- How might the solubility of peptides be influenced by the size c peptides? How might the R group of the amino acid influence

Explain how the tertiary structure of a protein is stabilized by various intermolecular forces and by disulfide bonds

1. Which peptide would be more soluble at pH 7.0, (Val)₂₀ or (Asp)₂₀ ? at pH 3.0, (Gly-Glu-Val)

Explain why the cartoon pictures of proteins often look like ribbons coiled and laying flat. Your description should include the shape of the NMA molecule's amide bond as well as the fact that all peptides that make up a protein are linked by amide bonds.

On 4. Below is a polypeptide with an unknown number of amino acids. On the diagram below: a. Circle EVERY peptide bond b. Circle and number each amino acid from 1, 2, 3, and so on; from left to right c. Label each amino acid as polar, non-polar, or electrically charged d. Label the N-terminus and C-terminus e. Select three pairs of amino acids that could potentially interact to influence tertiary structure AND state the bond/force/interaction type involved in each pair. H₂N-CH-C-N-CH-C- CH₂ CH₂ CH₂ NH CINH NH₂ Accessibility: Investigate CH₂ -NH -CH-C-N- CH-OH CH3 -CH-C-N CH₂ CH₂ -N- OH CHIC-OH CH₂ OH

in determining the structure of a fully folded protein? involving the amino acid side chains of the polypeptide. Which has the largest effect 5. hydrogen bonding ionic interactions a) b) c) d) hydrophobic interactions van der Waals interactions none of the above The misfolded, insoluble, and aggregated proteins characteristic of Alzheimer's disease and Parkinson's disease are known as: zymogens b) c) d) e) open quaternary structure proteins protein domains amyloid deposits molecular chaperones 6.

If you were to design a small peptide with a large net positive charge at physiological pH, which amino acid residues should predominate?

5. Refer to Model 2 for information relevant to this question. A sample of the peptide Lys-Glu-Ser has a net charge of zero between what two pH values? What is the pl of Lys-Glu-Ser? Model 2: The pl of a peptide is determined by examining the ionizable groups. The protonated and unprotonated forms of each ionizable group are in equilibrium. Consider the peptide Lys-Glu-Ser shown below at pH 7.2. The complete structure is on on the left and a stylized structure with just the ionizable groups is on the right. While the N-terminal is depicted as protonated, a sample of Lys-Glu-Ser is composed of a population of molecules and within that population some molecules contain a non-protonated N-terminal group at pH 7.2. may H3N* COO- H3N-CH-CIN-CH C N-CH C- H. pK 3.5 OH H. pK= 8.5 COO- CH2 CH2 CH2 NH, pK 10.0 pK 4.2 CH2 CH2 OH CH2 c=0

What charge is carried by the peptide FREEENERGY at pH 7? (pKas: N-terminus: 9; C-terminus: 3; Arginine 11.6; Glutamic acid, 4.3)

None