
Integrated Laboratory Class 6
Code: 100881Credits: 3
| Degree programme | Type | Course |
|---|---|---|
| Biochemistry | OB | 3 |
Contact lecturer
- Name :
- Nathalia Varejao Nogueira
- Email :
- nathalia.varejao@uab.cat
Teaching staff
- Jordi Vilardell Vila
- Alfredo Jesús Miñano Molina
- Margarida Julià Sapé
- Nathalia Varejao Nogueira
Group languages
You can consult this information at the end of the document.
Prerequisites
It's compulsory to have passed the laboratory safety test. All the required information is available at the Degree Moodle Classroom.
The students are adviced to study the specific contents of the subjects and to read carefully the laboratory protocol before startting each module.
Objectives
Integrated Laboratory VI is part of a set of practical subjects, which are distributed throughout the first six semesters of the Degree in Biochemistry.
The objective of these subjects is the development and acquisition of practical skills by students. The complexity of the contents increases gradually, associated with the requirements of the subjects taught each semester and with the acquisition of new theoretical knowledge.
During the Integrated Laboratory VI, students acquire practical skills associated with the following areas:
• Subcellular fractionation.
• Oximetry.
• Determination of cell viability and death.
• Cell signaling.
• Bioinformatics.
• Clinical biochemistry.
The laboratory sessions focus on learning basic and specialized techniques in each field, as well as on the development of the competencies necessary for laboratory work.
Learning outcomes
- CM22 (Clearly and concisely describe experimental results in the field of biochemistry, considering options for improvement.) Clearly and concisely describe experimental results in the field of biochemistry, considering options for improvement.
- CM23 (Work as a team when performing experiments and analysing their results.) Work as a team when performing experiments and analysing their results.
- CM24 (Understand disposal methods for the different types of waste generated in a biochemistry or molecular biology laboratory.) Understand disposal methods for the different types of waste generated in a biochemistry or molecular biology laboratory.
- KM26 (Identify cell systems useful for experimentation in biochemistry and molecular biology.) Identify cell systems useful for experimentation in biochemistry and molecular biology.
- KM27 (Describe the theoretical foundations and instrumentation used in basic and advanced biochemistry.) Describe the theoretical foundations and instrumentation used in basic and advanced biochemistry.
- SM25 (Use digital resources to search for information, study biomolecules and calculate key parameters.) Use digital resources to search for information, study biomolecules and calculate key parameters.
- SM26 (Interpret experimental results obtained using the main techniques of biochemistry.) Interpret experimental results obtained using the main techniques of biochemistry.
- SM27 (Apply the techniques and methods for addressing cell culture techniques, classical genetics, immunological detection, recombinant DNA, separation, purification and analysis of biomolecules in the biochemical field.) Apply the techniques and methods for addressing cell culture techniques, classical genetics, immunological detection, recombinant DNA, separation, purification and analysis of biomolecules in the biochemical field.
Contents
The sessions include the following contents, which can be carried out in simultaneous sessions.
Subcellular fractionation and oximetry assay.
2 sessions of 4 hours:
a) Extraction and homogenization of rat liver.
b) Subcellular fractionation by differential centrifugation.
c) Evaluation of the fractionation by determination of the enzymatic activity of different enzymatic markers specific of a subcellular location.
d) Determination of oxygen consumption by the mitochondrial fraction.
Genotyping. Determination of cell viability and type of cell death. Molecular Pathology and Cell signaling.
5 sessions of 4 hours:
a) Extraction and purification of genomic DNA.
b) Genotyping by PCR. Electrophoretic analysis.
c) Determination of the lethal dose 50 of a therapeutic drug on a human cell line.
d) Study of the type of cell death.
e) Hormone treatment of a human cell line.
f) Determination of the activation of a signaling pathway by western-blot.
BIOINFORMATICS
3 sessions of 2 hours and a fourth session of 3 hours. All the sessions are held in the computer room.
Students will carry out a miniproject that will consist of discovering a new gene, and characterizing it, using bioinformatics tools. As a \"new gene\", we understand one that has not been previously annotated.
Students will have to put into practice the knowledge acquired in the subject of Bioinformatics, for example: study of the characteristics of the starting protein, database searches, and advanced BLAST searches, multi-alignments and phylogenetic trees, and prediction of Three-dimensional structure, study of domains, comparison and structural classification.
