins in Figure 1.  Assume they are treated with chymotrypsin to cut them into fragments, and then the fragments are separated by gel electrophoresis.  What would the fragment patterns look like in the gel for the three different proteins, assuming we can separate polypeptides that differ in size by very small amounts?  Complete Figure 2 below to show the location of the uncut polypeptides (- enzyme lanes) and the cut fragments (+ enzyme lanes).

Consider the following properties of the protein components of a sample mixture as provided in the table below: 1. if the mixture is subjected to gel filtration chromotography which protein component elute first? 2. if the mixture is subjected to isoelectric focusing which protein will stop m oving nearest to the positive electrode? 3. if the mixture is subjected to cation-exchange chromotography using a buffer at ph 7 which protein will bind to the resin? 4.if the mixture is subjected to SDS-PAGE which protein will be at bottomost portion of gel? 5.if the mixture is subjected to hydrophobic interaction chromotography which protein will bind most strongly to the resin?

For the following proteins in the figure answer the questions below:   A) Oligomerization state of the protein and molecular weight of each protomer B) Number of domains of one protomer and its potential function. C) Based on the information obtained, how many bands will you observe if you run a solution of the spike oligomer in an SDS-PAGE get and in a native gel?