Consider a small protein containing 101 amino acid residues. Theprotein will have 200 bonds about which rotation can occur. Assumethat three orientations are possible about each of these bonds.(a) Based on these assumptions, about how many random-coil con-formations will be possible for this protein?(b) The estimate obtained in (a) is surely too large. Give one reason why.

Random coil conformations is the conformation in which the monomeric forms of amino acids are…

Answered: Consider a small protein containing 101…

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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Similar questions

At what level of protein structure (primary, secondary, tertiary or quarternary) does Hydrogen bonding is relevant ? Consider if there is no Hydrogen bonding that exists, and only van der Waals exists in this protein structure, what do you expect to happen in its property? Explain with examples.
Our growing understanding of how proteins fold allows researchers to make predictions about protein structure based on primary amino acid sequence data. Consider the following amino acid sequence.(a) Where might bends or β turns occur?(b) Where might intrachain disulfide cross-linkages be formed?(c) Assuming that this sequence is part of a larger globular protein, indicate the probable location (external surface or interior of the protein) of the following amino acid residues: Asp, Ile, Thr, Ala, Gln, Lys. Explain your reasoning.
Our understanding of how proteins fold allows us to make predictions about protein structure based on primary amino acid sequence data. Consider the following amino acid sequence :a)Where might bends or βturns occur? b)Where might intrachain disulphide cross-linkages be formed? c)Assuming that this sequence is part of a bigger globular protein, indicate the probable location (on the surface or interior of the protein) of the following amino acid residues: Asp, Ile, Thr, Ala, Gln and Lys. Explain your reasoning
Consider a small protein containing 101 amino acid residues. The proteinbackbone will have 200 bonds about which rotation can occur. Assume thatthree orientations are possible about each of these bonds.(a) Based on these assumptions, about how many random-coil conformationswill be possible for this protein?(b) The estimate obtained in (a) is surely too large. Give one reason why.
Why is the ionic bond between, say, the side chain of lysine and the side chain of glutamic acid stronger in the hydrophobic interior of a protein than in aqueous solvent (water)?
Which categories of amino acid would you expect to find on the surface of a soluble protein, and which would you expect to find in the interior? What distribution of amino acids would you expect to find in a protein embedded in a lipid bilayer? What does “polar” mean, in the case of an ionized molecule and how is this related to “charged” of a molecule? Explain the significance φ, ψ contour diagram in proteins and explore how is it interpreted?
Assume you have a long polypeptide chain of Gly-Val dipeptides linked end to end. Explain the likely tertiary structure of this polypeptide chain. For example, is the chain likely to form an alpha helix, a beta sheet, or some other structure? Is the structure likely to display lots of folding, or very little folding? Can you make any other predictions about the tertiary structure? Explain your reasoning in a well-developed paragraph.
Together, these monomers make up what type of polymer (macromolecule)? List at least three (broad) functions that these macromolecules can perform. What is an example protein that we’ve discussed that uses of these functions? Using R as the side chain, draw the basic structure of an amino acid.
In the illustration below, the blue squiggly line represents a protein. Notice that the amino acid that is colored red and the amino acid that is colored black are very close to each other in space, but they are far from each other in the primary structure of this protein. How can you explain why two amino acids that are so far from each other in the primary structure of a protein can be so close together in the tertiary structure of the same protein?
Helices can be described by the notation nm,where n is the number of residues per helical turn and m is the number of atoms, including H, in the ring that is closed by the hydrogen bond. Would a 310 helix be more or less steep than an α helix? why?
Structures of proteins comprising domains separated by flexible linker regions can be quite difficult to solve by x-ray crystallographic methods. Why might this be the case? What are possible experimental approaches to circumvent this barrier?
Hydrogen bonding is important at what level of protein structure (primary, secondary, tertiary, or quarternary)? Consider what would happen if there was no hydrogen bonding and just van der Waals in this protein structure. What would you anticipate to happen to its properties? Briefly explain with examples.

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