Teaching plan for the course unit

 

 

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General information

 

Course unit name: Molecular and Cell Bioengineering

Course unit code: 363746

Academic year: 2021-2022

Coordinator: Jordi Alcaraz Casademunt

Department: Department of Biomedical Sciences

Credits: 6

Single program: S

 

 

Estimated learning time

Total number of hours 150

 

Face-to-face and/or online activities

74

(In case of official restrictions caused by covid-19, a contingency plan will be applied to preserve students dedication.)

 

-  Lecture

Face-to-face

 

36

 

-  Group tutorial

Face-to-face

 

2

 

-  Laboratory session

Face-to-face

 

18

 

-  Seminar

Face-to-face

 

18

Supervised project

17

Independent learning

59

 

 

Recommendations

 

Students must have completed most first-year subjects, specifically Calculus of a Single Variable, Cell Biology and Biophysics.

 

 

Competences to be gained during study

 

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To be able to resolve problems with initiative and creativity and to take technological decisions in accordance with criteria of cost, quality, safety, sustainability, time and respect for the profession's ethical principles (Instrumental).

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To be able to analyse and summarize (Instrumental).

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To be able to work independently (Personal).

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To be able to work in a team or a multidisciplinary group (Personal).

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To be able to work in a multilingual environment and communicate and transmit knowledge, procedures, results, abilities and skills (oral and written) in a native and a foreign language (Instrumental).

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To gain knowledge of biomedical concepts and language.

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To know about and apply engineering concepts to the study of biological processes and the functions of the human organism. To gain knowledge of the atomic, molecular, cellular and organic levels of the physical mechanisms and phenomena that have an impact on health and disease.

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To know about alterations in the structure and function of the different types of cells.

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To use systems for the search and retrieval of biomedical information and procedures for clinical data. To be able to understand and critically interpret scientific texts and their sources.

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To know about cell function and structure and the techniques that are used to study this area.

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To know the basic aspects of descriptive and inferential statistical methods and to be able to use these in the biomedical sciences.

Learning objectives

 

Referring to knowledge

General skills

Upon completion of the course, students are able to:

— Understand the basic principles and the range of applicability of current bioengineering techniques used to study the fundamental aspects of physics underlying the functions of living cells and biomolecules.
— Understand the basis of current theoretical approaches used in the study of cell and molecular biophysics.
— Understand how bioengineering tools complement current techniques in cell and molecular cell biology and biochemistry.
— Use appropriate language for scientific communication (all lab reports will be written using the standard format required by peer-reviewed journals, i.e., introduction, material and methods, results, discussion, conclusions and references).
— Identify the essential physical principles underlying a given process in the context of biomolecules or cells.
— Improve their analytic and synthetic skills.
— Work in a multilingual environment and communicate knowledge, procedures, results and skills (spoken and written) in the student’s native language and in English.
— Work in teams and multidisciplinary groups.
— Work independently.

 

Referring to abilities, skills

Specific skills

Upon completion of the course, students are able to:

— Understand the basic unit of function and the concept of cellular microenvironment.
— Describe the main intermolecular forces in aqueous solutions.
— Describe the most common sources of noise in nanotechniques used in biology.
— Understand current techniques used to manipulate biomolecules and cells.
— Understand current techniques used to visualise physical processes in cells.
— Understand the passive physical processes that affect biomolecules.
— Understand the basics of molecular motors and other active physical processes that affect biomolecules.
— Understand the mechanical properties of biomolecules and cells.
— Understand the basic principles involved in the cellular transduction of physical cues.
— Understand the basic mechanisms of cell adhesion and migration.
— Describe the principal physical processes in cells.
— Describe the material properties of a cell.
— Understand the influence of cell shape on cellular functions.
— Understand and apply the concepts of engineering to the study of biological processes and the functions of the human body and know the physical processes at the atomic, molecular, cell and organism levels that are most relevant in normal and diseased conditions.
— Use biomedical language and understand biomedical concepts.
— Use appropriate search engines to find biomedical information and clinical documentation, and know how to read and interpret scientific literature and their sources.

