4. Tertiary structure of a protein describes:A. Sequence of amino acidsB. Location of disulphide bondsC. Amino terminal end amino acidD. The nature of protein folding5. Study of linear sequence of amino acids is done by all techniques listed except:A. End group analysisB. Hydrolysis by proteolytic enzymesC. Analyzing the content of each aminOacidD. Denaturing the protein6. Primary structure decides:A. Rate of synthesis of proteinB. Biological activity of the proteinC. Rate of degradation of the proteinD. Effect of proteolytic enzymes on protein

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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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A protein in its native three dimensional conformation is cleaved with trypsin. According to the amino acid sequence, there are 9 residues where trypsin could cleave, yet only 3 fragments were produced from the digest. What conclusion can be made about protein structure that would lead to this result? The protein has multiple domains b. The protein is highly compacted, minimally accessible by solvent molecules c. The protein has quaternary structure d. The protein has a dynamic structure, highly accessible by solvent molecules e. The protein is compromised only of alpha helices
A. One example of conjugated protein that contains the following Prosthetic groups: a. Iron Protein class, Example, b. Lipids Protein class, Example, c. Phosphate group Protein class, Example, d. Carbohydrate Protein class, Example, е. Heme Protein class, Example,
2. a. In the following diagram of a portion of a protein, label the types of interactions that are shown. b. What level of protein structure are these interactions producing? b. CH CH3 CH3 Polypeptide backbone CH2 H3C H3Ç 10 CH С—ОН - CH,-S-S-CH,- а. CH2 с. -CH,-CH,-CH2-CH2-NH 0-C-CH2- d.
3. A. Briefly discuss the four levels of structure in proteins. Knowing that the 3-dimensional shape of a protein is important to its function, discuss on a qualitative basis whether the changes below will likely alter the function of a protein, justifying your answer with why or why not. B. What would happen to a protein's functionality if a serine residue were replaced with threonine? C. What would happen if serine were replaced with leucine? D. What would happen if serine were replaced with cysteine? E. What would happen if aspartic acid were replaced with tryptophan in the part of the protein (an enzyme) that serves as an active site to catalyze a reaction? F. What would happen if aspartic acid were replaced with tryptophan in a non-active site?
4) For various amino acid pairs (for example: F to A, E to R, D to N, V to L, S to W), ask yourself: a) Based on what you know about the chemical properties of the side chains, what effect would you expect on the stability of the protein if you mutated one residue of the pair into the other in the interior of the protein? What forces might have an impact on this change (ie: what types of interactions would you expect that amino acid to be involved in?) How would your answer change if the amino acid were located on the surface of the protein? b) c)
A C2 G This a photograph of an actual polyacrylamide gel that has been run with samples of protein. For each question, write the letter from the item in the gel that best matches the word or concept that is described. Answers may be used once, more than once, or not at all. There may be more than one correct answer per question. 1. Band 2. Lane 3. Well 4. Will protein migrate through the gel from A to B or will it migrate from B to A? 5. Which end is nearest the negative electrode, A or B? 6. Which contains smaller protein fragments, F or G? 7. Which letter indicates the highest concentration of protein fragments that are the same size 8. Where would a sample of protein be loaded? B.
Case B: An oligopeptide has the ff amino acid composition: 2 Phe, 2 Met, 2 Glu, 1 Arg, 1 Val, 1 Leu, 1 Lys, 1 Gly, 1 Ser The reaction of the intact peptide with Sanger reagent followed by acid hydrolysis creates a derivative of Met. Specific cleavage of the intact peptide (using chymotrypsin) produces fragments with the ff sequences: Fragment A: Glu-Gly-Lys-Phe Fragment B: Met-Ser-Leu-Arg Fragment C: Met-Val-Glu-Phe Question: What information do these result give about the sequence of the peptide?
5. Indicate whether the following amino acid residues would be more likely to be found on the surface or in the interior of a folded protein: Leu, Arg, Phe, Asn, and Glu. Give your reasoning for each case (diagrams not required).
Which of the following statements are correct about the native state of a protein (select all that apply)? A. Polar sidechains commonly interact with water B. Hydrophobic amino acids tend to be on surface of protein C. The sidechains of polar amino acids are most commonly found in the central core of a protein D. Formation of an alpha-helix is primarily driven by hydrogen bonds between the protein main chain, not sidechains. E. Secondary structure is largely driven by hydrophobic interactions
9. A) Please write down the names of the following protein folds. A B C B) Which one(s) is made of more than one polypeptide? D E 000 C) Give an example of a protein containing the motif in C and explain how the structure of this motif facilitates function. 10. What is Levinthal's paradox? Describe the paradox and explain the conclusion to which it led.
The primary structure of a protein is shown below. Please answer the following questions. Leu-Arg-Ser-lle-Glu-Thr-Val-Val-Asn-Gln-Val-lle-Ser- Tyr a. Where is this section of the polypeptide most likely located [ Select ] completely embedded inside the protein partially exposed to the aqueous environment b. Is the above more likely an alpha helix or a beta-pleated sh completely exposed to the aqueous environment c. Which two amino acid residues are least likely to be in an alpha helix, but most likely to be a part of a beta turn? (Please select the amino acids in alphabetical order). [ Select ] [ Select ]
3a) Secondary (2°) structure in proteins refers to two specific conformations a region of a protein can take on, the a-helix and the b-pleated sheet. Briefly describe or explain how 2° structure forms/what causes 2° structure to form in a region of a protein.

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Tertiary structure of a protein describes: A. Sequence of amino acids B. Location of disulphide bonds C. Amino terminal end amino acid D. The nature of protein folding