BMB 401 Lecture Notes - Lecture 9: Steric Effects, Peptide, Protein Structure

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raspberrybear596

3 Apr 2019

School

University of Miami

Department

Biochemistry and Molecular Biology

Course

BMB 401

Professor

Farooq

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Document Summary

3d fold relative to each other: amino acids contain peptide bonds (assume trans conformation, steric hindrance is minimal for pro residues (able to exist in cis-trans) 310-helix (also right handed) it has three residues per helical turn: a pitch of 6. 0 per turn. Sheet conformation to as strand: a minimum of two strands running laterally to each other needed to generate a sheet. Inside sheet, the strands can run in the same direction, known as parallel. Type 1 and type 2 of terms are both stabilized by hydrogen bonding between the c=o group of ith residue and the nh group of (i+3) residue. Their differences arise due to the rotation of the peptide bond between residues (i+1) and (i+2) by 180 degrees. Unordered regions of a polypeptide chain interrupting secondary structures are known as loops. All 3d fold structures are stabilized by two major non-covalent forces between residues located.

Related Questions

1. A sequence of amino acids in a certain protein is found to be â Ser â Gly â Pro â Gly â

The sequence is most probably part of a(n):

a. beta turn

b. antiparallel beta sheet

c. alpha-helix

d. parallel beta-sheet

e. alapha-sheet

2. Which statement about peptides bonds is NOT TRUE?

There is perfectly free rotation about the peptide bond.

The peptide bond has partial double-bond character.

The peptide bond is shorter than a normal carbon-nitrogen single bond.

The peptide bond usually has a trans configuration with respect to the alpha-carbons of the two amino acids involved in the peptide bond.

Peptide bonds are made via condensation of an amine and a carboxylic acid with loss of water.

3. Which of the following statements about proteins is FALSE?

	Active proteins are generally very loosely structured.
	In water-soluble proteins, hydrophobic amino acid residues are generally buried and not exposed to water.
	Primary structure determines tertiary structure.
	Secondary structure is regular, recurring arrangements in space of nearby amino acid residues in a polypeptide.
	Quaternary structure involves the interaction of subunits in a protein with more than one polypeptide chain.

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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

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BMB 401 Lecture Notes - Lecture 9: Steric Effects, Peptide, Protein Structure

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