To take this course, it is not required to have passed any specific courses from previous years, although a solid foundation in Thermodynamics is necessary, which the student should have gained through the "Physics" course in the first year and "Thermodynamics and Chemical Kinetics" in the second year. The concepts acquired will be applied later in the degree program in the mandatory courses "Spectroscopy of biomolecules", "Advanced Methods in Biochemistry", and in some electives.



In the future practice of the profession, through this course, the student will improve their ability to abstract and tackle biological problems by applying general operational models or using new techniques, many of which are based on physical properties. If, in the future, they wish to focus their activity in this area, it is recommended that they read the information provided by the Biophysical Society, which can be found at:

http://www.biophysics.org/Education/WhatisBiophysics/tabid/2287/Default.aspx

Specific Competencies:



- Describe at the molecular level how living beings extract, transform, and use energy from their environment.

- Understand the structural and thermodynamic bases of membrane transport and electrical potentials.



Description of Content:

Reversible thermodynamics and its application in biology. Calorimetric techniques. Thermodynamics of irreversible processes. Properties of biological membranes. Diffusion: Thermodynamic and kinetic aspects. Study methods. Mediated transport. Transporters. Bioelectric phenomena. Nerve impulse. Ion channels. Energy-transducing membranes. Biological energy transduction: Oxidative phosphorylation.



The main objective is to familiarize the student with the conceptual and theoretical basis of biophysics applied to biological problems. Additionally, the structures of macromolecules involved in these processes, such as transporters and ion channels, are described. A practical and quantitative approach is achieved through problem solving and computer simulation exercises.

The course will be divided into 3 general sections, each of which consists of 2 subsections and 4 topics.



Syllabus:



SECTION 1 - THERMODYNAMICS OF BIOLOGICAL PROCESSES.



1.1 Thermodynamics: systems in equilibrium.

Topic 1. Reversible thermodynamics.

Topic 2. Gibbs free energy and biochemical and biophysical applications.

Topic 3. Gibbs free energy and physical equilibria.



1.2 Thermodynamics: systems not in equilibrium.

Topic 4. Theory of absolute reaction rates (ARRT) and thermodynamics of irreversible processes.



SECTION 2 - SOLUTE MOVEMENTS THROUGH MEMBRANES



2.1 Diffusion. Kinetic studies. Thermodynamics and molecular differences in diffusion.

Topic 5. Types of solute movements and properties of biological membranes.

Topic 6. Concept of diffusion and kinetic studies.

Topic 7. Thermodynamics and the molecular side of diffusion phenomena.



2.2 Mediated transport. Kinetics. Thermodynamic characteristics.

Topic 8. Concept of mediated transport and kinetic and thermodynamic studies.

ACTIVITY: Identification and characteristics of transporters.



SECTION 3 - BIOELECTRIC AND BIOENERGETIC PHENOMENA



3.1 Bioelectric phenomena. Research methods. Nerve impulse.

Topic 9. Electrical properties of the membrane and action potential.

Topic 10. Voltage-gated ion channels and patch clamp.

Topic 11. Synaptic transmission and nicotinic acetylcholine receptor.



3.2 Transduction membranes and chemiosmotic energy transduction.

Topic 12. Molecular aspects of bioenergetics and mitochondrial oxidative phosphorylation.

In the Lectures (M), the course content will be explained along with various problems, and in the Classroom Practices (GA), both quantitative and qualitative exercises and problems related to the concepts presented in the lectures will be addressed.



The computer lab sessions (GO) will be used to delve into:

1- The resting potential

2- The action potential

3- The properties of neuronal communication

For all these topics, the software Neurons in Action v.2 will be used, and a document detailing the group work will be prepared and submitted.



Finally, in relation to the seminars, as an in-depth exploration of what was learned in the second part of the course, a learning activity on "Identification and characteristics of membrane transporters" will be conducted.



Cases of duplication or plagiarism detected in the practice report or the team project will be penalized.

• Continuous Assessment System
• Final Assessment System
• Tools and qualification percentages:
  • Written test to be taken (%): 70
  • Realization of Practical Work (exercises, cases or problems) (%): 15
  • PERSONAL/GROUP WORK (%): 15

Evaluation System:



For the final evaluation, the following will be taken into account:



- Completion of exams. The final exam will consist of a theoretical section with multiple-choice, short answer, and essay questions, as well as a problem-solving section: it will be worth 70% of the final grade.



- Computer practice work, reflected through the preparation of a practice notebook: it will be worth 15%.



- Group work/presentation carried out during the activity: it will be worth 15%.



