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Code BIO 304
Term 201702
Title Biological Function and Structure
Faculty Faculty of Engineering and Natural Sciences
Subject Mol.Bio.Genetic&Bioengin.(BIO)
SU Credit 3
ECTS Credit 6.00 / 6.00 ECTS (for students admitted in the 2013-14 Academic Year or following years)
Instructor(s) Deniz Sezer,
Detailed Syllabus
Language of Instruction English
Level of Course Undergraduate
Type of Course Click here to view.
(only for SU students)
Mode of Delivery Formal lecture,Interactive lecture
Planned Learning Activities Interactive,Communicative,Discussion based learning

The course will treat the chemistry and structure of biological molecules as a basis for understanding and predicting their structures and structure-function relations. Emphasis will be on macromolecular assemblies and their interactions, structural transitions, ligand inter and analysis of the structural changes that lead to reactivity, stability and accomplishment of the function.


The aim of this course is to walk students through the main ideas and experimental
techniques in structural biology following the shortest path from the significant events in the history of the field to the recent research literature.

Learning Outcome

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.

Programme Outcomes
Common Outcomes For All Programs
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. 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 Identify, define, formulate and solve complex engineering problems; choose and apply suitable analysis and modeling methods for this purpose.
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.
4 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.
5 Design and conduct experiments, collect data, analyze and interpret the results to investigate complex engineering problems or program-specific research areas.
6 Knowledge of business practices such as project management, risk management and change management; awareness on innovation; knowledge of sustainable development.
7 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; understanding of professional and ethical responsibility.
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.
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.
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.
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.
3 Predicting and understanding the behavior of a material under use in a specific environment knowing the internal structure or vice versa.
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 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.
1 Use mathematics (including derivative and integral calculations, probability and statistics), basic sciences, computer and programming, and electronics engineering knowledge to design and analyze complex electronic circuits, instruments, software and electronics systems with hardware/software.
2 Analyze and design communication networks and systems, signal processing algorithms or software using advanced knowledge on differential equations, linear algebra, complex variables and discrete mathematics.
Assessment Methods and Criteria
  Percentage (%)
Final 25
Midterm 20
Assignment 15
Participation 15
Written Report 13
Presentation 12
Recommended or Required Reading

Branden and Tooze, Introduction to Protein Structure, 2nd edition, Garland Publishing, 1999.
Petsko and Ringe, Protein Structure and Function, New Science Press, 2004.


1. Linus Pauling, Robert B. Corey, and H. R. Branson, The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain, PNAS, 37, 205?211 (1951).
2. Linus Pauling and Robert B. Corey, Configurations of polypeptide chains with favored orientations around single bonds: two newpleated sheets, PNAS, 37, 729?740 (1951).

1. Linus Pauling and Robert B. Corey, A proposed structure for the nucleic acids, PNAS, 39, 84?97 (1953).
2. J. D. Watson and F. H. C. Crick, Molecular Structure of Nucleic Acids, Nature, 171, 737?738 (1953).
3. J. D. Watson and F. H. C. Crick, Genetical Implications of the Structure of Deoxyribonucleic Acid, Nature, 171, 964?967 (1953).

1. J. C. Kenrew, G. Bodo, H. M. Dintzis, R. G. Parrish, H. Wyckoff, and D. C. Phillips, A threedimensional model of the myoglobin molecule obtained by X-ray analysis, Nature, 181, 662?666 (1958).
2. J. C. Kendrew, R. E. Dickerson, B. E. Strandberg, R. G. Hart, D. R. Davies, D. C. Pillips, and V. C. Shore, Structure of Myoglobin: A Three-Dimensional Fourier Synthesis at 2 ?A Resolution, Nature, 185, 422?427 (1960).
3. J. C. Kendrew, H. C. Watson, B. E. Strandberg, R. E. Dickerson, D. C. Pillips, and V. C. Shore, A Partial Determination by X-ray Methods, and Correlation with Chemical Data, Nature, 190, 666?670 (1961).

1. M. F. Perutz, M. G. Rossmann, Ann F. Cullis, Hilary Muirhead, Georg Will, and A. C. T. North, Structure of Haemoglobin: A Three-Dimensional Fourier Synthesis at 5.5?A Resolution, Obtained by X-Ray Analysis, Nature, 185, 416?422 (1960).
2. Hilary Muirhead and M. F. Perutz, Structure Of Haemoglobin: A Three-Dimensional Fourier Synthesis of Reduced Human Haemoglobin at 5.5 ?A Resolution, Nature, 199, 633?638 (1963).

1. Declan A. Doyle, Jo?ao Morais Cabral, Richard A. Pfuetzner, Anling Kuo, Jacqueline M. Gulbis,
Steven L. Cohen, Brian T. Chait, and Roderick MacKinnon, The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity, Science, 280, 69?77 (1998).
2. Yufeng Zhou, Jo?ao H. Morais-Cabral, Amelia Kaufman and Roderick MacKinnon, Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 ?A resolution, Nature, 414, 43?48 (2001).

1. Jo?ao H. Morais-Cabral, Yufeng Zhou and Roderick MacKinnon, Energetic optimization of ion conduction rate by the K+ selectivity filter, Nature, 414, 37?42 (2001).
2. Simon Bern`eche and Beno??t Roux, Energetics of ion conduction through the K+ channel, Nature, 414, 73?77 (2001).

1. Elan Zohar Eisenmesser, Daryl A. Bosco, Mikael Akke, and Dorothee Kern, Enzyme Dynamics During Catalysis, Science, 295, 1520?3 (2002).
2. Elan Z. Eisenmesser, Oscar Millet, Wladimir Labeikovsky, Dmitry M. Korzhnev, MagnusWolf-Watz, Daryl A. Bosco, Jack J. Skalicky, Lewis E. Kay, Dorothee Kern, Intrinsic dynamics of an enzyme underlies catalysis, Nature, 438, 117?21 (2005).

1. James S. Fraser, Michael W. Clarkson, Sheena C. Degnan, Renske Erion, Dorothee Kern, Tom Alber, Hidden alternative structures of proline isomerase essential for catalysis, Nature, 462, 669?73 (2009).

1. Charalampos G. Kalodimos, Nikolaos Biris, Alexandre M. J. J. Bonvin, Marc M. Levandoski, Marc Guennuegues, Rolf Boelens, and Robert Kaptein, Structure and Flexibility Adaptation in Nonspecific and Specific Protein-DNA Complexes, Science, 462, 386?9 (2004).