Category: Biochemistry

PDB: 2PX6
The assignment should contain at least three figures: one (1) highlighting the secondary structure and two (2) active site images. Each Figure must have a caption for the active site images, be sure to describe the types of interactions you are showing in the image, and refer to any specific amino acid residues (involved in catalysis or inhibitor binding) by their amino acid number. I included an example on the file for how the assignment should look like. The three images need to be created using PyMOL for PDB: 2PX6 and using the white background.
Active site and enzyme-drug interactions
A. Include an image of the chemical structure of your drug molecule.
B. Create at least two PyMOL figures zoomed in on just the active site of your
enzyme. List the catalytic residues (e.g., Ser261, His342). Clearly show these
residues. Highlight other molecules in the structure that are involved in the reaction
catalyzed by your enzyme (substrates, products, cofactors, coenzymes, etc.). You
may hide the bound drug/inhibitor, or use a secondary, unbound structure to create
this image.
C. Zoom in on the drug bound to your enzyme (note that it may be in the active site, or
bound to another part of the protein, depending on the inhibitor type). Illustrate all
noncovalent interactions with measurements between this molecule and the
enzyme using at least one PyMOL figure. Include all hydrogen bonds and salt
bridges, clearly distinguishing these types of interactions. Also, show one nonpolar
interaction (3.3-4.0 Angstrom range).
D. Describe all of the interactions, referencing the specific amino acid side chain that is
involved in the interaction by its three-letter code and residue number and describing
the type of interaction with the drug. To save space, you may group them by type of
interaction.
VII. Figure Captions
For each figure, include a caption or description that helps the viewer understand
what they are seeing. A good figure caption briefly describes:
1. The figure content
2. Any coloring/labeling schemes to help the viewer interpret the image.

Calculate the molality of hydrochloric acid solution containing 48.5 g of hydrochloric acid in 248g of water.The molar mass of hydrochloric acid is 36.458 /mol

Here is the link of the assignment:https://drive.google.com/file/d/1vMBpHw8sfodWzya4u… Please read carefully. I also need Turnitin report with it. Rubric Name: Case Connections Written Response (Unit 1 and Unit 3)
CriteriaExcellentGood
Adequate
Attempted
Not Evident
Criterion Score
Logic and Understanding: First Case
22.5 points
Student logic is correct with clear rationalizations and references of their responses. All other choices are refuted using appropriate logic.
19 points
Student logic is correct with clear rationalizations and references; some but not all choices are refuted.
15.75 points
Student attempts to synthesize thoughts, but logic is flawed; Additional choices are not refuted or poorly explained.
12 points
Student does not synthesize thoughts and only provides a correct answer or logic is flawed.
0 points
Score of Logic and Understanding: First Case,
/ 22.5
Accuracy: First Case
20 points
Student accurately describes and applies appropriate Biochemistry concepts/details including the relevant metabolic pathways, enzymes, hormones and regulation, as related to the course material.
17 points
Student accurately describes all concepts/details as related to the course material.
14 points
Student correctly describes most concepts, but one or two may be incorrect or insufficient.
11 points
Many concepts are incorrectly or insufficiently described.
0 points
Score of Accuracy: First Case,
/ 20
Logic and Understanding: Second Case
22.5 points
Student logic is correct with clear rationalizations and references of their responses. All other choices are refuted using appropriate logic.
19 points
Student logic is correct with clear rationalizations and references; some but not all choices are refuted.
15.75 points
Student attempts to synthesize thoughts, but logic is flawed; Additional choices are not refuted or poorly explained.
12 points
Student does not synthesize thoughts and only provides a correct answer or logic is flawed.
0 points
Score of Logic and Understanding: Second Case,
/ 22.5
Accuracy: Second Case
20 points
Student accurately describes and applies appropriate Biochemistry concepts/details including the relevant metabolic pathways, enzymes, hormones and regulation, as related to the course material.
17 points
Student accurately describes all concepts/details as related to the course material.
14 points
Most concepts are correctly described, but one or two may be incorrect or insufficient.
11 points
Many concepts are incorrectly or insufficiently described.
0 points
Score of Accuracy: Second Case,
/ 20
Quality of Writing
15 points
Ideas are well organized and writing is clear and free of mechanical errors. All sources are cited with in-text citations, a link to the article, and AMA format for each resource.
12.75 points
Writing is well organized with no sentence level errors that impede meaning; source material is properly cited using AMA conventions.
10.5 points
Writing is mostly clear with minimal organizational or sentence-level errors that impede meaning; source material is cited but with some errors in AMA style.
8.25 points
Writing is often unorganized and/or has significant sentence errors that impede communication; source material is inconsistently cited with significant errors in AMA style.
0 points
Score of Quality of Writing,
/ 15

