Topic: HEMOGLOBIN This course is designed to introduce students to the various...

Question

Topic: HEMOGLOBIN

This course is designed to introduce students to the various technologies and their application to understanding the structure and function and of proteins. For your "
Protein Investigation Project
" you are to apply the knowledge gained throughout the semester to an in depth study of a human protein of your choosing. The protein could be from the sensory system (taste, sight, hearing, smell, touch) or other body systems such as the immune system.

TheProtein Investigation Projectis an individual project, but students canOpt-In to work together to prepare and submit as a group (2 - 4 students). Groups must notify the Course-Coordinator (A/Prof Paul Ramsland) by the end of Week 4. For group projects both assignments are to be co-developed and co-authored. Only one student from the group needs to submit the assignments.

During the semester you are to read primary peer-reviewed literature (original research articles), gain an understanding of the experiments and findings of these works and put this information together as a review of the literature in your "Final Project Report". You are also expected to use various bioinformatics tools and online databases to examine the relationship between the primary sequence of your protein, secondary structure, post-translational modifications, relationship to other proteins (network) and structure of the protein. This is the investigation part of your project.It is expected to have between 2 and 5 bioinformatic and database analysis aspects to your project.You are encouraged to explore various public source datasets to produce your written report in consultation with the teaching team and after demonstration of various data sources or predictive tools in training sessions that will be run during the semester.

The final written report should be around 2000 words (reports of 1500 to 2500 words are acceptable) and include illustrations (figures and tables) that provide a narrative about the protein you have selected. The scope and layout of your final report is flexible and you will receive feedback on your proposed plan as part of another assessable task (Project Report Outline). References could be in any format of a typical peer-reviewed journal (e.g., Journal of Biological Chemistry) and should be presented consistently. Reports should be written in scientific English and will vetted for plagiarism through Turnitin (<20% match="" is="" normally="">

Rubric

Final Project Report

Criteria

Ratings

Pts

This criterion is linked to a learning outcome

Title and Abstract/Summary

2.5
to >2.0
Pts

Exemplary

A clear descriptive title that immediately reflects the main content of the review and captures attention of the reader. A concise abstract/summary that provides a compelling narrative that generates interest in the reader.

2
to >1.5
Pts

Achieved

A clear descriptive title that relates to the topic of the review. A concise abstract/summary that captures the context, content and conclusions of the review.

1.5
to >0.0
Pts

Developing

A title that does not completely reflect the content of the review. An abstract/summary that only partly covers the topics discussed in the review.

0Pts

Not Demonstrated

Lack of a clear or missing title or abstract

2.5pts

This criterion is linked to a learning outcome

Introduction

5
to >4.0
Pts

Exemplary

The topic is introduced, and groundwork is laid as to the direction of the report. References are highly appropriate and information is correct.

4
to >3.0
Pts

Achieved

Readers are aware of the overall problem, challenge, or topic to be examined. Clear use of referencing and information generally correct.

3
to >0.0
Pts

Developing

Readers are somewhat aware of the overall problem, challenge, or topic to be examined. Some evidence for referencing of the information presented.

0Pts

Not Demonstrated

Neither implicit nor explicit reference is made to the topic that is to be examined. Information presented is not references or is incorrect.

5pts

This criterion is linked to a learning outcome

Content Coverage

20
to >16.0
Pts

Exemplary

The appropriate content in consideration is covered in depth without being redundant; High quality information and in sufficient quantity; Excellent use of online bioinformatics tools and databases to support the project; The content correctly related to the topic in each section of the review.

16
to >12.0
Pts

Achieved

All major sections of the pertinent content are included, but some areas could still be covered in more detail; Quantity and quality of information generally suitable; Strong use of online bioinformatics tools and databases to support the project; The content correctly relates to the topic selected in some sections of the review.

12
to >0.0
Pts

Developing

Some sections of the pertinent content are included, but not covered in as much depth, or as explicit, as expected; Information may be insufficient or excessive in parts; Use of online bioinformatics tools and databases to support the project somewhat lacking in scope and integration; The content poorly relates to the topic selected.

0Pts

Not Demonstrated

Major sections of pertinent content have been omitted or greatly run-on; There is no indication of an attempt to synthesize the information; No evidence for use of online bioinformatics tools and databases to support the project; The content is of little significance to the topic selected.

20pts

This criterion is linked to a learning outcome

Conclusions

2.5
to >2.0
Pts

Exemplary

The author was able to make succinct and precise conclusions based on the body of research article; Insights and relevance of the information is clear and well-articulated.

2
to >1.5
Pts

Achieved

The author provides concluding remarks that show an analysis and synthesis of ideas occurred. Some of the conclusions, however, are not supported in the body of the research article.

1.5
to >0.0
Pts

Developing

The author provides some concluding remarks, however these are of poor quality and are not supported in the body of the research article.

0Pts

Not Demonstrated

There is no indication of an attempt to make a conclusion based on the literature under review; New information is introduced in the conclusion.

