Spectroscopy in Biochemistry

Objectives

This curricular unit aims to provide a comprehensive understanding about spectroscopic techniques used in the field of biochemistry. In the continuity of other Physical-Chemistry classes provides complementary information on spectroscopic techniques that have significantly contributed to the advancement of knowledge in the field of life sciences.

General characterization

Code

10721

Credits

6.0

Responsible teacher

José Luís Capelo Martinez, Teresa Sacadura Santos Silva

Hours

Weekly - 4

Total - 55

Teaching language

Português

Prerequisites

Available soon

Bibliography

Book recommended by prof. J. L. Capelo for 1st semeter 2022/2023.

Daniel C. Harris

Quantitative Chemical Analysis. 6th edition.

Chapters 5, 18, 19, 20, 22

Adquiring this book is highly recommeded

Other books of interest.

Radiation in Bioanalysis: Spectroscopic Techniques and Theoretical Methods
Alice S. Pereira, Pedro Tavares, Paulo Limão-Vieira
Springer-Nature, Springer Bioanalysis series (16 Nov 2019)

Fundamentals of Molecular Spectroscopy
P.S. Sindhu
New Age International Pvt Ltd Publishers (30 Jan 2011)

Electron Paramagnetic Resonance: Elementary Theory and Practical Applications
John A. Weil and James R. Bolton
Wiley-Blackwell; 2nd Edition edition (22 Dec 2006)

Spectroscopy for the Biological Sciences
Gordon G. Hammes
Wiley-Blackwell (22 July 2005)

Teaching method

The syllabus will be presented through two types of classes:

Theoretical-Practical Classes: These will approach the fundamentals of the spectroscopic techniques studied, using practical cases whenever possible and solving problems aimed at training data analysis to facilitate understanding how to obtain information from each of the techniques discussed.
Practical Classes: In these, students will be given topics for the development of practical work related to the spectroscopies discussed.

During the theoretical-practical classes, the work groups will have to present a summary of the class assigned by the teacher. When deemed appropriate, the teacher may rate the presentation as "very good" or "improvable." In the first case, the group accumulates 0.1 points in the final grade; in the second case, -0.1.

A presentation with slides is generally considered "very good" when it meets various quality criteria, both in terms of content and delivery. Here are some points that can help evaluate or create a high-quality presentation:

Content:

Clarity and Objectivity: Slides should be clear and direct, presenting information concisely.
Relevance: The content should be relevant to the target audience and meet the objectives of the presentation.
Logical Structure: The presentation should have a well-defined introduction, development, and conclusion.
Data and Evidence: Use data, statistics, and examples to support arguments.
Visual Design: Slides should be visually appealing but without excessive elements that may distract.

Delivery:

Fluency and Tone of Voice: The delivery should be fluent, with a clear and varied tone to maintain interest.
Eye Contact: Maintain eye contact with the audience to create a connection.
Time: Respect the time allocated for the presentation.
Interactivity: Engage the audience with questions or discussions to add value.
Body and Gestural Language: Use gestures and movements to complement speech.

Extras:

Support Material: Provide support material like brochures, links, or references as a bonus.
Q&A: Be prepared for a Q&A session after the presentation.
Technology: Ensure all technical aspects, like the projector and remote control, work smoothly.

If a presentation meets most or all of these criteria, it is likely to be considered "very good."

A presentation with slides is generally considered "bad" when it fails in fundamental aspects of content, design, and delivery. Here are some points that can indicate a low-quality presentation:

Content:

Disorganization: Lack of a clear structure, making it difficult for the audience to follow the reasoning.
Irrelevant Information: Inclusion of information that does not add value or deviates from the main topic.
Lack of Depth: Superficial approach to topics that require more details.
Factual Errors: Presentation of incorrect or outdated information.

Design:

Excessive Text: Slides overloaded with text, making them hard to read or follow.
Poor Design: Use of incompatible colors, hard-to-read IGNOREs, or low-quality images.
Inconsistency: Variation in styles, IGNOREs, and colors without a defined pattern.
Unnecessary Animations: Excessive use of animations or transitions that do not add value and may distract.

Delivery:

Reading from Slides: Reading directly from the slides without adding additional information.
Lack of Preparation: Displaying nervousness, hesitation, or lack of knowledge about the topic.
Lack of Interactivity: Not engaging the audience or not adequately responding to questions.
Technical Issues: Failures in the use of technology, such as problems with the projector or remote control.

Other Aspects:

Exceeding Time: Extending far beyond the allocated time without justifiable reason.
Lack of Support Material: Not providing additional resources when necessary.
Lack of Context: Not establishing a clear context for the audience about the purpose or relevance of the presentation.

If a presentation exhibits several of these flaws, it is likely to be considered "bad." However, it''s important to remember that everyone can improve with practice and constructive feedback, which will be provided by the teacher.

Evaluation method

Please contact the professor responsible for this course.

Continuous Assessment will take into account attendance in practical classes and both practical and theoretical components:

Attendance:

To obtain attendance, students must attend all practical sessions. Attendance is required to successfully complete the course.

Theoretical Component (CT):

The assessment of the theoretical component consists of two tests that cover all the material taught (in classes of any type). The grade for this component is calculated through the simple arithmetic average of the grades obtained in the tests, rounded to the nearest tenth.

The assessment of the theoretical component consists of two tests that cover all the material taught (in classes of any type). The calculation of the grade for this component is done through the simple arithmetic average of the grades obtained in the tests, rounded to the nearest tenth.

