18. When oxygen binds to the heme group, by how many angstroms does the Fe2+ appear to shift?19. How far in Angstroms does the F8 histidine nitrogen appear to shift when oxygens binds to the Fe²+?20. Approximately how far in Angstroms does the Leu F7 appear to shift when oxygen binds to heme?21. Approximately how far in Angstroms does Helix F appear to shift when oxygen binds to heme? Whatwill happen to other helices in the subunit when helix F moves?

The heme group is a prosthetic group in oxygen-binding protein. Its primary function is to bind…

Answered: 8. When oxygen binds to the heme group,…

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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1. What is the length in AA’s of the LilP protein? Assume fMet is NOT CLEAVED. 2. Write out the sequence of the polypeptide in AA: use the three letter notation, e.g. Met-Ser-Pro-
Where do you predict the N- and C-termini are located for Max? Match the words in the left column to the appropriate blanks in the sentences on the right. electrostatic dispersion negative C-terminus positive positively negatively N-terminus The Reset Help is interacting with the DNA. The first reason for this is because the a-amino group is positively charged and will interact favorably with the of the charge on the phosphodiester backbone of the DNA. The second reason is that this orientation also situates the partial end of the helical macrodipole for favorable interactions with the charged phosphodiester backbone of the DNA
2. The diagram to the right shows the change in the structure of the C-terminal portion of each of the ẞ-subu- nits of human hemoglobin (HbA) in the oxyHb to deox- yHb or R-to-T transition. The hydrogen bonding interac- tion of the C-terminal ẞHis 146 residue with the side chain of Asp94, highlighted by the red ellipse, has been shown to be responsible for a major portion of the proton uptake associated with the Bohr effect. Treatment of HbA with the enzyme carboxypeptidase A (CPA) results in loss of the C-terminal ẞHis 146 and ẞTyr145 residues of the ẞ- subunits. (a) ( ) Draw a Hill plot [log(Y/[1-Y]) vs. log(pO2), Y = fraction of heme groups occupied by O2] to compare the values of the Hill coefficient nн and the O2-binding affinity at pH 7.4 of normal HbA before and after treat- ment of with CPA. (b) (' ) How will the plot for CPA-digested HbA change at pH 7.2? (c) 1 Hi5146 HN- ✓ Low PK B-chain. CH2 CH-NH-CO-CH-NH- CH₂ Tyr145 он HbO2 or R state Туг145 CH-CH2- OH co NH CH CH₂ His…
8. NMR measurements have shown that poly-lysine is a random coil at pH 7 but becomes a helix when the pH is raised above 10. If the same type of folding behavior is observed, what should be the pH dependence of poly-glutamate? A) Helix at pH 7 but random coil at pH 10 B) Random coil at pH 3 but helix at pH 7 C) Random coil at pH 7 but helix at pH 10 D) Helix at pH 3 but random coil at pH 7
6
If you want to purify a DNA-binding protein from a crude mixture of proteinsat pH 7, should you use a DEAE-cellulose or a CM-cellulose column(as shown)? Briefly explain your reasoning.
How will the temperature affect the sequence of proteins when ribosome stalling is done in vivo? 2 possible results? how might the temperature affect the sequence of proteins? is there less ribosome stalling at all sites or some locations specifically and why? where is the stalling happening specifically? is there less stalling at all sites or some locations? why might that be? how can raisning the tempreture affect the hydrogen bonds in the ribosome? how can raising the tempreture affect the hydrogen bonds in the ribosome?
Please don't provide handwritten solution .....
(a) 1 Normalized fluorescence 0.8 0.6 0.4 0.2 0 1.7.0- 50 55 OM 0.100 M 0.200 M 0.300 M 0.500 M 1.00 M 2.00 M Where is fully folded protein? • Where is fully unfolded protein? • Where is partially folded protein? 60 A 65 Temp. (°C) 70 75 80 To what does SYPRO orange bind? • Why does fluorescence increase as a function of temperature? • Define a melting temperature for a protein. • Demonstrate how an estimated melting temperature of the protein in zero molar ligand can be determined. • What is the effect of increasing the molar concentration on melting temperature for this protein? Why is melting temperature a useful measurement to make for a protein especially if you are interested in protein aggregation?
17. How would you computationally predict the thermodynamic stability of a long, extended RNA helix? Please explain in 1 sentence how structural "favorability" can be predicted
Compare the experimentally defined locations of the amino acids from the SCAM data with the positions predicted in the topological model. Comment on whether these experimental data are consistent with the topology model; do the data support this model? If not, how do they differ?
1.Draw these phosphorylated structures as they would be connected in a polinucleotide (e.g.RNA) in the order A-B. / Show how they combine to form the polynuleotide (i.e. only the end product). Show at any one of these structures where the glycosidic bond occurs 2.Sanger sequencing revealed the sequence of an oligonucleotide to be: d-AGATGCCTGACT. Draw a diagram of the gel banding pattern post capillary electrophoresis i.e. where on the gel would the fragments feature

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