Read the case report and be able to critique and analyze the methods, statistics and results. Find limitations and strengths
Find reliable data about the topic and background information to support your critique and analysis.
Approach it as a journal club assignment.
Be able to resume this report and further refer to past studies and cite them as well.

Read the case report and be able to critique and analyze the methods, statistics and results. Find limitations and strengths
Find reliable data about the topic and background information to support your critique and analysis.
Approach it as a journal club assignment.
Be able to resume this report and further refer to past studies and cite them as well.

The attachments below is the instructions needed for this notebook to be done (in word document)+ the experiments needed to be add in the notebook please write the experiments in the same order (note that the attachment below has the experiments in the wrong order so please start from the last experiment in the pdf -which is the actual first experiment- and end with the first experiment in the pdf – which is the actual last experiment-)

in the attachment below you will find the part that is already done (step 3 final draft 2 )and the other attachment has the information needed for this part that I need to work on now (step 4)
+ please not that I need you to only write
1-mutations or other impairments to the structural features
2-conclusions
3-acknowledge

Create one powerpoint slide for the poster. The poster should contain at least three figures: one (1) highlighting the secondary structure and two (2) active site images. Each Figure must have a caption—for the active site images, be sure to describe the types of interactions you are showing in the image, and refer to any specific amino acid residues (involved in catalysis or inhibitor binding) by their amino acid number. The PDB is 2Z5X. I included an example of how the poster should look like for the PyMOL image part in the file.
Full instruction:
A. Go to the RCSB PDB and examine all ligands bound to the protein structure. One of these
will be your drug, but there may be others. List all of the ligands and their role (e.g.,
substrate, product, coenzyme, inhibitor, cofactor, ions unrelated to function etc.) Note that
the ligands are listed on the structure’s PDB entry page. Insert at least one PyMOL image
zoomed out to show your entire enzyme. Be sure that each of these molecules is clearly
visible in your snapshot; you might label these in PyMOL or in the program you create
your poster in.
Some ligands are not relevant to your enzyme’s biological function (i.e., are only there due
to crystallization conditions and/or are not located at a site in the enzyme where they give
information about the true substrates, products, cofactors, or regulators). You will need to
read the manuscript and potentially the experimental procedures to figure out a molecule’s
role in the structure.
B. Create at least two PyMOL snapshots zoomed in on just the active site of your enzyme.
List the catalytic residues (e.g., Ser261, His342). Clearly show these residues in your
snapshots. Highlight other molecules in the structure that are involved in the reaction
catalyzed by your enzyme (substrates, products, cofactors, coenzymes, etc.). You may
hide the bound drug/inhibitor to create this image.
C. Zoom in on the drug bound to your enzyme (note that it may be in the active site, or bound
to another part of the protein, depending on the type of inhibitor). Name the molecule that
you have chosen. Illustrate all noncovalent interactions between this molecule and the
enzyme using at least one PyMOL snapshot. Include hydrogen bonds, hydrophobic
packing, and salt bridges. Describe all of the polar interactions, referencing the specific
amino acid side chain that is involved in the interaction by its three-letter code and residue
number and describing how it contacts the drug. Also highlight one nonpolar interaction. have attached exmples