 

 

Teaching blocks

 

1. Introduction

1.1. Conceptual framework: the physics of cells and biomolecules in the context of evolution

1.2. General strategies for building biophysical models

1.3. Overview of relevant biological entities: biomolecules, cells and tissues

1.4. Relevant biophysical scales

1.5. Relevant biophysical theoretical models

1.6. Basic statistical methods

2. Thermodynamic equilibrium in the living cell

2.1. Introduction

2.2. Classic thermodynamics revisited

2.3. Equilibrium states and free energy minimisation

2.4. Introduction to the tools of statistical mechanics

2.5. The Boltzmann distribution

2.6. Applications of the Boltzmann distribution; Equipartition of energy

3. Intermolecular surface forces in aqueous solutions

3.1. Introduction to intermolecular and surface forces in aqueous solutions

3.2. Useful techniques for probing intermolecular and surface forces: atomic force microscopy

3.3. Surface forces based on mechanical principles

3.4. Surface forces based on thermodynamic principles

3.5. Surface forces governed by electromagnetic principles: molecular recognition

4. Bioengineering approaches for manipulating single biomolecules and cells

4.1. Instrumentation requirements

4.2. Common noise sources: Fourier analysis

4.3. Nanoscopic techniques based on mechanical sensors and actuators

4.4. Nanoscopic techniques based on force fields

5. The biophysical context of biomolecules and cells

5.1. Passive versus active processes

5.2. Movement driven by external forces in the presence of damping

5.3. Movement driven by thermal energy: random walks

5.4. Physics of polymer chains

 

 

Teaching methods and general organization

 

The main objectives of the course are to introduce students to the main physical principles that underpin the essential processes in biomolecules and cells, and to present the current bioengineering approaches used in the study of these processes. Thus, the course is intrinsically multidisciplinary, combining topics from physics and engineering as well as from cell and molecular biology. Students work towards these objectives through lectures on the theory and in seminars involving the practical application of the main theoretical concepts. The course includes laboratory work in which students are given the opportunity to directly manipulate scientific data obtained in recent studies of cell and molecular biophysical processes, using state-of-the-art techniques. Students are also required to read scientific papers related to the data used in the laboratory sessions, as a means of learning about the general standards of scientific communication. In addition, the course includes a short group project in which students have to expand one of the topics of the course of their choice and make a final oral presentation. It is also important to note that this course is taught entirely in English.

In case of official restrictions caused by covid-19, a contingency plan will be applied to preserve students’ dedication. Teaching (including lectures, problem-solving sessions, seminars and laboratory work) will be held online through videos available in the Virtual Campus, and doubts will be solved through videoconference sessions, unless otherwise indicated.

 

 

Official assessment of learning outcomes

 

Students are assessed throughout the course, and the final grade combines the marks for assessed coursework (45% of the final grade) and a final examination (55% of the final grade).

a) Assessed coursework (45%)
Assessed coursework comprises a mid-semester test, covering almost half of the course content (worth 20% of the final grade), an extended individual written report on one of the laboratory assignments (12.5%), and a group research project expanding the topics covered in this course and orally presented (12.5%). Students who volunteer to solve selected problems in class are given extra credit.

b) Final examination (55%)
This examination assesses the students’ overall level of assimilation and understanding of the course content, including the theory, practical problem-solving exercises and laboratory work.

It may include any of the following: problem-solving exercises, multiple-choice questions and short-answer questions. 

Assessment focuses particularly on the following aspects:
— Understanding of the essential physical principles in the context of biomolecules and cells.
— Understanding of the essential physical principles underlying current techniques for studying biomolecules and cells.
— Skills applicable to producing quantitative solutions to physical problems involving biomolecules and cells.

A minimum grade of 3.5 in the final examination (55% of the final grade) is required to combine it with the marks of assessed coursework (45% of the final grade). Students must obtain a grade of at least 5 to pass the course. Students with a final grade lower than 5 are eligible to repeat assessment. The grade for the repeat assessment exam replaces that of the final examination to compute the final grade.

In case of official restrictions caused by covid-19, a contingency plan will be applied to ensure the continuity of continuous assessment and adapt this procedure as follows: (i) the oral presentation of the group project will be carried out via videoconference; (ii) the exams (mid-semester and final) will be carried out online by providing personalised problems to each student, who will have to scan the answers and upload them onto the Virtual Campus.

 

Examination-based assessment

Single assessment comprises an examination which assesses the students’ overall level of assimilation and understanding of the course content, including the theory, practical problem-solving exercises and laboratory work.

In case of official restrictions caused by covid-19, a contingency plan will be applied to adapt the final exam to online mode. In that case, personalised problems will be provided to each student, who will have to scan the answers and upload them onto the Virtual Campus.