BMB 401 Lecture Notes - Lecture 3: Hemoglobin, Oligomer, Ramachandran Plot

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aquamarinemink463

16 Dec 2016

School

University of Miami

Department

Biochemistry and Molecular Biology

Course

BMB 401

Professor

Farooq

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Document Summary

1 = linear amino acid sequence of a polypeptide. 2 = local ordered conformation of residues within a polypeptide chain. These secondary structure elements include a helices and b sheets (strands!) 3 = spatial arrangement of these secondary structures like the a helices and b sheets. They can be connected via b turns and loops into a 3d fold. 4 = spatial arrangement of individual chains when they come together to form a well-defined 3d structure. Not all proteins experience all 4 levels necessarily. A small protein may only be comprised of one pol(cid:455)peptide a(cid:374)d the(cid:396)efo(cid:396)e does(cid:374)"t ha(cid:448)e a (cid:395)uate(cid:396)(cid:374)a(cid:396)(cid:455) st(cid:396)u(cid:272)tu(cid:396)e fo(cid:396) e(cid:454)a(cid:373)ple. The bond itself is planar due to resonance interactions and it adopts this trans conformation because it reduces steric interference and therefore is thermodynamically favorable. The exception however is for proline which is the only fully cyclic amino acid. In this case steric interference is minimal so it can exist in a cis-trans e(cid:395)uili(cid:271)(cid:396)iu(cid:373)!

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

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BMB 401 Lecture Notes - Lecture 3: Hemoglobin, Oligomer, Ramachandran Plot

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