BIOL 200 Lecture Notes - Lecture 7: Van Der Waals Force, London Dispersion Force, Covalent Bond

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bluemosquito35

25 Sep 2017

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Secondary structure is made up of backbone interactions (h-bonds: results in the formation of alpha-helices and beta-pleated sheets. Tertiary and quaternary structures depends on side chain interactions (non-covalent and one covalent: hydrogen bonds, ionic bonds, van der waal forces (london dispersion forces, disulfide bonds. Primary structure: linear amino acid sequence of peptide bonded amino acids; this sequence determines the protein"s 3d structure. Secondary structure: local 3d structure stabilized by backbone h-bonding of the peptide; examples include alpha-helices and beta-sheets. Tertiary structure: overall 3d structure ( fold") of entire polypeptide; stabilized by side- chain interactions (non-covalent and disulfide bonds) as well as interactions between side chains and backbone atoms. Quaternary structure: 3d arrangement of polypeptides in a protein composed of multiple subunits; similar stabilization as tertiary. Similarities are driven by thermodynamics: both are driven by thermodynamics, non-covalent and covalent interactions ensure the most stable final conformational state, increase the stability of the system.

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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

The sequence of amino acids is considered to be the ________ structure of a protein.

Select one:

a. secondary

b. tertiary

c. quaternary

d. primary

The pattern the backbone folds, for example alpha-helix or beta pleated sheet, is the ________ structure of a protein.

Select one:

a. quaternary

b. secondary

c. tertiary

d. primary

Which type of forces stabilizes the primary structure of a protein?

Select one:

a. Salt bridges

b. Hydrogen bonding between the carbonyl group and amino group

c. Dipole-dipole

d. Peptide bonds

The interaction of the side chains on the amino acids, for example hydrophobic attractions, is the ________ structure of a protein.

Select one:

a. quaternary

b. secondary

c. tertiary

d. primary

violetyellowjacket662

Please I need help with these questions

1. The word "quaternary" structure refers to which case of "4"?

a)the 4^th residue in the sequence just those proteins with 4 total subunits, such as hemoglobin

b)proteins with any number of multiple subunits, regardless of the total number (2, 3, 4, 5, ...)

c) the number of residues per turn in an alpha helix (3.6 rounded off to the closest integer, which is 4)

d)the number of residues (4 total) needed to make a beta turn

2. The Ramachandran plot depicts which of the following?

a.sterically permitted rotational (dihedral) angles along the backbone chain

b.the polar and nonpolar sides of helices, using circular graph paper

c.the cysteine pairing pattern in a protein having several disulfide bonds

3. The "level" of protein structure involving repetition of a particular choice of phi and psi angles is which of the following?

a. primary structure

b. secondary structure

c. tertiary structure

d. quaternary structure

BIOL 200 Lecture Notes - Lecture 7: Van Der Waals Force, London Dispersion Force, Covalent Bond

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