CLINICAL BIOCHEMISTRY
3 sessions of 4 hoursand a fourth session in which the results obtained will be evaluated.
a) Measure the concentration of different analytes (urea, cholesterol, bilirubin ...) in serum by molecular absorption spectrometry in an automatic analyzer, using chemical and enzymatic reactions.
b) Determination of the limit of detection and of the linearity limit of the measurement of the concentration of urea.
c) Measurement of the catalytic activity of L-lactate dehydrogenase in serum using two continuous spectrometric methods recommended by the SEQC and by the ICCAT. Comparison of results.
d) Study of the effect of interfering substances (hemoglobin, bilirubin and lipids) in the measurement of the concentration of uric acid.
e) Application of an inter-laboratory quality external evaluation program to evaluate the results.
The subject will be taught in small groups of students in the laboratory and in the computer room (Bioinformatics).
Learning activities and methodology
| Title | Hours | ECTS | Learning outcomes |
|---|---|---|---|
| Study and presentations preparation | 8 | 0.32 | CM22, CM23, CM24, KM26, KM27, SM25, SM26, SM27 |
| Tutoring | 2.5 | 0.1 | CM22, CM23, CM24, KM26, KM27, SM25, SM26, SM27 |
| Laboratory sessions | 52 | 2.08 | CM22, CM23, CM24, KM26, KM27, SM25, SM26, SM27 |
| Laboratory reports and exams | 12.5 | 0.5 | CM22, CM23, CM24, KM26, KM27, SM25, SM26, SM27 |
Students will have a Laboratory Manual for each module before the start of the practical sessions and, when appropriate, a questionnaire. The documents will be available on the course Moodle site.
In order to attend the laboratory sessions, students must provide evidence of having passed the Biosafety and Laboratory Safety tests. Students must be familiar with and accept the operating rules of the laboratories of the Faculty of Biosciences.
For each laboratory session, it is mandatory that students bring their own lab coat, safety glasses, and the Laboratory Manual. They must also bring a notebook in which observations can be recorded, as well as a permanent marker.
During the laboratory sessions, students will work in pairs under the supervision of the professor responsible for the course. At the beginning of each session, the professor will provide a brief theoretical explanation of the practical content and of the experiments to be carried out by the students.
In the case of the computer-based bioinformatics sessions, a case study will be carried out in which students will work in pairs under the supervision of the professor responsible for the course. During the three practical sessions, students will develop the proposed mini-project, applying the tools used in the Bioinformatics course to the discovery and characterization of a previously unannotated protein. In solving this case study, students are expected to use the bioinformatics tools correctly, formulate appropriate research questions, develop a work plan and, finally, prepare a PowerPoint summary presentation of the information obtained together with its interpretation.
In order to achieve good performance and acquire the competencies corresponding to this course, it is essential that students carry out a thorough reading of the Laboratory Manual and become familiar with the practical activities to be carried out in each session, as well as with the methodology that will be applied in each case.
In order to acquire the specific competencies of the course, attendance at the practical sessions is mandatory. In the event that a student, due to a justified and unforeseen circumstance, is unable to attend one or more practical sessions, the student must notify the professor responsible for the course and submit the corresponding supporting documentation as soon as possible. Justified causes include health problems (the corresponding medical certificate must be submitted) or serious personal circumstances.
Assessment
Continuous assessment activities
| Title | Weight | Hours | ECTS | Learning outcomes |
|---|---|---|---|---|
| 1- Biochemistry: Subcellular fractionation and oximetry assay | 25% | 0 | 0 | CM22, CM23, CM24, KM26, KM27, SM25, SM26, SM27 |
| 3- Bioinformatics: In-class work and PowerPoint presentation | 25% | 0 | 0 | CM22, CM23, CM24, KM26, KM27, SM25, SM26 |
| 2- Biochemistry: Genotyping, assessment of cell viability and cell death, molecular pathology and cell signalling | 25% | 0 | 0 | CM22, CM23, CM24, KM26, KM27, SM25, SM26, SM27 |
| 4- Clinical Biochemistry: Assessment of practical results and written examination | 25% | 0 | 0 | CM22, CM23, CM24, KM26, KM27, SM25, SM26, SM27 |
General considerations:
Attendance at the laboratory/bioinformatics sessions is mandatory. The students will obtain the \"Non-Evaluable\" grade when the absence exceeds 20% of the programmed sessions.
The assessment will be based not only on different tests (written tests, laboratory reports) but also on the attitude and aptitude demonstrated by students during the sessions.
