Department of Biomedical Engineering

BME 315 | Course Introduction and Application Information

Course Name

Molecular Biophysics

Code	Semester	Theory (hour/week)	Application/Lab (hour/week)	Local Credits	ECTS
BME 315	FALL	3	0	3	5

Prerequisites	GBE 100 To succeed (To get a grade of at least DD)
Course Language	English
Course Type	ELECTIVE_COURSE
Course Level	First Cycle
Mode of Delivery	Face-To-Face
Teaching Methods and Techniques of the Course	-
National Occupational Classification Code	-
Course Coordinator	Doç. Dr. Osman Doluca
Course Lecturer(s)	Doç. Dr. Osman Doluca
Assistant(s)	-

Course Objectives

The aim of this course is to discuss the theories and applications of biophysics in the fields of nanomedicine and biomedical sciences. Biophysics is a promising interdisciplinary field that combines the principles and concepts of physics, biology, chemistry, biochemistry, medicine, and engineering. The objective of this course is to provide a comprehensive introduction to biological systems at the molecular and subcellular levels, with an emphasis on electrical and dynamic behavior. Additionally, the course aims to discuss fundamental theories in biomedicine and their applications through current examples.

Learning Outcomes

The students who succeeded in this course;

Name	Description	PC Sub	* Contribution Level
Name	Description	PC Sub	1	2	3	4	5
LO1	Will be able to explain the terminology related to biophysics,	1.2		X
LO2	Will be able to identify biological structures and biomedical samples,	1.5			X
LO3	Will be able to describe the radiation function, the interaction of light with matter and biophysical methods,	1.2			X
LO4	Will be able to explain the applicability of biophysical principles to the biomedical field,	1.5		X
LO5	Will be able to discuss new and cutting-edge technologies in the field of biomedicine and nanobiomedicine.	5.1		X

Course Description

This course covers the binding interactions of biomolecules/biopolymers, structural-functional and dynamic properties of biomolecules (nucleic acids, proteins, lipids, etc.), enzyme mechanisms, cell membrane dynamics, membrane proteins, transport, physics of neurons, thermodynamics, bioenergetics, radiation processes, biomedical spectroscopy, infrared spectroscopy, and new approaches in nanobiomedicine and biomedical fields.

Related Sustainable Development Goals

Course Category	Core Courses
	Major Area Courses	X
	Supportive Courses
	Media and Managment Skills Courses
	Transferable Skill Courses

WEEKLY SUBJECTS AND RELATED PREPARATION STUDIES

Week	Subjects	Required Materials	Learning Outcome
1	Molecular forces in biological structures: interactions, bonding, force fields, energy functions	Chapter 2, Jackson, M. B. (2006). Molecular and Cellular Biophysics. Cambridge University Press. ISBN 052162441	LO1
2	Organelles and molecular structure of cells	Chapter 1, Abeles, R. H., Frey, P. A., & Jencks, W. P. (1992). Biochemistry. Jones & Bartlett Publishers. ISBN-13 978-0867202120	LO2
3	Structural and functional properties of biomolecules - nucleic acids	Chapter 7,12,19, Abeles, R. H., Frey, P. A., & Jencks, W. P. (1992). Biochemistry. Jones & Bartlett Publishers. ISBN-13 978-0867202120	LO2
4	Structural and functional properties of biomolecules - proteins	Chapter 7,12,19, Abeles, R. H., Frey, P. A., & Jencks, W. P. (1992). Biochemistry. Jones & Bartlett Publishers. ISBN-13 978-0867202120	LO2
5	Enzyme mechanisms, Enzyme reactions and kinetics	Chapter 10, Jackson, M. B. (2006). Molecular and Cellular Biophysics. Cambridge University Press. ISBN 052162441	LO2
6	Thermodynamics, bioenergetics, ionization of biological molecules	Chapter 13, Jackson, M. B. (2006). Molecular and Cellular Biophysics. Cambridge University Press. ISBN 052162441	LO3
7	Ion permeability and membrane potential, neuron physics, nerve signals, action potential	Chapter 13, Jackson, M. B. (2006). Molecular and Cellular Biophysics. Cambridge University Press. ISBN 052162441	LO3
8	Midterm		-
9	Interaction of IR radiation with biomolecules, vibration modes; Infrared Spectroscopy in Biomedical field	Chapter 12, Atkins, P., De Paula, J., & Keeler, J. (2022). Atkins’ physical chemistry. Oxford University Press. ISBN 9780198847816	LO4
10	Radiation processes (emission, scattering, absorption) and properties of light; UV-Vis Spectroscopy, CD Spectroscopy, Fluorescence Spectroscopy, and Biomedical applications - II	Chapter 12, Atkins, P., De Paula, J., & Keeler, J. (2022). Atkins’ physical chemistry. Oxford University Press. ISBN 9780198847816	LO4
11	Radiation processes (emission, scattering, absorption) and properties of light; UV-Vis Spectroscopy, CD Spectroscopy, Fluorescence Spectroscopy, and Biomedical applications - II	Chapter 12, Atkins, P., De Paula, J., & Keeler, J. (2022). Atkins’ physical chemistry. Oxford University Press. ISBN 9780198847816	LO4
12	X-ray crystallography, diffraction; Drug/ligand interactions	Lecture notes	LO5
13	Nanobiomedicine, Drug delivery, Characterization	Lecture notes	LO5
14	Studies from recent literature on the application of biomedical and biophysical techniques to biological samples	Lecture notes	LO5
15	Review	Lecture notes	-
16	Final Exam		-

