What would you predict about the ratio of hydrophilic to hydro- phobic amino acid residues in a series of monomeric globular proteins that range in size from a molecular weight of 10,000 g/mole to a molecular weight of 100,000 g/mole? Note that the volume of a sphere is 4/3nr³, while the sur- face area of the outside of a sphere is 4nr².
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- What would you predict about the ratio of hydrophilic to hydro- phobic amino acid residues in a series of monomeric globular proteins that range in size from a molecular weight of 10,000 g/mole to a molecular weight of 100,000 g/mole? Note that the volume of a sphere is 4/3nr³, while the sur- face area of the outside of a sphere is 4nr². How would your prediction change if the monomeric proteins were fibrous instead of globular?Bacteriorhodospin (Mw = 26 kDa) is a protein with purple colour. The protein acts as a light-activated proton pump that provides energy for cellular functions. The structure, revealed by both electron microscopy and X-ray crystallography, showed that the protein consists of 7 transmembrane spanning helices (TMH). Each TMH traverses the lipid bilayer completely (thickness of 45 Å). a)Calculate the minimum number of amino acid residues needed per TMH to completely cross the membrane. b)Estimate how large a fraction of the bacteriorhodopsin protein that is made up by TMHs. c)Now that you know the fraction of the protein that is made up by TMHs, at which ψ/φangles will the amino acids cluster in a Ramachandran plot?Consider a protein in which a negatively charged glutamic acid side chain (pKa = 4.2) makes a salt bridge (ion-ion interaction) with a positively charged histidine side chain (pKa = 6.5). Part A Do you predict that this salt bridge will become stronger, become weaker, or be unaffected as pH increases from pH = 7.2 to pH = 7.8? The salt bridge will become stronger. The salt bridge will become weaker. The salt bridge will be unaffected. Submit Part B Previous Answers Correct At pH = 7.2 the glutamic acid (Glu) side chain will carry a charge of ~ -1 (at 3 pH units above the pKa for Glu, the side chain will be almost fully ionized); whereas the histidine (His) side chain will carry a charge of < +0.5 (at pH = pK₂ the charge on His would be +0.5; since pH = 7.2 is above its pKa, it will carry less (+) charge as it becomes more deprotonated). As the pH increase to 7.8, the charge on Glu will remain ~ -1 and the charge on His will decrease; thus, this salt bridge is predicted to become weaker…
- Consider an amino acid (A) with no ionizable side chains, and call the three species involved in the acid/base equilibria H2A+, HA, and A- (see scheme below). Assume that pKa(1) = 2.0 and that pKa(2) = 9.0. Suppose that the total concentration of the amino acid is 1.0 mM. Report to two significant digits. pH [H2A+] (mM) [HA] (mM) [A-] (mM) 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0 11.0 12.0In the molecule of oligomeric protein there are 19 lysine residues. 12 of them may be easily acetylated with anhydrides of dicarbon acids (it react with NH2-groups). The acetylation of extra two residues of lysine will dissociate the protein to the subunits. The rest 5 lysine residues may be modified only after denaturation of the protein. Suggest, how many lysine residues are: a) on a surface of protein globule; b) inside globule: c) in a site which is responsible for the contact within subunitsHair is comprised largely of keratin, a fibrous protein consisting of two a-helices wrapped around each other in a left-handed coiled-coil. The diagram below compares a partial alignment of the amino acid sequences of a form of human keratin and of ovine keratin. For each pair of dissimilar aligned amino acids, (i) indicate if a side chain is associated with a discrete charge by writing or (at pH 7) adjacent to the letter; and (ii) indicate whether each amino acid is polar (p) or apolar (a) in the case of aligned, electrostatically-neutral, side chains. In the diagram, 219 and 158 designate se-quence positions of the first aligned residue in each polypeptide strand. human II 5 219 ovine II 7c 158 FEQYINNLRRQLDSIVGERGRLDSELRNMQDLVEDFKNKYEDEINKRTTAE FEGYIETLRREAECVEADSGRLSSELNHVQEVLEGYKKKYEQEVALRATAE
- Consider a protein in which a negatively charged glutamic acid side chain (pKa = 4.2) makes a salt bridge (ion–ion interaction) with a positively charged histidine side chain (pKa = 6.5). (a) Do you predict that this salt bridge will become stronger, become weaker, or be unaffected as pH increases from pH = 7.0 to pH = 7.5? (b) Justify your answer with calculations of partial charges on these amino acid side chains.Consider a protein in which a negatively charged glutamic acid side chain(pKa = 4.2) makes a salt bridge (ion–ion interaction) with a positively charged histidine side chain (pKa = 6.5).(a) Do you predict that this salt bridge will become stronger, become weaker, or be unaffected as pH increases from pH = 7.0 to pH = 7.5?(b) Justify your answer with calculations of partial charges on these aminoacid side chains.At physiological pH (i.e. 7.4), polylysine assumes a random structure in solution. Given that the pKa for the e-amino group of lysine is 10.5, under what conditions would you expect polylysine to form an a-helix? Explain your reasoning. Under what conditions would you expect polyglutamate to form an a-helix, given that the pKa for the side-chain COOH group is 4.3?
- Which intermolecular forces are important in acetic acid, CH3 –(C=0)-oh? A particular amino acid contains a- CHNH3+ group. Is this amino acid more likely to be found on the inside or the outside of the folded protein? Briefly explain. The addition of ethanol, CH3CHOH, t an aqueous solution lowers the surface tension of the solution. Predict whether adding ethanol to an aqueous protein solution will tend to stabilize or unfold the protein. Briefly explain.After staining an SDS-PAGE gel with Coomassie Blue G-250, the protein bands are visualized by de-staining the gel in a Coomassie Blue G-250 de-staining solution. This solution is made up of 10% acetic acid, 50% methanol, and 40% distilled water. How much of each of these components do you need to prepare 5 liters of Coomassie Blue G-250 de-staining solution?Peptides and small proteins fold spontaneously in aqueous solution at room temperature. Thus, for a small protein in water, we can say ΔG FOLD < 0. Denoting the unfolded protein as Unf and the folded protein as Fld, we can write the following equation:Unf(aq)--DELTA G FOLD----> Fld(aq)Considering the transition from the unfolded state (in which there are many possible conformations) to the folded state (only one conformation), there is clearly a decrease in the entropy of the protein. However, protein folding is (correctly) described as an entropically driven process.a) Resolve this apparent paradox by identifying the enthalpy (ΔH) and entropy (−TΔS)components involved in protein…