B8777 - Clinical Biochemistry and Molecular Biology

Learning outcomes

At the end of the course the student is able to work in a biochemistry laboratory. The student knows the fundamental rules regarding safety and environmental sustainability principles in the biochemistry laboratory; the student will be able to safely use the instruments used for the study of macromolecules, nucleic acid sequencing techniques and bioinformatics analysis of genomic data.

Course contents

This course is part of the Integrated Course “ATTIVITÀ SPERIMENTALE NEL LABORATORIO BIOTECNOLOGICO”.

At the of the Integrated Course unit, the student will be able to understand the functioning of a biochemistry and cell culture laboratory. The student is able to use the instruments in the biochemistry laboratory, perform cell cultures, perform sequencing techniques and evaluate gene expression. The student is also able to process collected data and plan an experimental design.

SPECIFIC PREREQUISITES FOR THIS COURSE:

To better understand the topics covered in this course, students are advised to have already acquired knowledge in the following areas: general chemistry, cell biology, and biochemistry, with particular emphasis on the structure and function of biomolecules (proteins, carbohydrates, lipids, nucleic acids) and the main metabolic pathways. A good understanding of fundamental laboratory methods (e.g., use of scales, pH meters, and centrifuges) is also helpful.

COURSE CONTENTS:

MODULE 1 – Giulia Andreani 3 CFU

The syllabus is structured as follows:

Lectures:

• Introduction to the clinical biochemistry laboratory (4 hours) (analytical and biological variability, analytical interference, method validation, sampling of biological matrices useful for performing clinical biochemistry tests)
• Protein quantification in biological matrices (6 hours) (UV-VIS spectrophotometry, calibration curves and automatic analyzers, enzymatic assays)
• Purification and study of a proteome using qualitative techniques (3 hours) (chromatography, 1D and 2D electrophoresis, and mass spectrometry)
• Study of metals in biological systems and their interactions with protein molecules (3 hours) (coupled techniques such as chromatography-AAS).

Laboratory/Practical Sessions: each lab session will begin with a brief introduction to contextualize the purpose of the analysis and explain the protocol the student will perform. Using the analytical technique explained in the protocol, the student will obtain results that he will be able to interpret. The techniques covered in the labs will include:

• Quantification of proteins in biological matrices using colorimetric techniques in UV-VIS spectrophotometry (5 hours)

• Separation of a complex biological matrix using gel filtration chromatography (5 hours)

• Separation of a proteome using 1D SDS-PAGE electrophoresis (6 hours)

MODULE 2 - 2 CFU Fabio Gentilini

This highly practical course provides students with in-depth training in molecular biology techniques applied to the diagnosis of genetic and neoplastic diseases, as well as in parentage identification in domestic animals. Each lab activity is preceded by a brief theoretical introduction to contextualize the objectives and procedures of the experiments.

The course begins with the fundamental methods of molecular biology, including DNA extraction, PCR, Sanger sequencing, fragment analysis, and the study of single nucleotide polymorphisms (SNPs). These techniques are applied to the genetic characterization and molecular diagnosis of biological samples.

Students will explore the molecular diagnostics of neoplastic diseases, focusing on the genetic basis of immunoglobulins, the concept of lymphoid markers, and the gene rearrangement of Ig and TCR loci. Techniques such as heteroduplex analysis and geneScanning will be used for lymphoid clonality assessment in hands-on lab sessions.

The role of somatic mutations in cancerogenesis will be addressed by distinguishing between driver and passenger mutations. Practical sessions will include detection of such mutations in tumor tissues using real-time PCR and high-resolution melting (HRM) analysis.

Another module covers the analysis of repetitive DNA, particularly microsatellites, which serve as polymorphic markers in both parentage testing and pedigree analysis. Through laboratory exercises, students will perform targeted amplifications and interpret genetic profiles.

Germline mutation genotyping techniques will also be addressed, employing restriction enzymes, real-time PCR, HRM, and primer extension methods, with hands-on work on both pathological and healthy samples.

The course concludes with an introduction to data analysis and bioinformatics. Students will learn how to select molecular targets and mine genetic sequences for diagnostic assay design. They will use online tools to design primers and become familiar with sequencing data formats (e.g., FASTA, FASTQ). Practical training will be provided on the Galaxy platform (GUI Galaxy), where students will carry out basic workflows such as trimming, mapping, and visualizing sequencing results.

Readings/Bibliography

MODULE 1

The teaching materials for this course are available on the Virtuale Learning Environment (https://virtuale.unibo.it/?lang=en ).

