BIOLOGY 2B03 Lecture Notes - Lecture 6: Peptide, Partial Charge, Lysine

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10 Apr 2018

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Polypeptides fold spontaneously and assume a random-coil structure o random-coil is a periodically ordered structure of the protein. Structure that the polypeptide assumes most of the time, or native structure, is the functional structure. Ionic bond - attraction between a positively charged cation and negatively charged anion lomoar cpsd| 2151316: ex. Interaction between negatively charged anion on glutamate side chain and positively charged cation on lysine side chain. Ionic interaction is assisting in holding the 2 arms of the polypeptide together in its shape o one bond is not strong enough to do this o accumulation of interactions can maintain protein shape. Interaction between a partially positively-charged hydrogen atom in a molecular dipole and unpaired electrons from another atom: ex. In water, oxygen has a partial negative charge, a negative dipole, whereas the hydrogen exhibits a partial positive charge, or a positive dipole: happens in other covalent bonds as well.

Related Questions

1. The level of protein structure that is stabilized primarilyby non-covalent interactions between the side chains within asingle polypeptide chain is refered to as its:

A) primary structure

B) secondary structure

C) tertiary structure

D) quaternary structure

E) none of the above

2. Collagen, a strong fibrous protein found in connectivetissue, bone, and the extracellular matrix, has a structure inwhich three left-handed helices wind around each other to form aright-handed triple helix. The primary structure of collagen has arepeat unit of -(Gly-X-Pro)- Which of the following bonds stabilizethe collagen triple helix? (mark all that apply)

A) Hydrogen bonds between hydroxyproline residues

B) Hydrogen bonds between N-H and C=O

C) Ionic bonds between amino acid side chains

D) Hydrogen bonds between charged amino acids

3. The non-covalent forces that stabilize the Beta-strandconformation of peptides include:

A) H-bonds between amide C=O and amide NH

B) Van der Waals packing between the peptide backbone atoms

C) Van der Waals packing due to side chain interdigitation

D) Only A and B above

E) None of the above

4. What is the approximate length difference of a 22-kDasingle-stranded ?-helical protein segment vs. a 22-kDasingle-stranded ?-strand protein segment? Assume a mean residuemass of 110 Da. Show work.

5. Circular dichroism measurements have shown that the peptidebackbone of poly-l-lysine (KKKKKKK) adopts a random coilconformation at pH 7.0, but becomes ?-helical as the pH is raisedabove 10. This observation is known as the

magentaotter572

Is DNA a protein if so what makes up proteins, if not what it is and what are its monomers called? Describe the primary, secondary, tertiary, and quaternary structure of DNA (this sub-question is independent of the answer to the first question).

Describe electrostatic bonds, covalent bonds, van der Waals interactions, and hydrogen bonds and give an example of each.

Which of the four classes of amino acids has side chains with the greatest hydrogen-bond-forming potential?

Which has the greatest potential to form electrostatic interactions?

Which class has the greatest potential for hydrophobic interactions?

Of the following amino acids, (K), (Y), and (F), which side-chains would you expect to be the most soluble in a polar aqueous solution? Which the least?

Would you agree with the statement that many different amino acid sequences can fold into the same basic tertiary structure? What data can you cite as evidence for your position?

Some proteins, once folded âassociateâ to form higher order structures (i.e., quaternary structure). Within these structures the single protein chain is known as a âsubunitâ (not to be confused with a protein domain). If two identical protein chains fold and associate, the quaternary structure is named âhomodimerâ (and the individual subunits are sometimes referred to as âmonomersâ); for three âhomotrimerâ and so on. If, on the other hand, the two protein chains that associate have different primary structures, the quaternary structure is named âheterodimerâ. Using the dimer as an example, we know that the respective regions of the protein subunit surfaces that are interfaced, are responsible for the âfavorable energy of interactionâ which stabilizes the dimeric protein complex.

(a). Although, noncovalent bonding interactions are used both for stabilization of the folded protein molecule and its dimerization, the contribution of the âhydrophobic effectâ to chain folding is significantly greater than its contribution to subunit association. Define the âhydrophobic effectâ and explain why you would expect it to have a more pronounced role in chain folding compared to dimerization of the folded molecules.

(b) As the protein chain folds to the native structure, it loses entropy. Upon dimerization, more protein entropy is lost. Compare and contrast the source of protein entropy loss, which occurs with folding, with that which occurs with dimerization.

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BIOLOGY 2B03 Lecture Notes - Lecture 6: Peptide, Partial Charge, Lysine

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