Question

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Discuss how the properties of acidity, basicity, and polarity arise for some amino acids. 8. How does water interact with hydrophobic and hydrophllic molecules? How does water interact with amino acid side chains, and how does this facilitate the folding of proteins? 9. Describe how amino acids are linked together to form protein chains. 10. What does the Ramachandran plot describe? How is it useful in describing protein structure? 11. What physical forces act on the amino acid chain to fold it into a compact structure? Explain the role of hydrophobicity in inducing the spontaneous folding of protein chains. 12. What is hydrogen bonding? How does it arise? Explain the role of hydrogen bonding in stabilizing protein folds. 13. "The stable folded state of a protein represents a state of low energy." Be able to expound on this fundamental idea. 14. What is the protein folding problem? Be able to describe the need for the computational solution to the protein folding problem. What are the two major challenges to the computational solution to the protein folding problem?

Answer 1

10) A Ramachandran plot (also known as a Ramachandran diagram or a [φ,ψ] plot), originally developed in 1963 by G. N.Ramachandran, C. Ramakrishnan, and V. Sasisekharan. In fact, it is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure. A Ramachandran plot is a way to visualize backbone dihedral angles ψ against φ of amino acid residues in protein structure. A Ramachandran plot can be used in two somewhat different ways. One is to show in theory which values, or conformations, of the ψ and φ angles are possible for an amino-acid residue in a protein. A second is to show the empirical distribution of data points observed in a single structure.
The colouring/shading on the plot represents the different regions described in Morris et al. (1992): the darkest areas correspond to the "core" regions representing the most favorable combinations of phi-psi values.
Ideally, one would hope to have over 90% of the residues in these "core" regions. The percentage of residues in the "core" regions is one of the better guides to stereochemical quality. The different regions were taken from the observed phi-psi distribution for 121,870 residues from 463 known X-ray protein structures. The two most favoured regions are the "core" and "allowed" regions which correspond to 10° x 10° pixels having more than 100 and 8 residues in them, respectively. The "generous" regions were defined by Morris et al. (1992) by extending out by 20° (two pixels) all round the "allowed" regions. In fact, the authors found very few residues in these "generous" regions, so they can probably be treated much like the "disallowed" region and any residues in them investigated more closely.

12) The hydrogen bond is really a special case of dipole forces. A hydrogen bond is an attractive force between the hydrogen attached to an electronegative atom of one molecule and an electronegative atom of a different molecule. Usually, the electronegative atom is oxygen, nitrogen, or fluorine, which has a partial negative charge. The hydrogen then has the partial positive charge.

It basically plays an indispensable role in association with protein interaction as well as with regard to protein folds, some of them are as follows: -

• A hydrogen bond is formed by the interaction of a hydrogen atom that is covalently bonded to an electronegative atom (donor) with another electronegative atom (acceptor).

• Hydrogen bonding confers rigidity to the protein structure and specificity to intermolecular interactions.

• The accepted (and most frequently observed) geometry for a hydrogen bond is a distance of less than 2.5 Å (1.9 Å) between hydrogen and the acceptor and a donor‐hydrogen‐acceptor angle of between 90° and 180° (160°).

• During protein folding, the burial of hydrophobic side‐chains requires intramolecular hydrogen bonds to be formed between the main chain polar groups.

• The most stable conformations of polypeptide chains that maximize intrachain hydrogen‐bonding potential are α helices and β sheets.

• Specificity in molecular recognition is driven by the interaction of complementary hydrogen‐bonding groups on interacting surfaces.