Course Notes/Textbooks	Jackson M. B. (2006). Molecular and Cellular Biophysics. Cambridge University Press. ISBN 052162441 Atkins P. De Paula J. & Keeler J. (2022). Atkins’ physical chemistry. Oxford University Press. ISBN 9780198847816 Abeles R. H. Frey P. A. & Jencks W. P. (1992). Biochemistry. Jones & Bartlett Publishers. ISBN-13 978-0867202120
Suggested Readings/Materials	-

EVALUATION SYSTEM

Semester Activities	Number	Weighting	LO1	LO2	LO3	LO4	LO5
Quizzes / Studio Critiques	1	30		X	X	X	X
Midterm	1	30	X	X	X
Final Exam	1	40	X	X	X	X	X
Total	3	100

ECTS / WORKLOAD TABLE

Semester Activities	Number	Duration (Hours)	Workload
Participation	-	-	-
Theoretical Course Hours	16	3	48
Laboratory / Application Hours	-	-	-
Study Hours Out of Class	14	2	28
Field Work	-	-	-
Quizzes / Studio Critiques	1	15	15
Portfolio	-	-	-
Homework / Assignments	-	-	-
Presentation / Jury	-	-	-
Project	-	-	-
Seminar / Workshop	-	-	-
Oral Exams	-	-	-
Midterms	1	27	27
Final Exam	1	32	32
		Total	150

COURSE LEARNING OUTCOMES AND PROGRAM QUALIFICATIONS RELATIONSHIP

#	PC Sub	Program Competencies/Outcomes	* Contribution Level
#	PC Sub	Program Competencies/Outcomes	1	2	3	4	5
1	Engineering Knowledge: Knowledge of mathematics, science, basic engineering, computation, and related engineering discipline-specific topics; the ability to apply this knowledge to solve complex engineering problems.
	1	Mathematics
	2	Science		LO1	LO3
	3	Basic Engineering
	4	Computation
	5	Related engineering discipline-specific topics		LO4	LO2
	6	The ability to apply this knowledge to solve complex engineering problems
2	Problem Analysis: Ability to identify, formulate and analyze complex engineering problems using basic knowledge of science, mathematics and engineering, and considering the UN Sustainable Development Goals relevant to the problem being addressed.
3	Engineering Design: The ability to devise creative solutions to complex engineering problems; the ability to design complex systems, processes, devices or products to meet current and future needs, considering realistic constraints and conditions.
	1	Ability to design creative solutions to complex engineering problems
	2	Ability to design complex systems, processes, devices or products to meet current and future needs, considering realistic constraints and conditions
4	Use of Techniques and Tools: Ability to select and use appropriate techniques, resources, and modern engineering and computing tools, including estimation and modeling, for the analysis and solution of complex engineering problems, while recognizing their limitations.
5	Research and Investigation: Ability to use research methods to investigate complex engineering problems, including literature research, designing and conducting experiments, collecting data, and analyzing and interpreting results.
	1	Literature research for the study of complex engineering problems		LO5
	2	Designing experiments
	3	Ability to use research methods, including conducting experiments, collecting data. analyzing and interpreting results
6	Global Impact of Engineering Practices: Knowledge of the impacts of engineering practices on society, health and safety, economy, sustainability, and the environment, within the context of the UN Sustainable Development Goals; awareness of the legal implications of engineering solutions.
	1	Knowledge of the impacts of engineering practices on society, health and safety, economy, sustainability, and the environment, within the context of the UN Sustainable Development Goals
	2	Awareness of the legal implications of engineering solutions
7	Ethical Behavior: Acting in accordance with the principles of the engineering profession, knowledge about ethical responsibility; awareness of being impartial, without discrimination, and being inclusive of diversity.
	1	Acting in accordance with the principles of the engineering profession, knowledge about ethical responsibility ethical responsibility
	2	Awareness of being impartial and inclusive of diversity, without discriminating on any subject
8	Individual and Teamwork: Ability to work effectively, individually and as a team member or leader on interdisciplinary and multidisciplinary teams (face-to-face, remote or hybrid).
	1	Ability to work individually and within the discipline
	2	Ability to work effectively as a team member or leader in multidisciplinary teams (face-to-face, remote or hybrid)
9	Verbal and Written Communication: Taking into account the various differences of the target audience (such as education, language, profession) on technical issues.
	1	Ability to communicate verbally
	2	Ability to communicate effectively in writing
10	Project Management: Knowledge of business practices such as project management and economic feasibility analysis; awareness of entrepreneurship and innovation.
	1	Knowledge of business practices such as project management and economic feasibility analysis
	2	Awareness of entrepreneurship and innovation
11	Lifelong Learning: Lifelong learning skills that include being able to learn independently and continuously, adapting to new and developing technologies, and thinking questioningly about technological changes.