Učni načrt predmeta

Predmet:
Proteinsko in celično inženirstvo
Course:
Protein and Cell Engineering
Študijski program in stopnja /
Study programme and level		 Študijska smer /
Study field		 Letnik /
Academic year		 Semester /
Semester
Nanoznanosti in nanotehnologije, 3. stopnja 1 1
Nanosciences and Nanotechnologies, 3rd cycle 1 1
Vrsta predmeta / Course type
Izbirni / Elective
Univerzitetna koda predmeta / University course code:
NANO3-825
Predavanja
Lectures		 Seminar
Seminar		 Vaje
Tutorial		 Klinične vaje
work		 Druge oblike
študija		 Samost. delo
Individ. work		 ECTS
15 15 15 105 10

*Navedena porazdelitev ur velja, če je vpisanih vsaj 15 študentov. Drugače se obseg izvedbe kontaktnih ur sorazmerno zmanjša in prenese v samostojno delo. / This distribution of hours is valid if at least 15 students are enrolled. Otherwise the contact hours are linearly reduced and transfered to individual work.

Nosilec predmeta / Course leader:
prof. dr. Jože Pungerčar
Sodelavci / Lecturers:
Jeziki / Languages:
Predavanja / Lectures:
slovenščina, angleščina / Slovenian, English
Vaje / Tutorial:
slovenščina, angleščina / Slovenian, English
Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti:
Prerequisites:

Zaključena druga stopnja bolonjskega študija ali diploma univerzitetnega študijskega programa.

Potrebna so tudi osnovna znanja s področij biokemije, molekularne in celične biologije, molekularne genetike in proteinske/encimske strukture.

Completed Bologna second level study program or an equivalent pre-Bologna university study program.

Basic knowledge of biochemistry, molecular and cell biology, molecular genetics and protein/enzyme structure is also requested.

Vsebina:
Content (Syllabus outline):

- Proteinsko inženirstvo: zgodovinski pregled, osnovni pojmi, racionalni dizajn in usmerjena evolucija.
- Mutageneza: različni pristopi in najpogostejše tehnike.
- Neomejeni potencial celičnega inženirstva.
- Uporaba različnih proteinskih označevalcev.
- Načrtovanje usmerjenih mutacij na izbrani proteinski molekuli.
- Uvedba mutacij(e) na nukleotidnem nivoju.
- Pridobitev mutiranega rekombinantnega proteina in njegova osnovna karakterizacija.
- Priprava izbranega označenega proteina v sesalskih celicah.
- Analiza dobljenih rezultatov.
- Priprava zaključne seminarske naloge.

- Protein engineering: historical view, basic concepts and terms, rational design and directed evolution.
- Mutagenesis: various approaches and common techniques.
- Unlimited potential of cell engineering.
- Use of various protein tags and markers.
- Design of site-directed mutations on a selected protein molecule.
- Introduction of mutation(s) at the nucleotide level.
- Production of a mutant recombinant protein and its basic characterization.
- Preparation of a selected labeled protein in mammalian cells.
- Analysis of the obtained results.
- Preparation of a final seminar work.

Temeljna literatura in viri / Readings:

Ausubel, F.M. et al. /Eds./ (2007): Current Protocols in Molecular Biology. John Wiley and Sons, Inc., New York, USA; Continuously updated.
Robertson, D.E. and Noel, J.P. /Eds./ (2004): Protein Engineering. In: Methods in Enzymology, Vol. 388, Elsevier Academic Press, Amsterdam, The Netherlands.
Wittrup, K.D. and Verdine G.L. /Eds./ (2012): Protein Engineering for Therapeutics, Parts A & B. In: Methods in Enzymology, Vols. 502 & 503, Elsevier Academic Press, Amsterdam, The Netherlands.
Al-Rubeai, M. and Fussenegger, M. /Eds./ (2007): Cell Engineering, Vol. 5 (Systems Biology), Springer Verlag, New York, USA.
Saltzman, W.M. (2015): Biomedical Engineering - Bridging Medicine and Technology, 2nd edn., Cambridge University Press, New York, USA.

Current research and review articles from the field.

