The subject "Basic Biochemical Methodology" is mainly a practical subject. In Basic Biochemical Methodology, students will acquire basic knowledge about the techniques commonly used in biochemistry laboratories. The knowledge acquired in this subject is of vital importance for the subsequent academic and professional development.

The use of scientific literature, experimental design, laboratory safety, and ethics will be covered during the first semester.

During the second semester, the teaching activities are focused on acquiring sufficient knowledge and skills for the proper performance of the laboratory practices that will take place throughout the degree program. The various teaching activities in this semester of "Basic Biochemical Methodology" are closely aligned with the subject "Instrumental Techniques" offered in the second year. In "Instrumental Techniques," students will delve deeper into the concepts previously learned in "Basic Biochemical Methodology," specifically regarding chromatography, electrophoresis, and protein purification.

The general objective of this subject is to provide training that will enable students to work in the future in research centres, biotechnological industries, or educational institutions. To this end, the specific (M) and transversal (G) competencies and their learning outcomes (LO) detailed below will be addressed:



Specific Competencies



M04.1 - Understand the principles, instrumentation, and applications of the main techniques of Biochemistry and Molecular Biology and their usefulness in Biotechnology.



RA1 - The student will be able to explain the knowledge related to the separation and analysis of biomolecules.

RA2 - The student will be able to design and interpret experimental protocols to solve specific biochemical problems.



M04.2 – Execute properly laboratory protocols in Biotechnology and in Biochemistry and Molecular Biology.



RA3 - The student will be able to use skillfully basic instrumentation and the most commonly used experimental methods in biochemistry.

RA4 - The student will be able to explain and implement good laboratory practices.

RA5 - The student will be able to solve theoretical-practical exercises to obtain precise quantitative data.



M04.7 – Extract and analyse information from bibliographic sources, biological databases, and other bioinformatics tools.



RA6 - The student will be able to manage the scientific-technical literature in their field and apply it to the acquired knowledge.



Transversal Competencies



G001 - Acquire adequate capacity for analysis, synthesis, and critical reasoning in the application of the scientific method.



RA7 - The student will be able to describe, quantify, analyze, and critically evaluate the experimental results obtained and draw conclusions from them.



G002 - Develop continuous autonomous learning, fostering initiative and adaptation to new situations.



RA8 - The student will be able to manage the decisions they make, the knowledge they apply, the difficulties they encounter in learning, and how to overcome them.



G003 - Acquire the ability to convey ideas and communicate them to both professional and non-professional audiences, promoting the use of foreign languages, especially English.



RA9 - The student will be able to use structures and norms in specialized written communication for the preparation of academic and/or scientific documents.



RA10 - The student will be able to communicate orally their ideas and arguments in a comprehensible manner and in accordance with established formal criteria.

Syllabus:



BLOCK 1: Introduction to Experimentation and Information and Communication Technologies



Topic 1: Scientific Articles and Journals. Bibliographic Searches. Data Repositories for Scientific Articles. PubMed. Science Citation Index.



Topic 2: The Scientific Method in Biochemical Research and Ethical Considerations. The Scientific Method in Biochemical Research. Formulating a Hypothesis. Experimental Design. Data Treatment and Evaluation. Drawing Conclusions. Ethical Considerations.



Classroom Practices: How many types of scientific articles can we find? Reading opinion articles about the editorial system and predatory journals. Reviewing basic laboratory calculations (concentrations, dilutions, etc.). Analysing the results of a Bradford experiment (using Excel: inserting a chart, linear regression, etc.). Guidelines and recommendations on writing a scientific paper (bias in writing lab reports, etc.).



Computer Practices: Bibliographic search and bibliometrics.



BLOCK 2: Experimentation in Biochemistry. Cellular Systems and Subcellular Fragmentation



Topic 3: Good Practices in a Biochemistry Laboratory: Identification of Hazards (physical, chemical, biological, and radiological). General and Personal Safety Measures. Safety Regulations. Behaviour in Emergency Situations.



