Nevşehir Hacı Bektaş Veli University Course Catalogue
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| 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 |
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| 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 | ||