2.5pts

This criterion is linked to a learning outcome

Images, Tables and References

5
to >4.0
Pts

Exemplary

Visually appealing, creative, relevant original image(s) and/or table(s) are created by the author and the originality is identified by author. All references are of high quality and appropriate.

4
to >3.0
Pts

Achieved

Relevant images(s) and/or table(s) obtained externally and appropriately sourced (not an original image or table); OR, reasonable and somewhat relevant original image(s) and table(s) are created by the author and the originality is identified by author. Most references are suitable and of high quality.

3
to >0.0
Pts

Developing

Image(s) and/or table(s) are not visually appealing or are irrelevant to the content; OR, image(s) and table(s) are appealing and relevant but from an unidentified source (reader is unable to identify if image or table is original or sourced externally). Some suitable references are included.

0Pts

Not Demonstrated

No image(s) or table(s) included. Insufficient and/or poor quality references used.

5pts

Total points:35

Dr Shweta · Accepted Answer

Role of Bioinformatics in the investigation of 3 -D structure of Hemoglobin
· Introduction:
Hemoglobin or the ball of blood is an iron containing oxygen and carbon-dioxide carrying protein which is located in the red blood cells. It helps in the transfer of oxygen from lungs to tissues and body's organs and transports of carbon dioxide from tissues and organs back to the lungs. This oxygen is then utilized in the cells for the aerobic respiration of food to generate chemical energy in the form of ATP required for the sustainment of life [1]. A healthy person contains approximately 12 to 20 grams of Hemoglobin/100 mL of blood.  The oxygen-binding capacity of Hemoglobin is 1.34 mL O2 per gram of Hemoglobin and hence it upsurges the total oxygen carrying capacity of blood by seventy-fold as compared to the oxygen directly dissolved in the blood. Deficiency of Hemoglobin is known as anemia in which due to low count of red blood cells, the oxygen content of the blood reduces leads to fatigue and weakness [2]. 
· Role of Bioinformatics in the analysis of structure of Hemoglobin: 
To study the molecular structure of Hemoglobin X-ray analysis or Nuclear magnetic resonance (NMR) spectroscopy method is used. And its secondary structure is analysed via bioinformatics with the help of its primary sequence and subunit gamma-2 protein sequence using the UNIPROT database in FASTA file format. UNIPROT is a collection of freely available database of sequence of proteins and their functions sequenced and arranged during the different Genome sequencing projects. It works along with the FASTA which is a sequence alignment software for DNA and protein [3]. Other than this, for its comparative analysis other bioinformatics tools can also be used. For instance, Chou and Fasman secondary structure prediction server [CFSSP] that helps in the prediction of secondary structure of Hemoglobin via its amino acid sequence. The Garnier–Osguthorpe Robson [GOR] method which also helps in the prediction of secondary structure of Hemoglobin via the method based on the information theory. It specifically analyses the amino acid sequences to predict the alpha helices, beta sheets, turns, and randomly coil secondary structures in the secondary structure of Hemoglobin. Self-optimized prediction method with alignment [SOPMA] is also an efficient tool used to predict the secondary structure of Hemoglobin according to its primary sequence [4]. 
Based on the results of X-ray analysis, NMR and bioinformatics data the molecular structure of Hemoglobin is explained as below: 
· Molecular structure of Hemoglobin:
Molecular structure of Hemoglobin molecule is studied by the technique of X-ray crystallography and it is found that Hemoglobin is a complex tetrameric protein with a protein molecule with a 4-chain quaternary structure known as the tetramer. Its molecular structure is symbolized as (αβ)2 as it is made up of four polypeptide chains two Alpha chains and two beta chains arranges alternately as alpha then Beta then again Alpha and finally Beta. These chains are joined with each other with the help of non-covalent bonds. Along with this, Hemoglobin contains heme cofactor that has iron. In total there are four heme-iron complexes present in its structure with one haem in each of the polypeptide chain.  The haem group present in each polypeptide chain has one iron in its ferrous Fe++ form and this hydrophobic heme is specifically joined with the hydrophobic protein pocket with the help of explicit non-covalent bonds. The red colour of Hemoglobin is due to the presence of this heme-iron complex which is composed of the elements carbon (C), hydrogen (H), oxygen (O), nitrogen (N) and iron (Fe) [5]. The space-filling model of the molecular structure of haemoglobin as detected by the X-ray crystallography is shown as below in Figure 1. 
Figure 1: Molecular structure of Haemoglobin
Image Courtesy: http://bioinformatics.org/jmoltutorials/jtat/hemoglobin/contents/contents.htm
In the lungs, where oxygen is present in large quantity, the molecule of oxygen (O2) binds with that of the atom of iron which is present in the ferrous form and transported with the blood. Later when it approaches near the tissue which requires oxygen the binding between ferrous and oxygen breaks and oxygen is released. Elemental oxygen occupied position in the pocket of the polypeptide chain of Hemoglobin and gets anchored there with the help of the nitrogen atom of histidine.

Topic: HEMOGLOBINThis course is designed to introduce students to the various technologies and their application to understanding the structure and function and of proteins. For your "Protein...

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