Chapter 6, Proteins: Secondary, Tertiary, and Quaternary Structure Video Solutions, Biochemistry

Problem 1

The central rod domain of a keratin protein is approximately 312 residues in length. What is the length (in $\AA$ ) of the keratin rod domain? If this same peptide segment were a true $\alpha$ -helix, how long would it be? If the same segment were a $\beta$ -sheet, what would its length be?

Ronald Prasad

Numerade Educator

01:09

Problem 2

A teenager can grow 4 inches in a year during a "growth spurt." Assuming that the increase in height is due to vertical growth of collagen fibers (in bone), calculate the number of collagen helix turns synthesized per minute.

Hast Aggarwal

Numerade Educator

11:40

Problem 3

Discuss the potential contributions to hydrophobic and van der Waals interactions and ionic and hydrogen bonds for the side chains of Asp, Leu, Tyr, and His in a protein.

Khalida Dawar

Numerade Educator

00:39

Problem 4

Pro is the amino acid least commonly found in $\alpha$ -helices but most commonly found in $\beta$ -turns. Discuss the reasons for this behavior

Shazia Naz

Numerade Educator

01:04

Problem 5

For flavodoxin (pdb id $=$ 5NLL), identify the right-handed cross-overs and the left-handed cross-overs in the parallel $\beta$ -sheet.

Kelsey Dondelinger

Numerade Educator

01:06

Problem 6

Choose any three regions in the Ramachandran plot and discuss the likelihood of observing that combination of $\phi$ and $\psi$ in a peptide or protein. Defend your answer using suitable molecular models of a peptide.

Sohini Lahiri

Numerade Educator

01:33

Problem 7

A new protein of unknown structure has been purified. Gel filtration chromatography reveals that the native protein has a molecular weight of 240,000 . Chromatography in the presence of $6 M$ guanidine hydrochloride yields a single peak corresponding to a protein of $M_{r} 60,000 .$ Chromatography in the presence of $6 M$ guanidine hydrochloride and $10 \mathrm{m} M$ $\beta$ -mercaptoethanol yields peaks for proteins of $M_{r} 34,000$ and 26,000 Explain what can be determined about the structure of this protein from these data.

Madi Sousa

Numerade Educator

01:18

Problem 8

Two polypeptides, $A$ and $B$, have similar tertiary structures, but $A$ normally exists as a monomer, whereas $\bar{B}$ exists as a tetramer, $B_{4}$ What differences might be expected in the amino acid composition of A versus B?

Banhishikha Sinha

Numerade Educator

03:19

Problem 9

The hemagglutinin protein in influenza virus contains a remarkably long $\alpha$ -helix, with 53 residues.
a. How long is this $\alpha$ -helix (in nm)?
b. How many turns does this helix have?
c. The typical residue in an $\alpha$ -helix is involved in two H bonds. How many $\mathrm{H}$ bonds are present in this helix?

Ronald Prasad

Numerade Educator

01:39

Problem 10

It is often observed that Gly residues are conserved in proteins to a greater degree than other amino acids. From what you have learned in this chapter, suggest a reason for this observation.

Prashant Bana

Numerade Educator

01:06

Problem 11

Which amino acids would be capable of forming H bonds with a lysine residue in a protein?

Lottie Adams

Numerade Educator

01:52

Problem 12

Poly-L-Glutamate Structure Poly-Lglutamate adopts an $\alpha$ -helical structure at low $\mathrm{pH}$ but becomes a random coil above pH $5 .$ Explain this behavior.

Danielle Ashley

Numerade Educator

02:30

Problem 13

Imagine that the dimensions of the alpha helix were such that there were exactly 3.5 amino acids per turn instead of $3.6 .$ What would be the consequences for coiled-coil structures?

Shiksha Dutta

Numerade Educator

03:52

Problem 14

In addition to domains and modules, there are other significant sequence patterns in proteins - known as linear motifs - that are associated with a particular function. Consult the biochemical literature to answer the following questions:
$\bullet $What are linear motifs?
$\bullet $How are they different from domains?
$\bullet $ What are their functions?
$\bullet $How can they be characterized?
There are several papers that are good starting points for this problem:
Neduva, V., and Russell, R., 2005. Linear motifs: evolutionary interaction switches. FEBS Letters $579: 3342-3345$

Gibson, $\mathrm{T},, 2009$. Cell regulation: determined to signal discrete cooperation. Trends in Biochemical Sciences $34: 471-482$
Diella, F., Haslam, N., Chica,, C. et al., 2009. Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Frontiers of Bioscience $13: 6580-6603$

