Tt7. What is the driving force that promotes secondary structure formation of alpha helicesand beta sheets? How is this force arranged to make an alpha helix or beta sheet? Whatpromotes turns or kinks in these structures? You can describe and/or draw it but pleaseshow what are the interactions facilitating this effect.

Two types of secondary structures are abundant in protein: alpha helix and beta sheets.The alpha…

Answered: 7. What is the driving force that…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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18. Amino acids at the N-terminal end of eukaryotic polypeptides that contain information required for post-translational processing and determining the extra-cellular destination of the nascent polypeptides. Group of answer choices 1. Sigma Sequence 2. Signal Sequence 3. Chaperone Sequence 4. Kozak Sequence
3. Approximate molecular weight for an unknown protein from gel-filtration experiment is 130 kDa. Thirty six mg of this pure protein was treated with excess of fluorodinitrobenzene. After the reaction and complete acid hydrolysis the mixture was found to contain 356 µg of dinitrobenzene derivative of methionine (free acid) and no other amino acid-dinitrobenzene derivatives. Is this protein consisting of single polypeptide chain or multiple subunits? If it consists of multiple subunits, then how many? From these data, can you calculate the molecular weight of the protein more precisely?
2. RNA is almost never found in its primary structure and will form secondary structures based on the cellular environment in which it is found. i) Describe why RNA preferentially forms secondary structures and also discuss the major chemical interactions that are facilitating that structure. ii) Below is a structure of an RNA that is folded. This RNA structure can be easily interrupted by addition of Mg2+ to the system. Describe why the secondary RNA structure would change as a result of the addition of this ion. knot 20A 250 S2G 29 G 3" 13 U 10 5' C5 GS1
2. The 64 codons are shown in Table 1. Notice that the first two nucleotides of each codon (abbreviated by their first letter) are shown in the column on the left. To find out the amino acid specified by a given codon, find the first two letters in the column on the left, then follow that row to the column showing the last nucleotide (letter) of the codon. Note that most amino acids are coded for by more than one codon. Table 1. The Genetic Code: Codons and Their Amino Acids First Two Mocleotides af Codons Last Nocleotide of Codons A The Amino Acids phe phe leu leu Abbreviations Names UC gly glycine alanine ser ser ser ser ala UA tyr tyr term term val valine UG cys cys term trp ile isoleucine cu leu leu leu leu leu leucine serine threonine ser CC pro pro pro pro thr gin proline aspartate glutamate lysine arginine asparagine glutamine cysteine methionine CA his his gin pro asp CG arg arg arg arg glu lys AU ile ile ile met AC thr thr thr thr arg asn AA asn asn lys lys gln AG ser ser arg…
1. What is the length in AA’s of the LilP protein? Assume fMet is NOT CLEAVED. 2. Write out the sequence of the polypeptide in AA: use the three letter notation, e.g. Met-Ser-Pro-
1. If a single transition occurs in a codon that specifies Phe. List all the possible mutated codons and the amino acids they specify.
2. The diagram to the right shows the change in the structure of the C-terminal portion of each of the ẞ-subu- nits of human hemoglobin (HbA) in the oxyHb to deox- yHb or R-to-T transition. The hydrogen bonding interac- tion of the C-terminal ẞHis 146 residue with the side chain of Asp94, highlighted by the red ellipse, has been shown to be responsible for a major portion of the proton uptake associated with the Bohr effect. Treatment of HbA with the enzyme carboxypeptidase A (CPA) results in loss of the C-terminal ẞHis 146 and ẞTyr145 residues of the ẞ- subunits. (a) ( ) Draw a Hill plot [log(Y/[1-Y]) vs. log(pO2), Y = fraction of heme groups occupied by O2] to compare the values of the Hill coefficient nн and the O2-binding affinity at pH 7.4 of normal HbA before and after treat- ment of with CPA. (b) (' ) How will the plot for CPA-digested HbA change at pH 7.2? (c) 1 Hi5146 HN- ✓ Low PK B-chain. CH2 CH-NH-CO-CH-NH- CH₂ Tyr145 он HbO2 or R state Туг145 CH-CH2- OH co NH CH CH₂ His…
2. Chymotrypsin, trypsin, and elastase are members of a family of enzymes referred to as serine proteases. The enzyme papain (found in papaya) is also a protease but is a member of a family of enzymes referred to as cysteine proteases. The amino acid residues in the active site of papain critical for peptide bond hydrolysis are a protonated histidine and a deprotonated cysteine residue. The cysteine residue functions as the nucleophile similarly to the serine residue in serine proteases. (a) Using what you know about chymotrypsin's mechanism, draw a reaction mecha- nisn for the hydrolysis of a peptide bond by papain. Does the mechanism you have drawn employ acid-base catalysis, covalent catalysis, (b) or both? (c) The pKa values of the active site residues that control the pH profile of the activity of pa- pain are 4.2 and 8.2. The pH optimum for the reaction is 6.0. Through the many years of re- search carried out on cysteine proteases, it has been demonstrated that the pKa of 4.2…
8. NMR measurements have shown that poly-lysine is a random coil at pH 7 but becomes a helix when the pH is raised above 10. If the same type of folding behavior is observed, what should be the pH dependence of poly-glutamate? A) Helix at pH 7 but random coil at pH 10 B) Random coil at pH 3 but helix at pH 7 C) Random coil at pH 7 but helix at pH 10 D) Helix at pH 3 but random coil at pH 7
9. Put the following events in the synthesis of a polypeptide in the proper order. An initiator tRNA already bound to the small subunit binds to an mRNA. An aminoacyl tRNA matches its anticodon to the codon in the A site. The large subunit attaches to the small subunit, with the initiator tRNA in the P site. A peptide bond forms. A tRNA translocates from the A site to the P site, and an empty tRNA exits from the E site.
2. A mutation that changes an alanine residue in the interior of a protein to valine (A157 → V157) is found to lead to a loss of proper folding and activity. However, proper folding and activity are regained when a second mutation at a different position changes a leucine residue to glycine (L185 G185). Based on these observations, you → hypothesize that amino acid residues 157 and 185 are spatially close to each other in the folded and active protein. How does your hypothesis explain the data, that the double mutant (A¹57 → V157; L185 → G185) has activity that the single mutant (A¹57 → V157) lacks?
4. Why would a tetra peptide e.g. H-Gly-His-Gly-His-NH2 accumulate in the lysosome in a biological cell? Is it related to the acidic pH of the lysosome?

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