Cilji in kompetence:
Objectives and competences:

Študent poglobi svoje znanje s področja razumevanja odnosov med strukturo in funkcijo proteinov. Nauči se samostojno načrtovati ustrezne eksperimente in uporabljati različne pristope proteinskega inženirstva. Prav tako se nauči uporabljati različne celične sisteme za študij in razumevanje biološkega delovanja izbranih proteinov ter molekulskih celičnih mehanizmov.

Splošne kompetence:
- Obvladanje raziskovalnih metod, analitičnih postopkov in molekularnobioloških procesov.
- Razvoj kritične in samokritične presoje.
- Sposobnost uporabe pridobljenega znanja v praksi.
- Samostojno raziskovalno delo.
- Kooperativnost ter delo v skupini in kompetitivnem mednarodnem raziskovalnem okolju.

Predmetnospecifične kompetence:
- Predmet pripravlja študente na konkretno delo s proteini/encimi v raziskovalnem molekularnobiološkem laboratoriju.
- Daje tudi dobra izhodišča za delo v ustreznem polindustrijskem laboratoriju.

A student is expected to acquire in-depth knowledge and understanding of structure-function relationships in proteins. He/she learns how to independently design appropriate experiments and to use different approaches in protein engineering. The student also learns how to exploit various cell systems for studying and understanding the biological roles of proteins of interest and molecular cell mechanisms.

General Competences:
- The student will master research methods, analytical procedures and molecular biology processes.
- Development of a critical and self-critical judgment.
- Transfer of the acquired knowledge to practical use.
- Individual research work.
- Cooperativity and team work in a competitive international research environment.

Course Specific Competences:
- This course prepares students for practical work on proteins/enzymes in a molecular biology research laboratory.
- The course provides a good background for work in an appropriate semi-industrial laboratory.

Predvideni študijski rezultati:
Intendeded learning outcomes:

Znanje in razumevanje:
- Poglobljeno razumevanje osnovnih pristopov proteinskega inženirstva.
- Razumevanje in vrednotenje različnih možnosti celičnega inženirstva in njihove smiselne uporabe.

Knowledge and Understanding:
- In-depth understanding of basic approaches to protein engineering.
- Understanding and evaluation of different possibilities of cell engineering and their rational use.

Metode poučevanja in učenja:
Learning and teaching methods:

Predavanja (opcijsko).
Seminarji, tutorstvo in seminarska naloga.
Laboratorijsko ali in silico individualno in timsko delo, usmerjeno v študentovo raziskovalno problematiko.

Lectures (optional).
Seminar work and tutorial.
Individual and team work in the laboratory or in silico that is student research-oriented.

Načini ocenjevanja:
Delež v % / Weight in %
Assesment:
Seminarska naloga
50 %
Seminar work
Ustni zagovor seminarske naloge
50 %
Oral defense of seminar work
Reference nosilca / Lecturer's references:
1. Požek, K., Leonardi, A., Pungerčar, J., Rao, W., Gao, Z., Liu, S., Laustsen, A.H., Trampuš Bakija, A., Reberšek, K., Podgornik, H. and Križaj, I. (2022): Genomic confirmation of the P-IIIe subclass of snake venom metalloproteinases and characterization of its first member, a disintegrin-like/cysteine-rich protein. Toxins 13, 232.
2. Pungerčar, J., Bihl, F., Lambeau, G. and Križaj, I. (2021): What do secreted phospholipases A2 have to offer in combat against different viruses up to SARS-CoV-2? Biochimie 189, 40–50.
3. Latinović, Z., Leonardi, A., Koh, C.Y., Kini, R.M., Trampuš Bakija, A., Pungerčar, J. and Križaj, I. (2020): The procoagulant snake venom serine protease potentially having a dual, blood coagulation factor V and X-activating activity. Toxins 12, 358.
4. Leonardi, A., Sajevic, T., Pungerčar, J. and Križaj, I. (2019): Comprehensive study of the proteome and transcriptome of the venom of the most venomous European viper : discovery of a new subclass of ancestral snake venom metalloproteinase precursor-derived proteins. J. Proteome Res. 18, 2287–2309.
5. Latinović, Z., Leonardi, A., Šribar, J., Sajevic, T., Žužek, M.C., Frangež, R., Halassy, B., Trampuš-Bakija, A., Pungerčar, J. and Križaj, I. (2016): Venomics of Vipera berus berus to explain differences in pathology elicited by Vipera ammodytes ammodytes envenomation: Therapeutic implications. J. Proteomics 146, 34–47.