Create one powerpoint slide for the poster. The poster should contain at least three figures: one (1) highlighting the secondary structure and two (2) active site images. Each Figure must have a caption—for the active site images, be sure to describe the types of interactions you are showing in the image, and refer to any specific amino acid residues (involved in catalysis or inhibitor binding) by their amino acid number. The PDB is 2Z5X. I included an example of how the poster should look like for the PyMOL image part in the file.
Full instruction:
A. Go to the RCSB PDB and examine all ligands bound to the protein structure. One of these
will be your drug, but there may be others. List all of the ligands and their role (e.g.,
substrate, product, coenzyme, inhibitor, cofactor, ions unrelated to function etc.) Note that
the ligands are listed on the structure’s PDB entry page. Insert at least one PyMOL image
zoomed out to show your entire enzyme. Be sure that each of these molecules is clearly
visible in your snapshot; you might label these in PyMOL or in the program you create
your poster in.
Some ligands are not relevant to your enzyme’s biological function (i.e., are only there due
to crystallization conditions and/or are not located at a site in the enzyme where they give
information about the true substrates, products, cofactors, or regulators). You will need to
read the manuscript and potentially the experimental procedures to figure out a molecule’s
role in the structure.
B. Create at least two PyMOL snapshots zoomed in on just the active site of your enzyme.
List the catalytic residues (e.g., Ser261, His342). Clearly show these residues in your
snapshots. Highlight other molecules in the structure that are involved in the reaction
catalyzed by your enzyme (substrates, products, cofactors, coenzymes, etc.). You may
hide the bound drug/inhibitor to create this image.
C. Zoom in on the drug bound to your enzyme (note that it may be in the active site, or bound
to another part of the protein, depending on the type of inhibitor). Name the molecule that
you have chosen. Illustrate all noncovalent interactions between this molecule and the
enzyme using at least one PyMOL snapshot. Include hydrogen bonds, hydrophobic
packing, and salt bridges. Describe all of the polar interactions, referencing the specific
amino acid side chain that is involved in the interaction by its three-letter code and residue
number and describing how it contacts the drug. Also highlight one nonpolar interaction. have attached exmples

PyMOL Project
Create one powerpoint slide for the poster. The poster should contain at least three figures: one (1) highlighting the secondary structure and two (2) active site images. Each Figure must have a caption—for the active site images, be sure to describe the types of interactions you are showing in the image, and refer to any specific amino acid residues (involved in catalysis or inhibitor binding) by their amino acid number. The PDB is 2Z5X. I included an example of how the poster should look like for the PyMOL image part in the file.
Full instruction:
A. Go to the RCSB PDB and examine all ligands bound to the protein structure. One of these
will be your drug, but there may be others. List all of the ligands and their role (e.g.,
substrate, product, coenzyme, inhibitor, cofactor, ions unrelated to function etc.) Note that
the ligands are listed on the structure’s PDB entry page. Insert at least one PyMOL image
zoomed out to show your entire enzyme. Be sure that each of these molecules is clearly
visible in your snapshot; you might label these in PyMOL or in the program you create
your poster in.
Some ligands are not relevant to your enzyme’s biological function (i.e., are only there due
to crystallization conditions and/or are not located at a site in the enzyme where they give
information about the true substrates, products, cofactors, or regulators). You will need to
read the manuscript and potentially the experimental procedures to figure out a molecule’s
role in the structure.
B. Create at least two PyMOL snapshots zoomed in on just the active site of your enzyme.
List the catalytic residues (e.g., Ser261, His342). Clearly show these residues in your
snapshots. Highlight other molecules in the structure that are involved in the reaction
catalyzed by your enzyme (substrates, products, cofactors, coenzymes, etc.). You may
hide the bound drug/inhibitor to create this image.
C. Zoom in on the drug bound to your enzyme (note that it may be in the active site, or bound
to another part of the protein, depending on the type of inhibitor). Name the molecule that
you have chosen. Illustrate all noncovalent interactions between this molecule and the
enzyme using at least one PyMOL snapshot. Include hydrogen bonds, hydrophobic
packing, and salt bridges. Describe all of the polar interactions, referencing the specific
amino acid side chain that is involved in the interaction by its three-letter code and residue
number and describing how it contacts the drug. Also highlight one nonpolar interaction.Attached good examples