Topic 4: Levels of Experimentation in Biochemistry: Studies with Intact Animals, Isolated Organs, Tissues, or Cells. Molecular Studies (Structural or Functional). Cellular Systems. Techniques for Separating Different Cell Types. Cell Cultures. Cell Quantification and Viability. The Hemocytometer.



Topic 5: Subcellular Fractionation: Methods for Homogenization and Obtaining raw Extract. Preparative Centrifugation (Differential and Density Gradient). Marker Enzymes to Identify Various Cellular Organelles. Organelle Viability. Analytical Centrifugation.



Classroom Practices: Solving exercises and problems related to centrifugation. Designing workflows for conducting experimental sessions.



Laboratory Practices:



Cell Fragmentation and Protein Quantification.

Isolation of Chloroplasts by Sucrose Gradient Centrifugation.

Mitochondria Purification. Determination of Mitochondrial Viability.



BLOCK 3: Basic Techniques Used in the Biochemistry Laboratory



Topic 6: Preparation and Separation Techniques. Chromatography. Electrophoresis Techniques. Agarose Gels, Native Gels, SDS-PAGE. Isoelectric Focusing. Two-Dimensional Electrophoresis. Capillary Electrophoresis. Chromatography. Types of Chromatography. Electrophoretic Techniques: Electrophoresis in Agarose Gels, Gradient Gels, SDS-PAGE, Isoelectric Focusing, Two-Dimensional Electrophoresis, Capillary Electrophoresis.



Topic 7: Analytical Techniques. Spectrophotometry Techniques. Equipment: Visible and Ultraviolet Spectroscopy. Design of Enzymatic Assays. DNA Denaturation and Renaturation. Polymerase Chain Reaction (PCR). RT-PCR. DNA Chips.



Topic 8: General Techniques for Macromolecule Labelling and Their Applications. Radiochemical Techniques. Immunochemical Techniques. Immunoprecipitation. Immunoassays (ELISA, RIA). Identification Techniques. Western Blot, Dot Blot.



Classroom Practices: Simple practical problems on chromatography. Electrophoresis Experiment Simulator: SDS-PAGE. Enzyme Reaction Calculation Problems. Simple practical problems on PCR and qPCR. Simple practical problems on Immunotechniques. Radioactivity Calculation Exercises and Problems. Complex Theoretical-Practical Experimental Exercises. How to Give a Good Oral Presentation Using ICT Resources.



Laboratory Practices:



Gel Filtration Chromatography. Determination of the Molecular Mass of a Protein.

Purification of Lysozyme from Egg White by Ion Exchange Chromatography.

Protein Electrophoresis in Polyacrylamide-SDS Gel.

Nucleic Acid Electrophoresis in Agarose Gel. Characterization of Plasmid DNA.

Seminars:



Seminars. Communication (written and oral) of a Current Scientific Topic Related to the SDGs (Sustainable Development Goals)

The teaching methodology includes lectures, classroom practices, seminars, computer practices, and laboratory practices:



Lectures: The instructor will present the course content using a digital presentation and links to audiovisual content (available on Egela). Students will be encouraged to ask questions, and the instructor will also pose questions to prompt student reflection and communication. This approach allows for necessary feedback during each lecture.



Classroom Practices: Students will solve scheduled problems and questions. These practices are typically used as supplementary material to the theoretical lectures or laboratory practices.



Computer Practices: Students will apply their knowledge related to bibliographic searches and bibliometric analyses (quality indicators). Additionally, they will attend a seminar on databases and complete practical exercises using information from the lectures.



Laboratory Practices: This methodology is designed for students to acquire the appropriate skills for working in a laboratory. Students will develop manual skills to observe and obtain results, analyze and reflect on them, and communicate their findings through practice reports. Laboratory practices are closely related to the theoretical content of the course, allowing students to apply the knowledge gained in lectures to real experimental work situations.



Seminar Sessions: Students will develop a topic related to Biotechnology or Biochemistry and the Sustainable Development Goals (SDGs) outlined in the EHUagenda. They will communicate their findings both in writing and orally in the format of scientific dissemination.

