Nevşehir Hacı Bektaş Veli University Course Catalogue

Information Of Programmes

INSTITUTE OF SCIENCE / MBG625 - MOLECULAR BIOLOGY AND GENETICS (PHD)

Code: MBG625 Course Title: PROTEOMICS BIOINFORMATICS Theoretical+Practice: 3+0 ECTS: 6
Year/Semester of Study 1 / Fall Semester
Level of Course 3rd Cycle Degree Programme
Type of Course Optional
Department MOLECULAR BIOLOGY AND GENETICS (PHD)
Pre-requisities and Co-requisites None
Mode of Delivery Face to Face
Teaching Period 14 Weeks
Name of Lecturer NAŞİT İĞCİ (nasitigci@nevsehir.edu.tr)
Name of Lecturer(s)
Language of Instruction Turkish
Work Placement(s) None
Objectives of the Course
To give a practical knowledge about the aims of bioinformatics approaches in the field of proteomics studies.

Learning Outcomes PO MME
The students who succeeded in this course:
LO-1 can explain current bioinformatics strategies used in proteomics. PO-1 Have information about current issues in molecular biology and genetics.
PO-3 Make use of the knowledge they have in order to find a solution to problems by analyzing, comparing and questioning them and can carry out original research in the related field on their own
PO-6 Ability to design a research project in the field of molecular biology and genetics and to evaluate and present the results related to it
Examination
Presentation
LO-2 can perform some important bioinformatic analyses in proteomics. PO-3 Make use of the knowledge they have in order to find a solution to problems by analyzing, comparing and questioning them and can carry out original research in the related field on their own
PO-6 Ability to design a research project in the field of molecular biology and genetics and to evaluate and present the results related to it
Examination
Presentation
LO-3 gains knowledge about proteomics databases and can explain when to use which database in researches. PO-1 Have information about current issues in molecular biology and genetics.
PO-3 Make use of the knowledge they have in order to find a solution to problems by analyzing, comparing and questioning them and can carry out original research in the related field on their own
PO-4 Evaluate the knowledge and skills in a critical way in every activity regarding the field, thereby guiding their learning
PO-6 Ability to design a research project in the field of molecular biology and genetics and to evaluate and present the results related to it
Examination
Presentation
PO: Programme Outcomes
MME:Method of measurement & Evaluation

Course Contents
Current proteomics strategies, use of proteomics bioinformatics, analysis in gel-based expression studies, use of protein databases, mass spectrometry based proteomics experimental approaches and protein identification with bioinformatics tools, bioinformatics approaches in protein 3 dimensional structure model.
Weekly Course Content
Week Subject Learning Activities and Teaching Methods
1 Current strategies and data sources of proteomics. Lecture, Discussion, Question Answer, Literature Search
2 The place of bioinformatics in proteomics and their applications. Lecture, Discussion, Question Answer, Literature Search
3 Expression analysis with gel-based methods and evaluation and presentation of the results using softwares. Lecture, Discussion, Question Answer, Literature Search
4 Introduction of protein databases and methods of obtaining amino acid sequences in databases. Lecture, Discussion, Question Answer, Literature Search
5 The use of protein databases to achieve the desired knowledge and their use for specific purposes. Lecture, Discussion, Question Answer, Literature Search
6 Mass spectrometers and their use in proteomics. Lecture, Discussion, Question Answer, Literature Search
7 Structure and information of the spectrum obtained by mass spectrometry. Lecture, Discussion, Question Answer, Literature Search
8 mid-term exam
9 Protein identification by mass spectrometry I: Peptide Mass Fingerprint Analysis. Lecture, Discussion, Question Answer, Literature Search, Computer Work
10 Protein identification by mass spectrometry II: Peptide Fragment Fingerprint Analysis. Lecture, Discussion, Question Answer, Literature Search, Computer Work
11 Mass spectrometry based de novo amino acid sequencing and software that can be used for this purpose. Lecture, Discussion, Question Answer, Literature Search
12 Uses and applications of Protein BLAST. Lecture, Discussion, Question Answer, Literature Search, Computer Work
13 Methods used in quantitative proteomics. Lecture, Discussion, Question Answer, Literature Search
14 Use of bioinformatic analyses in quantitative proteomics. Lecture, Discussion, Question Answer, Literature Search
15 Determining of protein 3 dimensional structures, software used in modeling and homology based structure modeling. Use of artificial intelligence in this field. Lecture, Discussion, Question Answer, Literature Search, Computer Work
16 final exam
Recommend Course Book / Supplementary Book/Reading
1 Hubbard SJ, Jones AR. 2010. Proteome Bioinformatics. Springer.
2 Campbell AM, Heyer LJ. 2006. Discovering Genomics, Proteomics and Bioinformatics. Benjamin Cummings.
3 Eidhammer I, Flikka K, Martens L, Mikalsen S-O. 2007. Computational Methods for Mass Spectrometry Proteomics. Wiley.
4 Özel Demiralp F, İğci N, Peker S, Ayhan B. 2014. Temel Proteomik Stratejiler. Ankara Üniversitesi Yayınevi, Ankara.
Required Course instruments and materials
Lecture notes, books, related articles, computer.

Assessment Methods
Type of Assessment Week Hours Weight(%)
mid-term exam 8 2 20
Other assessment methods
1.Oral Examination
2.Quiz
3.Laboratory exam
4.Presentation 15 2 20
5.Report
6.Workshop
7.Performance Project
8.Term Paper
9.Project
final exam 16 2 60

Student Work Load
Type of Work Weekly Hours Number of Weeks Work Load
Weekly Course Hours (Theoretical+Practice) 3 14 42
Outside Class
       a) Reading 3 14 42
       b) Search in internet/Library 3 14 42
       c) Performance Project 0
       d) Prepare a workshop/Presentation/Report 2 7 14
       e) Term paper/Project 0
Oral Examination 0
Quiz 0
Laboratory exam 0
Own study for mid-term exam 2 7 14
mid-term exam 2 1 2
Own study for final exam 2 7 14
final exam 2 1 2
0
0
Total work load; 172