Information Package / Course Catalogue
Proteins Structures and Functions
Course Code: ZBY506
Course Type: Area Elective
Couse Group: Second Cycle (Master's Degree)
Education Language: Turkish
Work Placement: N/A
Theory: 3
Prt.: 0
Credit: 3
Lab: 0
ECTS: 8
Objectives 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. 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.

Course Content

This course includes that information about structural and functional relationship of proteins at molecular level; problem solving on novel areas such as rational drug design; analyzing and manipulating the chemical and physical interactions between groups and atoms functional in assuming the different hierarchical organization levels of protein structure.

Name of Lecturer(s)
Lec. Murat Kemal AVCI
Learning Outcomes
1.Distinguish the structural and functional relationship of proteins at molecular level
2.Apply his/her structural knowlodge and ability to problem solving capacity to novel areas such as rational drug design
3.Analyze and manipulate the chemical and physical interactions between groups and atoms functional in assuming the different hierarchical organization levels of protein structure with the aid of DeepView program and use this it to desigh economic and effective wet lab experiments
4.Get knowledge about protein synthesis
5.To be able to search information about protein structure functions at academic level
Recommended or Required Reading
1.Protein Structure and Fuction, Petsko G, A and Ringe D; Introduction to protein structure, Branden C; Introduction to Protein Architecture, Lesk A, M; Lehninger Principles of Biochemistry,David L. Nelson, Michael M. Cox. M. Cox
Weekly Detailed Course Contents
Week 1 - Theoretical
Structural Genomics and Proteomiks
Week 2 - Theoretical
Structure determination; X-Ray crystallography and NMR interpretation of structural information
Week 3 - Theoretical
Importance and determinants of secondary structure. Properties of alpha helix and beta sheets. Prediction of secondary structure
Week 4 - Theoretical
Tertiary structure and stability. Weak interactions, Protein flexibility
Week 5 - Theoretical
Control of protein function. Mechanism of regulation
Week 6 - Theoretical
The structural basis of protein function.
Week 7 - Theoretical
Control of protein function. Mechanism of regulation
Week 8 - Theoretical
Relations of Amino asit structure and protein function
Week 9 - Theoretical
Motor protein switches. Protein degradation and other regulatory modifications.
Week 10 - Theoretical
Strategies for determining binding sites and catalytic residues.
Week 11 - Theoretical
Homology modeling, profile based threading and ab-inito modeling
Week 12 - Theoretical
Analyzing and manuplating protein structure for ligand binding sites and catalytic sequences
Week 13 - Theoretical
Techniques for probing the functions of proteins
Week 14 - Theoretical
Fusion proteins
Assessment Methods and Criteria
Type of AssessmentCountPercent
Midterm Examination1%30
Final Examination1%70
Workload Calculation
ActivitiesCountPreparationTimeTotal Work Load (hours)
Lecture - Theory14103182
Midterm Examination1819
Final Examination1819
TOTAL WORKLOAD (hours)200
Contribution of Learning Outcomes to Programme Outcomes
PÇ-1
PÇ-2
PÇ-3
PÇ-4
PÇ-5
OÇ-1
5
5
5
4
5
OÇ-2
5
5
4
4
5
OÇ-3
5
5
5
3
5
OÇ-4
4
3
4
3
4
OÇ-5
4
3
2
4
5
Adnan Menderes University - Information Package / Course Catalogue
2026