The final grade will be obtained by adding the partial grades from the three evaluated sections. For the exam, both parts count equally towards the average grade. It is mandatory to obtain a minimum grade of 4.5/10 to compute the exam grade with the other activities, and a grade lower than 3.5/10 cannot be obtained in either part of the exam. To pass the course, a minimum score (45%) in each of the mentioned sections is required.



The completion of computer practices is mandatory.



The assessment and withdrawal from examination regulations will follow the current guidelines (BOPV March 13, 2017, 1311).



According to article 8.3, 'Students wishing to withdraw from continuous assessment shall have a period of 9 weeks from the start of the course to notify the responsible teacher of such withdrawal.' Activities not assessed through continuous assessment will be incorporated into the examination assessment period in agreement with the students involved one week after the withdrawal.



EXAMINATION WITHDRAWAL: In accordance with article 12.2, 'It shall be submitted in writing to the responsible teacher at least one month before the end date of the teaching period of the corresponding subject, i.e., in week 11 of the academic year.'



The assessment guidelines for this subject are based on the documents: “Normativa reguladora de la Evaluación del alumnado en las titulaciones oficiales de Grado” and “Protocolo sobre ética académica y prevención de las prácticas deshonestas o fraudulentas en las pruebas de evaluación y en los trabajos académicos en la UPV/EHU” (https://www.ehu.eus/es/web/estudiosdegrado-gradukoikasketak/akademia-araudiak)

If the subject is not passed in the regular examination period, the partial grades of the approved sections will be saved for the extraordinary examination period of the current academic year (July).

Open eGela course page: additional information will be provided

Basic bibliography

- Physical Biology of the Cell 2nd ed. R. Phillips, J. Kondev, J. Theriot, H.G.Garcia. Garland Science 2013

- Biophysics: A physiological Approach. P.F. Dillon. Cambridge University Press 2012.

- Biological Thermodynamics 2nd ed .D.T.Haynie. Cambridge University Press, 2008

- Membrane structural Biology 2nd ed. M. Luckey. Cambridge University Press , 2014

- Bioenergetics 4th ed D.G.Nicholls y S.J. Ferguson. Elsevier. 2013

- Molecular Biology of the Cell.7th ed Alberts et al.Garland 2022

- The molecules of life: Physical and Chemical Principles. J. Kuriyan, B. Konforti y D. Wemmer. Garland Science 2013.

- Cell Biology by the numbers. R. Millo y R. Phillips.Garland Science, 2016.

In-depth bibliography

- Comprehensive Biophysics (10 vols) Edward Engelman (Ed.) Academic Press, 2012
- Mechanics of the cell. 2nd ed . David Boal . Cambridge University Press, 2012.
- Single-Molecule Cellular Biophysics. M.C.Leake. Cambridge University Press, 2013.
- Methods in Molecular Biophysics: Structure, Dynamics, Function for Biology and Medicina. N.R.Zaccai, I.N. Serdyuk y J. Zaccai. Cambridge University Press, 2017.
- Advanced Techniques in Biophysics. J.L.R.Arrondo y A.Alonso. Springer, 2006
- Biocalorimetry 2: Applications of Calorimetry in the Biological Sciences. John E. Ladbury (Editor), Michael L. Doyle (Editor) Wiley, 2004
- Molecular and Cellular Biophysics. M.B. Jackson. Cambridge University Press, 2006
- Principles and Problems in Physical Chemistry for Biochemists.3rd ed N.C.Price, Raymond A. Dwek, R.G. Ratcliffe y Mark Wormald. 3ª ed. Oxford Univ Press 2001
- Cell Biology 4th ed. T.D.Pollard, W.C.Earshaw, J. Lippincott-Schwartz y Graham Johnson. Elsevier 2023

Journals

Annual Review of Biophysics: http://www.annualreviews.org/loi/biophys
Biophysical Journal: http://www.cell.com/biophysj
Science: http://www.science.com/science/index.htlm
Nature: http://www.nature.com/nature/index.htlm

Web addresses

Selected Topics in Biophysics from Biophysical Society: https://www.biophysics.org/education-careers/education- resources/selected-topics-in-biophysics
Structural Biophysics: http://blanco.biomol.uci.edu/WWWResources.html
Membrane proteins: https://blanco.biomol.uci.edu/mpstruc/
ATPsintase: http://www.csun.edu/~hcchm001/wwwatp2.htm
Ion channels: http://www.neuro.wustl.edu/neuromuscular/mother/chan.html
Electrophysiology: http://nerve.bsd.uchicago.edu
iBioseminars: http://www.ibiology.org/ibioseminars.html