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Syllabus ( MBG 424 )


   Basic information
Course title: Protein Structure - Function Relationships
Course code: MBG 424
Lecturer: Dr. Muslum YILDIZ
ECTS credits: 5
GTU credits: 3 (3+0+0)
Year, Semester: 4, Spring
Level of course: First Cycle (Undergraduate)
Type of course: Area Elective
Language of instruction: English
Mode of delivery: Face to face
Pre- and co-requisites: Biochemistry I
Professional practice: No
Purpose of the course: The fundemental outcome of this course is to enable students comprehend the relationships between protein structures and functions on atomic level while doing these they will acquire the means of visualizing and manuplating protein 3D structures using DeepView. This course will also introduce them to in silico rational drug design concept widely exploited by structure based biotech companies seeking novel chemicals to target cancer, neurologic disorders etc.
   Learning outcomes Up

Upon successful completion of this course, students will be able to:

  1. Apply his/her ability to investigate macromolecules at atomic level to related areas such as rational drug design, protein-protein interactions and protein engineering.

    Contribution to Program Outcomes

    1. To be able to define the structure-function relationship at the molecular level in cells and organisms.
    2. To be able to work individually, make independent decisions and participate actively in multidisciplinary group studies.
    3. To be able to follow current scientific and technological innovations with the awareness of continuous learning and to apply them in the field.
    4. To be able to present their studies in scientific talks and written texts in national and international scientific platforms by a foreign language.

    Method of assessment

    1. Homework assignment
    2. Laboratory exercise/exam
  2. Distinguish the relationship between the structure and functions of the proteins.

    Contribution to Program Outcomes

    1. To be able to define the structure-function relationship at the molecular level in cells and organisms.
    2. To be able to work individually, make independent decisions and participate actively in multidisciplinary group studies.

    Method of assessment

    1. Written exam
   Contents Up
Week 1: Protein function general overview (Pymol)
Week 2: Noncovalent interactions between atoms in biomolecules (PyMol)
Week 3: Hierarchy in protein structure, Primary structure, Amino acids ( Chemical and physical properties).
Week 4: Hierarchy in protein structure, Secondary structure (PyMol)
Week 5: Hierarchy in protein structure, Tertiary and quaternary structures (PyMol)
Week 6: post-translational modifications and metal centers (PyMol)
Week 7: Midterm exam


Week 8: energetics and protein stability, CD, flouresence, Thermal melting, spectroscopy ( Spartan)
Week 9: Protein-Ligand Interactions (Docking)
Week 10: Methods of Structure Determination x-ray, nmr, epr and hdx-ms (Docking)
Week 11: The structure of the Membrane proteins, channels and transporters (Docking)
Week 12: The structure of the Membrane proteins, channels and transporters (Docking)
Week 13: Protein structure and a molecular approach to medicine (Docking)
Week 14: Protein structure and a molecular approach to medicine (Docking)
Week 15*: General review.
Week 16*: Final exam
Textbooks and materials:
Recommended readings: 1. Protein Structure and Fuction, Petsko G, A and Ringe D;
2. Introduction to protein structure, Branden C;
3. Introduction to Protein Architecture, Lesk A, M;
4. Lehninger Principles of Biochemistry,David L. Nelson, Michael M. Cox
5. http://structome.org/index.php/Main_Page http://spdbv.vital-it.ch/
http://dock.compbio.ucsf.edu/DOCK_6/index.htm
  * Between 15th and 16th weeks is there a free week for students to prepare for final exam.
Assessment Up
Method of assessment Week number Weight (%)
Mid-terms: 7 25
Other in-term studies: 0 0
Project: 0 0
Homework: 5,11 30
Quiz: 0 0
Final exam: 16 45
  Total weight:
(%)
   Workload Up
Activity Duration (Hours per week) Total number of weeks Total hours in term
Courses (Face-to-face teaching): 3 14
Own studies outside class: 1 14
Practice, Recitation: 0 0
Homework: 5 1
Term project: 5 1
Term project presentation: 0 0
Quiz: 1 6
Own study for mid-term exam: 6 1
Mid-term: 1 1
Personal studies for final exam: 8 2
Final exam: 2 1
    Total workload:
    Total ECTS credits:
*
  * ECTS credit is calculated by dividing total workload by 25.
(1 ECTS = 25 work hours)
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