During the theoretical-practical classes led by Professor J. L. Capelo, predefined work groups will have to present the corresponding summary of the class assigned by the teacher. When deemed appropriate, the teacher may grade the presentation as either "very good" or "needs improvement." In the first case, the group accumulates 0.1 points on the final grade; in the second case, they lose 0.1 points.

A slide presentation is generally considered "very good" when it meets several quality criteria, both in terms of content and delivery. Here are some points that can help evaluate or create a high-quality presentation:

Content:

Clarity and Objectivity: Slides should be clear and straightforward, presenting information concisely.
Relevance: The content should be relevant to the target audience and meet the objectives of the presentation.
Logical Structure: The presentation should have a well-defined introduction, development, and conclusion.
Data and Evidence: Use data, statistics, and examples to support arguments.
Visual Design: Slides should be visually appealing but without excessive elements that may distract.

Delivery:

Fluency and Tone of Voice: The delivery should be fluent, with a clear and varied tone to maintain interest.
Eye Contact: Maintain eye contact with the audience to create a connection.
Timing: Respect the time allocated for the presentation.
Interactivity: Engaging the audience with questions or discussions can add value.
Body and Gesture Language: Use gestures and movements to complement speech.

Extras:

Support Material: Providing support material like pamphlets, links, or references can be a bonus.
Q&A: Be prepared for a Q&A session after the presentation.
Technology: Ensure all technical aspects, like the projector and remote control, work smoothly.

If a presentation meets most or all of these criteria, it is likely to be considered "very good."

A slide presentation is generally considered "poor" when it fails in fundamental aspects of content, design, and delivery. Here are some points that can indicate a low-quality presentation:

Content:

Disorganization: Lack of a clear structure, making it difficult for the audience to follow the reasoning.
Irrelevant Information: Inclusion of information that does not add value or deviates from the main topic.
Lack of Depth: Superficial approach to topics that require more details.
Factual Errors: Presentation of incorrect or outdated information.

Design:

Excessive Text: Slides overloaded with text, making them hard to read or follow.
Poor Design: Use of incompatible colors, hard-to-read IGNOREs, or low-quality images.
Inconsistency: Variation in styles, IGNOREs, and colors without a defined pattern.
Unnecessary Animations: Excessive use of animations or transitions that do not add value and may distract.

Delivery:

Reading from Slides: Reading directly from the slides without adding additional information.
Lack of Preparation: Showing signs of nervousness, hesitation, or lack of knowledge about the topic.
Lack of Interactivity: Failing to engage the audience or not responding adequately to questions.
Technical Issues: Failures in the use of technology, such as problems with the projector or remote control.

Other Aspects:

Exceeding Time: Going far beyond the allocated time without justifiable reason.
Lack of Support Material: Not providing additional resources when necessary.
Lack of Context: Not establishing a clear context for the audience about the purpose or relevance of the presentation.

If a presentation shows several of these flaws, it is likely to be considered "poor." However, it''s important to remember that everyone can improve with practice and constructive feedback from the teacher.

Practical Component (CP):

The assessment of the practical component involves the preparation and execution of a practical test in the laboratory. The grade obtained is rounded to the nearest tenth. Additionally, the preparation of a seminar based on a scientific paper with a public defense will also be evaluated.

The practical component assessment also includes the preparation and execution of a practical test in the laboratory. The grade obtained is rounded to the nearest tenth. The preparation of a questionnaire and a seminar based on a scientific paper with a public defense will also be evaluated: practical test = 50%; seminar = 40%; questionnaire = 10%.

Final Grade (CF):

The final grade is calculated based on the weighted arithmetic average of the CT (0.60) and CP (0.40) components. All intermediate calculations will be rounded to the nearest tenth, and the final grade will be rounded to the nearest whole number.

For students who have obtained attendance in years prior to 2020/2021, their final grade will be given only by the CT.

Students can also pass through the Resit Exam. In this case, the resit exam grade replaces the CT.

Grade Improvement:

Without prejudice to the FCT NOVA regulations, you can only attempt to improve the final grade of the course once. This improvement can be made in a resit exam, in which case the grade obtained replaces the CT.

If the attempt to improve the final grade is made in another type of exam, the grade obtained will be equal to the final grade.

ATTENTION:

Oral assessment will be carried out for students who obtain a CT > 17 as a methodology for defending the grade obtained. In any other case, the course coordinator reserves the right to conduct an oral exam for any student enrolled in the course.

Subject matter

Electronic and vibrational absorption. UV and visible spectra of nucleic acids and protein cofactors. Infrared spectroscopy. Equipment used in absorption spectroscopy. Study cases.

Linear and circular dichroism. Optical rotatory dispersion (ORD), Circular dichroism (CD), Linear dichroism. Equipment used in ORD and CD spectroscopies. CD and ORD and the macromolecular structure of proteins. Use of CD and ORD in nucleic acid studies. Study cases.

Fluorescence and phosphorescence spectroscopy. Fluorescence Resonant Energy Transfer and it’s application to biological systems. Equipment used in emission spectroscopy. Study cases.

Light dispersion in solutions of macromolecules. Dynamic light dispersion (DLS). Equipment used in DLS. Study cases.

Electron Paramagnetic Resonance spectroscopy (EPR). Basic principles and procedures to study paramagnetic centers. Hyperfine interaction. Systems with more than a single unpaired electron. Equipment used in EPR measurements. Study cases.

Programs

Programs where the course is taught:

Biochemistry