The assessment will be divided into different blocks that will serve to establish the degree of fulfillment in the acquisition of knowledge about the contents proposed.
Students who do not obtain the required minimum grade (4.0 or higher in each block) will not pass the course. In this case, the maximum final grade for the course will be 4.0.
In the event of not passing the course, from the second enrolment onwards, students will only be required to complete the assessment of those specific blocks that they have not passed. This exemption will remain valid for two additional enrolment periods.
Subcellular fractionation and oximetry assay.
Students must prepare a report, where the results obtained during the practical sessions will be presented and discussed. This report will represent 80% of the note in this module. The date of the delivery will be fixed by the teacher.
The remaining 20% of the grade will correspond to students' attitude and participation during the sessions.
The grade for this block will represent 25% of the overall course grade.
Genotyping. Determination of cell viability and type of cell death. Cell signaling.
Students must prepare a report presenting and discussing the results obtained during the practical sessions. This report will account for 75% of the grade for this block. The submission deadline will be set by the professor.
In addition, the practical ability of each group of students will be evaluated, taking into account theresults obtained in the genotyping test, which will represent 25% of the note in this section.
The grade for this block will represent 25% of the overall course grade.
Bioinformatics.
The evaluation will be done by submitting the results obtained via Moodle. The format will be a PowerPoint presentation.
The deadline for submission will be at the end of the last practical session. This work will be presented to the professor and to the rest of the students on the last day of class in a short presentation (5-10 min).
This PowerPoint presentation will allow you to obtain 25% of the overall course grade. Of this 25%, 20% will correspond to the instructor's assessment and 5% will be obtained through peer assessment of the work presented.
Clinical Biochemistry.
The student will have to answer a written test about the practices, which will represent 75% of the mark of the module. The remaining 25% will be determined by an evaluation of the practical results.
The grade for this block will represent 25% of the overall course grade.
Single assessment.
For those students who take the single assessment is compulsory to do the laboratory practices (PLAB) in the scheduled sessions with the rest of the group.
The single assessment consists of a single synthesis test with questions from all the blocks of the integrated laboratory, except for Bioinformatics, on the day scheduled in the academic calendar.
The grade obtained in the synthesis test is 57.5% of the final grade of the subject. The oral presentation of the Bioinformatics module, the attitude during the practices and the results obtained will be the remaining 42.5%. Only if all members of the Bioinformatics working group have selected the single assessment option, this presentation can be made on the day scheduled in the calendar for the single assessment. In this case, the single assessment will be 82.5% of the final grade.
Use of AI and Fraud
Any irregularity committed during an assessment activity (academic misconduct, plagiarism, or improper use of AI, unless such use is expressly authorized in the course syllabus) that may lead to a significant alteration of the grade will result in that activity being graded as 0. If the course syllabus stipulates that obtaining a minimum mark in this assessment is an essential requirement to pass the course, or if multiple irregularities occur in the assessment activities of the same course, the final grade for the course will be 0. Furthermore, disciplinary proceedings may be initiated against any student who incurs any of these irregularities.
Bibliography
The bibliography of each block is indicated in the syllabus of the corresponding theoretical subject
Software
The programs, webpages, and webservers used in this laboratory are listed below:
Programs:
Jalview: https://www.jalview.org/
MEGA X: https://www.megasoftware.net/
Notepad++: https://notepad-plus-plus.org/downloads/ç
Icn3d: https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.2.0.zip
PyMol: https://pymol.org/2/
Webpages and Webservers:
https://services.healthtech.dtu.dk/
Course groups and languages
The information provided is provisional until November 30. After this date, you will be able to consult the language of each group through this link. To access the information, you will need to enter the course CODE
| Type of teaching | Group | Language | Semester | Shift |
|---|---|---|---|---|
| (PLAB) Practical laboratories | 331 | Catalan/Spanish | second semester | afternoon |
| (PLABs) Suport a les pràctiques de laboratori | 331 | Catalan/Spanish | second semester | afternoon |
| (PLAB) Practical laboratories | 332 | Catalan/Spanish | second semester | afternoon |
| (PLABs) Suport a les pràctiques de laboratori | 332 | Catalan/Spanish | second semester | afternoon |
| (PLAB) Practical laboratories | 333 | Catalan/Spanish | second semester | afternoon |
| (PLABs) Suport a les pràctiques de laboratori | 333 | Catalan/Spanish | second semester | afternoon |