• Continuous Assessment System
• Final Assessment System
• Tools and qualification percentages:
  • Exhibition of works, readings ... (%): 10
  • In this section, the sum of the percentages corresponding to theory (45%), laboratory practices (30%), computer exercises (5%), and problem-solving exercises (10%) is included. (%): 90

The assessment of the "Basic Biochemical Methodology" course is divided into five sections:



-Written Exam 45%: Correct answers, expression, argumentation, and use of scientific terminology will be taken into consideration. A minimum of 50% correct answers is required.

-Laboratory Practical Session 30%: Attendance, attitude, and cleanliness; accuracy and clarity of the report/exam will be taken into account, with a requirement to pass at least 50% of the questions.

-Computer Practical Session 5%: Attendance, attitude, and completion of exercises.

-Seminar 10%: Attendance, attitude, organization of information, analytical and synthesis skills, clarity of presentation, and participation in the debate.

-Problem-solving 10%: Attendance, correct resolution of problems posed during classroom exercises; exam, requiring a minimum of 50% correct answers.

In the case of taking partial exams, it will be necessary to obtain a minimum of 50% correct answers to pass the subject.

Attendance to the different teaching modalities throughout the course will be mandatory to be eligible to take the exams in the regular session. A minimum of 50% correct answers will be required to pass the exam.

Waiving: Failing to take the final exam is sufficient to waive the final grade.

Not taking the final exam is enough to receive a grade of "not presented" for the course.

The use of books, notes, phones, electronic devices, computers, or other equipment is not allowed during assessment tests (except for a calculator*). If any academic dishonesty or fraudulent practices are detected, the protocol on academic ethics and prevention of such practices at UPV/EHU will be enforced.

The final grade will be calculated by adding the grades obtained in the following sections:

-Written Exam 45%

-Laboratory Practical Session 30%.

-Computer Practical Session 5%.

-Seminar 10%.

-Problem-solving 10%.

Participation in the different teaching modalities throughout the course will be mandatory to be eligible to take the exams in the extraordinary session. A minimum of 50% correct answers will be required to pass the exam.

The grades of the sections passed will be kept for the extraordinary assessment session of that school year if the subject is failed in the ordinary call.

Not taking the written test will be qualified as "not presented" in the final grade for the course.

The eGela webpage (http://egela.ehu.eus) will be used to publish the course guide and information about the activities performed in the laboratory, computer room and classroom.
Before entering the laboratory, students must carefully read the protocol for the corresponding session. This protocol will be uploaded to eGela.

Basic bibliography

- Wilson, K. and Walker, J. (eds.)(2018). Principles and Techniques of Biochemistry and Molecular Biology. 8th edn. Cambridge University Press.

- Lesk, A."Introduction to Protein Science: Architecture, Function, and Genomics". Oxford University Press, 2017.

- Roca, P. y cols. (2003). Bioquímica. Técnicas y Métodos. Editorial Hélice

- Freifelder, D. (2003). Técnicas de Bioquímica y Biología Molecular. Editorial Reverté.

- García-Segura, J.M. y cols. (2002). Técnicas instrumentales de análisis en Bioquímica. Editorial Síntesis

In-depth bibliography

- Boyer, R. F. (2009). Biochemistry laboratory: modern theories and techniques. Pearson Education.
- Serdyuk, I.N., Zaccai, N. Zaccai, J. Methods in molecular biophysics Ed. Cambridge University Press, 2007.

Journals

The journal of biological chemistry, Crc critical reviews in biochemistry, European journal of biochemistry/febs, Journal of biochemical and biophysical methods, Bioscience, biotechnology, and biochemistry, Progress in biochemical pharmacology, Archives of biochemistry and biophysics, European journal of medicinal chemistry, Clinical physiology and biochemistry, J capillary electrophor, , Appl theor electrophor, J. of chromatography, Analytica chimica acta.

Web addresses

http://ocw.mit.edu/OcwWeb/web/home/home/index.htm
http://www.sciencedirect.com/science/journal/00219673
http://workbench.concord.org/database/
http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-376-9_6
http://www.ncbi.nlm.nih.gov/pubmed
https://apps.webofknowledge.com/