On the same site, the instructor also provides supplementary materials for further study and videos related to the laboratory activities.

Scientific articles illustrating the application of the techniques studied will be distributed during the course.

For the section on proteomics, the following text is recommended:

Proteomics T. Alberio, M. Fasano, P. Roncada (EdiSES, 2021)

MODULE 2

The preparation for the final exam is based exclusively on the teaching materials provided by the teacher, including lecture slides, handouts, selected scientific articles, and laboratory protocols used during practical sessions. All materials will be made available through the channels announced at the beginning of the course. Non-attending students are strongly advised to consult the full set of materials, as they represent the sole source of reference for the exam.

Teaching methods

The course includes both theoretical lectures and practical/laboratory sessions.

According to the students, a topic may be explored in depth through group work. Innovative teaching techniques will be employed during the lessons, aimed at encouraging active student participation, including the use of interactive quizzes to test learning.

Regarding laboratory activities, to facilitate the learning process, each student will be provided with a handout explaining the protocols for the practical activities. The handout will also contain worksheets that each student will complete, collecting the data obtained from their experimental work. At the end of the practical activity, students should be able to process the collected data using appropriate spreadsheets and discuss the final results in group work.

Considering the types of activities and teaching methods adopted, attendance for this course requires the successful completion of Modules 1 and 2 via e-learning, and Module 3 on health and safety training in study environments. Information about the schedule and access to Module 2 is available in the dedicated section of the Degree Program website.

Participation in practical and laboratory sessions requires wearing a lab coat and appropriate footwear. Suitable personal protective equipment (PPE), such as disposable latex gloves, will be provided as needed.

Assessment methods

The assessment for the Integrated Course “EXPERIMENTAL ACTIVITY IN THE BIOTECHNOLOGY consists of 2 parts:

First part: written test including module 1 and module 2 of APPLIED EXPERIMENTAL BIOLOGY (https://www.unibo.it/en/study/course-units-transferable-skills-moocs/course-unit-catalogue/course-unit/2025/543766). 

Second part: written test including module 1 and module 2 of Biochemistry and Clinical Molecular Biology

The written test consisting of 26 multiple-choice and 2 open-choice, the latter mainly related to the laboratory activity. Maximum duration of the exam 60 minutes.

During the test, the use of support material or devices such as calculators, tablets, smartwatches, computers is not allowed, except for those that may be permitted by the teacher.

The evaluation of the answers of the test involves: multiple-choice exact answers 1 point; answers to open questions up to a maximum of 2.

The test is considered to be passed with a minimum score of 18/30. 

The exam is considered passed only if all parts are successfully completed. The final grade is determined by the the average of the grades from the various parts of the exam, expressed out of 30). A minimum final grade of 18/30 is required.

Negative results are not graded numerically but recorded as “withdrawn” or “failed” in the electronic transcript on AlmaEsami, and do not affect the student’s academic record.

Grades for individual parts and the final grade will be published on the Virtuale Learning Environment (https://virtuale.unibo.it/?lang=en ) by the designated course contact within 5 working days of the exam.

Students may reject the final grade 1 time by informing the course examiner via email within 5 working days.

The designated course contact for this course is prof. Chiara Bernardini.

Students can register for exams through the AlmaEsami platform (http://almaesami.unibo.it/ ). Exams are scheduled during the designated periods in the academic calendar. Additional sessions are available for students beyond the standard program duration.

Students with learning disorders and/or temporary or permanent disabilities: please, contact the office responsible (https://site.unibo.it/studenti-con-disabilita-e-dsa/en/for-students ) as soon as possible so that they can propose acceptable adjustments. The request for adaptation must be submitted in advance (15 days before the exam date) to the lecturer, who will assess the appropriateness of the adjustments, taking into account the teaching objectives.

Teaching tools

PowerPoint presentations will be used for lectures and Excel spreadsheets for demonstrations of data processing methods; both presentations and spreadsheets will be uploaded to the instructor's EOL website. Databases and other online teaching resources will be consulted, including virtual labs. Digital tools will be used during lectures to support and complement lectures, as well as specific apps for conducting surveys and self-assessment tests.

For practical exercises, students will have access to individual workstations equipped with suitable laboratory equipment for the practical activities.

In case of difficulty understanding the course content, the instructor is available for clarification meetings, which must be scheduled via email.

Office hours

See the website of Giulia Andreani

See the website of Fabio Gentilini