Biological Function and Structure (BIO 304)

2022 Spring
Faculty of Engineering and Natural Sciences
Canan At─▒lgan,
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Formal lecture,Interactive lecture,Seminar,Group tutorial
Interactive,Communicative,Discussion based learning,Task based learning,Simulation
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The course will treat the chemistry and structure of biological molecules as a basis for understanding and predicting their function as nanomachines. Emphasis will be on proteins and their interactions, structural transitions, ligand interactions and analysis of the structural changes that lead to reactivity, stability, and accomplishment of the function.


To equip the students with (i) a basic understanding of structure - function relationships in biological macromolecules, (ii) convey the fundamental principles of experimental and computational techniques utilized for this purpose, (iii) reconsider evolution from the perspective of molecular structures.


  • Upon successful completion of this course students are expected to: Describe the basic steps in using X-ray crystallography for determination of macromolecular structure
  • Describe the basic ideas behind using NMR spectroscopy for determination of protein structures
  • Be aware of the fact that NMR experiments can be used to acquire information about the dynamics of the macromolecule on various time scales
  • Have a basic understanding of how molecular dynamics simulations of biomolecules work
  • Utilize available software for visualizing the structure of biomolecules
  • Understand the source and magnitude of the physical driving forces responsible for the spontaneous folding and interactions of biomolecules
  • Read and understand the main ideas of a research article in the field of structural biology
  • Present coherently, using the correct terminology, the findings of a research article in the field of structural biology that they may have read.


1. Understand the world, their country, their society, as well as themselves and have awareness of ethical problems, social rights, values and responsibility to the self and to others. 3

2. Understand different disciplines from natural and social sciences to mathematics and art, and develop interdisciplinary approaches in thinking and practice. 4

3. Think critically, follow innovations and developments in science and technology, demonstrate personal and organizational entrepreneurship and engage in life-long learning in various subjects; have the ability to continue to educate him/herself. 3

4. Communicate effectively in Turkish and English by oral, written, graphical and technological means. 5

5. Take individual and team responsibility, function effectively and respectively as an individual and a member or a leader of a team; and have the skills to work effectively in multi-disciplinary teams. 3

1. Possess sufficient knowledge of mathematics, science and program-specific engineering topics; use theoretical and applied knowledge of these areas in complex engineering problems. 2

2. Identify, define, formulate and solve complex engineering problems; choose and apply suitable analysis and modeling methods for this purpose. 4

3. Develop, choose and use modern techniques and tools that are needed for analysis and solution of complex problems faced in engineering applications; possess knowledge of standards used in engineering applications; use information technologies effectively. 5

4. Have the ability to design a complex system, process, instrument or a product under realistic constraints and conditions, with the goal of fulfilling specified needs; apply modern design techniques for this purpose. 4

5. Design and conduct experiments, collect data, analyze and interpret the results to investigate complex engineering problems or program-specific research areas. 3

6. Possess knowledge of business practices such as project management, risk management and change management; awareness on innovation; knowledge of sustainable development. 1

7. Possess knowledge of impact of engineering solutions in a global, economic, environmental, health and societal context; knowledge of contemporary issues; awareness on legal outcomes of engineering solutions; knowledge of behavior according to ethical principles, understanding of professional and ethical responsibility. 3

8. Have the ability to write effective reports and comprehend written reports, prepare design and production reports, make effective presentations, and give and receive clear and intelligible instructions. 4

8. Have the ability to write effective reports and comprehend written reports, prepare design and production reports, make effective presentations, and give and receive clear and intelligible instructions. 5

1. Comprehend key concepts in biology and physiology, with emphasis on molecular genetics, biochemistry and molecular and cell biology as well as advanced mathematics and statistics. 5

2. Develop conceptual background for interfacing of biology with engineering for a professional awareness of contemporary biological research questions and the experimental and theoretical methods used to address them. 5

1. Use mathematics (including derivative and integral calculations, probability and statistics, differential equations, linear algebra, complex variables and discrete mathematics), basic sciences, computer and programming, and electronics engineering knowledge to (a) Design and analyze complex electronic circuits, instruments, software and electronics systems with hardware/software or (b) Design and analyze communication networks and systems, signal processing algorithms or software 1

1. Applying fundamental and advanced knowledge of natural sciences as well as engineering principles to develop and design new materials and establish the relation between internal structure and physical properties using experimental, computational and theoretical tools. 5

2. Merging the existing knowledge on physical properties, design limits and fabrication methods in materials selection for a particular application or to resolve material performance related problems. 2

3. Predicting and understanding the behavior of a material under use in a specific environment knowing the internal structure or vice versa. 5

1. Familiarity with concepts in statistics and optimization, knowledge in basic differential and integral calculus, linear algebra, differential equations, complex variables, multi-variable calculus, as well as physics and computer science, and ability to use this knowledge in modeling, design and analysis of complex dynamical systems containing hardware and software components. 2

2. Ability to work in design, implementation and integration of engineering applications, such as electronic, mechanical, electromechanical, control and computer systems that contain software and hardware components, including sensors, actuators and controllers. 2


  Percentage (%)
Final 30
Midterm 25
Assignment 15
Participation 10
Presentation 20



1. Branden and Tooze, Introduction to Protein Structure, 2nd edition, Garland Science, 1999.
2. Bahar, Jernigan and Dill, Protein Actions, Taylor & Francis, 2017.
3. Petsko and Ringe, Protein Structure and Function, New Science Press, 2004.