A lysine is burined inside a protein surrounded by hydrophobic resiudes, how does this affect the pKa of lysine?
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A lysine is burined inside a protein surrounded by hydrophobic resiudes, how does this affect the pKa of lysine?
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- A lysine is on the surface of a protein near an arginine, how does this alter pKa of lysineAssume that the 3 polypeptide strands shown below form a parallel B-sheet. Select amino acids AA1, AA2, and AA3 so that the parallel B-sheet is amphipathic and remains stable. Glu-lle-Asn-AA1-Cys-Val Ser-AA2-GIn-Leu-Lys-Phe Lys-Met-Cys-Leu-AA3-Val O AA1 = Pro, AA2 = Leu, AA3 = lle O AA1 = Val, AA2 = Leu, AA3 = Asn O AA1 = Ala, AA2 = Gly, AA3 = Leu AA1 = Phe, AA2 = Arg, AA3 = Ala O OThe activity provides you with a version of the NGF pathway, an example of a RTK. All of the proteins involved can be in ON/OFF states. Using this cell signaling pathway you will be asked a variety of questions to determine how the molecules are regulated, but also how a cell would respond if this cell signaling party steps were interrupted or activated. Neural Growth Factir (NGF) Ras- Ras- GDP GTP Trk-A Ras-GEF braf braf МЕК МЕК ERK ERK ERK ERK STAT STAT Spiouty DNA Nucleus Cytosol
- On average, how many phosphoanhydride bonds (P;-P; bonds) are directly hydrolyzed in thecourse of synthesizing a 200 amino acid protein? Assume that you begin with the mature mRNA,ribosomal subunits, tRNAs, free amino acids, and all necessary factors.What is the length in AA’s of the LilP protein? Assume fMet is NOT CLEAVED. Write out the sequence of the polypeptide in AA: use the three letter notation, e.g. Met-Ser-Pro-In the protein adenylate kinase, the C-terminal region has the sequence Val-Asp-Asp-Val-Phe- Ser-Gin-Val-Cys-Thr-His-Leu-Asp-Thr-Leu-Lys The hydrophobic residues in this sequence are presented in boldface type. Use helix wheel to demonstrate this peptide is an amphipathic helix.
- One of the amino acid sequences in the lysozyme protein from the bacterial virus T4 studiesby Streisinger and co-worker was .... Lys – ser – pro – ser – leu – asn – ala – ala – lys. Thisparticular amino acid was found to have changed to lys – val – his –his –leu –met –ala –ala–lys... as a result of a single nucleotide deletion and addition approximately 15 bases apartin the mRNA. Which base was deleted and which was added? Give the altered sequence of bases inthe altered amino acid.One of the amino acid sequences in the lysozyme protein from the bacterial virus T4 studiesby Streisinger and co-worker was .... Lys – ser – pro – ser – leu – asn – ala – ala – lys. Thisparticular amino acid was found to have changed to lys – val – his –his –leu –met –ala –ala–lys... as a result of a single nucleotide deletion and addition approximately 15 bases apartin the mRNA.a. What is the sequence of the nucleotides that produce the original protein.b. Which base was deleted and which was added? Give the altered sequence of bases inthe altered amino acid.Describe the general structure of a type 2 alpha helix protein. Explain how type 2 alpha helix transmembrane domains can be used to form pathways for large polar and charged molecules to traverse the lipid bilayer of the cell membrane.
- A protein substrate is known to be multi-monoubiquitinated. The control lane "C" in the SDS-PAGE gel shows a properly ubiquitinated protein substrate. Please draw out what the lane would look like if all lysine residues except for one are mutated to alanine residues in the protein substrate. Use one sentence to explain your rationale. C 1 Protein Substrate ||||Amino acids project from each polypeptide backbone in a β-sheet in an alternating fashion (oneabove the plane and the next below the plane – see Fig 3.8B). Consider the following proteinsequence: Leu-Lys-Val-Asp-Ile-Ser-Leu-Arg-Leu-Lys-Ile-Arg-Phe-Glu.a. Is there a pattern to these amino acids? If so, what is it? b. What does this sequence of amino acids mean for the hydrophobicity/hydrophilicity of theresulting β-sheet? c. Can you make a prediction about how the β-sheet will be arranged in higher levels of protein structure? If so, what prediction would you make?In the peptidoglycan layer of bacterial cells: give a reason why the tetrapeptide side chain is only binding to the NAM molecule and not to the NAG?