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Chapter 31: Problem 8

The amino acid sequence deduced from the nucleotide sequence of a newly discovered human gene begins: MRSLLILVLCFLPLAALGK ... Is this a signal sequence? If so, where does the signal peptidase act on it? What can you surmise about the intended destination of this protein?

Short Answer

Expert verified
Yes, the given sequence appears to be a signal sequence. Signal peptidase is likely to act on the alanine residue. Given the presence of the signal sequence, the protein is likely destined for the endoplasmic reticulum.

Step by step solution

01

Identifying the signal sequence

First, observe that the given sequence begins with M (methionine), which is common for many proteins including those with signal sequences. Further, there is a stretch of hydrophobic amino acids, L, L, I, V, L, C, (leucine, leucine, isoleucine, valine, leucine, and cysteine), which are typical for a signal sequence. Therefore, it could be surmised that this is a signal sequence.
02

Identifying the action of signal peptidase

Signal peptidase would act to cleave this signal sequence. Its action is typically after a small and neutral amino acid, which would be A (alanine) in this case.
03

Determining the protein's destination

Based on the presence of the signal sequence, the intended destination of this protein is likely the endoplasmic reticulum (ER). This is because proteins that are intended for secretion or for placement in the plasma membrane typically contain an N-terminal signal sequence that directs the protein to the ER during translation.

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Most popular questions from this chapter

Not only is the Sec61p translocon complex essential for translocation of proteins into the ER lumen, it also mediates the incorporation of integral membrane proteins into the ER membrane. The mechanism for integration is triggered by stop-transfer signals that cause a pause in translocation. Figure 31.5 shows the translocon as a closed cylinder spanning the membrane. Suggest a mechanism for lateral transfer of an integral membrane protein from the protein-conducting channel of the translocon into the hydrophobic phase of the ER membrane.

Fluorescence resonance energy transfer (FRET) is a spectroscopic technique that can be used to provide certain details of the conformation of biomolecules. Look up FRET on the Web or in an introductory text on FRET uses in biochemistry, and explain how FRET could be used to observe conformational changes in proteins bound to chaperonins such as GroEL. A good article on FRET in protein folding and dynamics can be found here: Haas, E., 2005. The study of protein folding and dynamics by determination of intramolecular distance distributions and their fluctuations using ensemble and single-molecule FRET measurements. ChemPhysChem \(6: 858-870 .\) Studies of GroEL using FRET analysis include the following: Sharma, S., et al., 2008. Monitoring protein conformation along the pathway of chaperonin-assisted folding. Cell \(133: 142-153\); and \(\mathrm{Lin}, \mathrm{Z},\) et al. \(, 2008 .\) GroEL stimulates protein folding through forced unfolding. Nature Structural and Molecular Biology \(15: 303-311\)

The GroEL ring has a 5 -nm central cavity. Calculate the maximum molecular weight for a spherical protein that can just fit in this cavity, assuming the density of the protein is \(1.25 \mathrm{g} / \mathrm{mL}\)

As described in this chapter, the most common post-translational modifications of proteins are proteolysis, phosphorylation, methylation, acetylation, and linkage with ubiquitin and SUMO proteins. Carry out a Web search to identify at least eight other post translational modifications and the amino acid residues involved in these modifications.

(Integrates with Chapter 24 .) Acetyl-CoA carboxylase has at least seven possible phosphorylation sites (residues 23,25,29,76,77 \(95,\) and 1200 ) in its 2345 -residue polypeptide (see Figure 24.4 ). How many different covalently modified forms of acetyl-CoA carboxylase protein are possible if there are seven phosphorylation sites?
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