Drawn below is a schematic of a transmembrane protein.ExtracellularCellmembraneCytosolic side(a) From the list below, select the amino acid(s) that might by more common in the extracellular domain ofthis membrane protein and whose side- chain can form hydrogen bonds with the surrounding watermolecules. Explain why you selected this option(s).LysineSerinePhenylalanineMethionine(b) From the list below, select the amino acid(s) that would likely be found in the transmembrane/membrane spanning domain of this protein and whose side- chain interacts with the lipid bilayer.LysineSerinePhenylalanineMethionine

Amino acids are the building blocks of proteins which is linked by peptide/amide bond to form…

Answered: (a) From the list below, select the…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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(b) Hemoglobin is made of B-globin subunits. The first few mRNA nucleotides for B- globin are given by: (1) (iii) (iv) Write down the DNA sequence that has led to this mRNA and indicate the sense and non-sense strands and the polarity. CE Derive the polypeptide for the sequence using the table of the genetic code (Table Q1 below) and indicate the polarity of the polypeptide chain. First Position (5' end) U A single point mutation in mRNA sequence can cause sickle cell anemia by changing the amino acid Glu to Val. For the given mRNA, indicate the point mutations for the first Glu in the polypeptide sequence that can cause this disease. 5'-AUGGUCCACCUGACUCCUGAGGAGAAG...UGA-3' C The polypeptide of B-globin contains the amino acid Leu. Write down all the anticodons of the tRNA molecules that can potentially code for Val. Indicate the polarity of the anti-codon. A G Table 1. The Codons of the Genetic Code Second Position U Phe Phe Leu Leu Leu Leu Leu Leu Ile Ile Ile Met-Start Val Val Val…
The 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
Soap, phospholipids and cholesterol are all amphipathic molecules. Provide a drawing of each and label the polar and non polar areas.
2. The following tyrosine-phosphorylated polypeptides were tested as substrates of protein tyrosine phosphatase, an important enzyme in cellular signal transduction. The pTyr in bold signifies the tyrosine residue that is phosphorylated. The binding affinities of the polypeptide substrates to the enzyme were found to follow the order: (a) > (c) - (d) >> (b). (a) Asp-Ala-Asp-Glu-pTyr-Leu-lle-Pro-Gln-Gln-Gly (b) Pro-Val-Pro-Glu-pTyr-lle-Asn-Ala-Ser-Val (c) Asp-Ala-Glu-Glu-pTyr-Leu-Val-Pro-Gln-Gln-Gly (d) Asp-Asn-Leu-Tyr-pTyr-Trp-Asp-Glu-Asn-Ser-Ser In addition to the presence of the phosphorylated tyrosine residue, what amino acid a) properties of the polypeptides accounts for the relative order of binding affinities to the enzyme? b) the active site of the phosphatase enzyme that are responsible for the affinity of substrate binding? Assume a pH of 7.4 at the enzyme active site. (Note a phosphatase uses phosphate substrate) What amino acids have side chains that would indicate they are…
I’m having hard time drawing the graph to answer these questions can you show how to approach them?
A recent genome sequencing project for the bacterium Burkholderia mallei has identified a new protein with high similarity to the lysylphosphatidylglycerol flippase enzyme. A short section of the new protein sequence is shown below. TVEVNAPGDVQKALSELQQINDGRLDIRI (a) Are any reverse turns likely to be present? Explain your answer. (b) Are any beta-strands likely to be present? Explain your answer. (c) Are any alpha helices likely to be present? Explain your answer. (d) Is any supersecondary structure likely to be present? Explain your answer. (e) Identify two residues that are likely to be buried in the core of the folded protein. Explain your answer. (f) Identify two residues that are likely to be hydrogen bonded to each other. Explain your answer.
Membrane-spanning proteins are notoriously difficult to characterize by x-ray crystallography. Hollonut of VISA Toplon a. Explain how the information in the diagrams below can be used in the detection of membrane- spanning proteins consisting of alpha helices, given that the lipid portion of a typical bilayer is approximately 30 Å thick. Amino terminus 5.4 A (3.6 residues) b. Identify and briefly describe how the features of a transmembrane protein composed of ß-sheets differ from that above.
6) Proteins can be modified by phosphorylation, which adds a phosphate group to the hydroxyl group of serine, threonine, or tyrosine residues. The R-group for phosphoserine is shown at right. A) The image below is an Isoelectric focusing strip that shows the unphosphorylated protein-of-interest (in blue). To which side of the unphosphorylated protein would you expect to see the phosphorylated protein? (Draw an arrow to indicate direction). Briefly justify your answer. un-phosphorylatable: Low pH Justify: B) To study the effects of phosphorylation, researchers often mutate a Ser/Thr to appear as though it is always phosphorylated or never phosphorylated at a particular site. What amino acid substitution should you use to preserve similar dimensions as Ser (or Thr) but make the side chain appear to be: constitutively (always) phosphorylated: Justify: Ser or Thr → O O=P-O O I CH₂ Ser or Thr➜ Phosphoserine High pH
Many transmembrane proteins have a large series of hydrophobic amino acids such as those in the middle of the protein (around b). Why would this make sense, and where would you expect these to be located in the final protein structure?
Do you expect a Pro → Gly mutation in a surface-loop region of a globular protein to be stabilizing or destabilizing? Assume the mutant folds toa native-like conformation. Explain your answer in terms of the predictedenthalpic and entropic effects of the mutation on the ∆G for protein foldingcompared to ∆G of folding for the wild-type protein
(c) The tube and cylinder diagram to the right illus- trates schematically the potassium channel protein from a bacterium. This channel protein consists of four identical polypeptide chains each comprised of 119 residues. The cyan ribbon illustrates only two of the polypeptide chains. The relative positions of 4 α-helices, one from each poly- peptide chain, are shown as cylinders. The red sphere in the central part of the diagram shows the position of a potas- sium ion identified by X-ray structure analysis. A cesium ion (green sphere) was also found to be stabilized in the same position when cesium chloride was introduced into the crys- tals. The cylinders each represent an α-helix running from Tyr62 to Thr74. Considering the position of the potassium ion, in- dicate on one of the cylinders at which end of the cylinder residue Tyr62 is found and at which end residue Thr74 is found. Explain the basis of your answer? Ala23 Thr119 (d) The N- and C-terminal residues of one of the…
Bovine insulin is composed of two polypeptide chains that are linked together covalently. The two chains have the following sequences: GIVEQCCASVCSLYQLENYCN - A chain FVNQHLCGSHLVEALYLVCGERGFFYTPKA - B chain a. Through which amino acids are these two chains linked together covalently? b. How many different ways can these two chains be linked? c. Of the different connectivities you enumerated in part b, which is the biologically active form?

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