Sana Riaz

Numerade Educator

00:55

Problem 15

How do proteins interact? When one protein binds to another, one or both changes conformation. Two hypotheses have been proposed to describe such binding: In the induced fit model, the interaction between a protein and a ligand induces a conformation change (in the protein or ligand) through a stepwise process. In the conformational selection model, the unliganded protein (in the absence of the ligand) exists as an ensemble of conformations in a dynamic equilibrium. The binding ligand interacts preferentially with one among many of these conformations and shifts the equilibrium in favor of the selected conformation. Three recent papers shed light on this question:
Boehr, D., and Wright, P. E., 2008. How do proteins interact? Science $320: 1429-1430$
Gsponer, J., et al., 2008. A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction. Structure $16: 736-746$ Lange, $O .,$ et al., $2008 .$ Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science $320: 1471-1475$
Consult these papers and answer the following questions:
$\bullet$What proteins were studied in these papers? $\bullet$What techniques were used, and what time scales of protein motion were studied?

$\bullet$What were the conclusions of these papers, and how do these results illuminate the choice between induced fit and conformational selection in protein-protein interactions?

Josee Pacheco

Numerade Educator

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Problem 16

How do proteins accomplish conformational changes? How is it that proteins convert precisely and efficiently from one conformation to another? Recall from Figure 6.34 that any folding/unfolding transition must involve movement across a free-energy landscape, and try to imagine the nature of a conformational transition. Are bonds formed and broken along the way? What kinds of bonds and interactions might be involved? Suggest how such conformational transitions might occur. One reference that will be useful in this regard is:
Boehr, D., 2009. During transitions proteins make fleeting bonds. Cell $139: 1049-1051$

Brett Donadeo

Numerade Educator

01:11

Problem 17

Who was Herman Branson? What was his role in the elucidation of the structure of the $\alpha$ -helix? Did he receive sufficient credit and recognition for his contributions? And how did the rest of his career unfold? Do a Google search on Herman Branson to learn about his life, and read the article by David Eisenberg under Further Reading. You may also wish to examine the original paper by Pauling, Corey, and Branson, as well as the following Web site:
Pauling, L., Corey, R. B., and Branson, H. R., 1951. The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proceedings of the National Academy of Sciences, USA $37: 235-240$

Joanna Quigley

Numerade Educator

01:01

Problem 18

Consider the following peptide sequences:
EANQIDEMLYNVQCSLTTLEDTVPW LGVHLDITVPLSWTWTLYVKL
QQNWGGLVVILTLVWFLM
CNMKHGDSQCDERTYP YTREQSDGHIPKMNCDS AGPFGPDGPTIGPK
Which of the preceding sequences would be likely to be found in each of the following:
a. A parallel $\beta$ -sheet
b. An antiparallel $\beta$ -sheet
c. $\quad$ A tropocollagen molecule
d. The helical portions of a protein found in your hair

Narayan Hari

Numerade Educator

01:27

Problem 19

To fully appreciate the elements of secondary structure in proteins, it is useful to have a practical sense of their structures. On a piece of paper, draw a simple but large zigzag pattern to represent a $\beta$ -strand. Then fill in the structure, drawing the locations of the atoms of the chain on this zigzag pattern. Then draw a simple, large coil on a piece of paper to represent an $\alpha$ -helix. Then fill in the structure, drawing the backbone atoms in the correction locations along the coil and indicating the locations of the $\mathrm{R}$ groups in your drawing.

Lottie Adams

Numerade Educator

00:16

Problem 20

The dissociation constant for a particular protein dimer is 1 micromolar. Calculate the free energy difference for the monomer-to-dimer transition.

Dr. Satish Ingale

Numerade Educator

01:10

Problem 21

Consider a protein that can exist in two forms: folded and unfolded. Calculate the free energy difference at $298 \mathrm{K}$ between a state in which $80 \%$ of the protein is folded and a state in which $80 \%$ of the protein is unfolded.

Lottie Adams

Numerade Educator

00:41

Problem 22

Using the ActiveModel for concanavalin A, discuss an example in which a difference in protein primary structure leads to a difference in protein function.

Yokshitha Reddy Bathula

Numerade Educator

01:13

Problem 23

Describe the secondary structure of each subdomain of malonylCoA: ACP transferase. Explain the difference between parallel and antiparallel beta sheets.

Sohini Lahiri

Numerade Educator