Učni načrt predmeta

Predmet:
Proteoliza
Course:
Proteolysis
Študijski program in stopnja /
Study programme and level		 Študijska smer /
Study field		 Letnik /
Academic year		 Semester /
Semester
Nanoznanosti in nanotehnologije, 3. stopnja Bioznanosti 1 1
Nanosciences and Nanotechnologies, 3rd cycle Biosciences 1 1
Vrsta predmeta / Course type
Izbirni / Elective
Univerzitetna koda predmeta / University course code:
NANO3-826
Predavanja
Lectures		 Seminar
Seminar		 Vaje
Tutorial		 Klinične vaje
work		 Druge oblike
študija		 Samost. delo
Individ. work		 ECTS
30 30 30 210 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:
akad. prof. dr. Vito Turk
Sodelavci / Lecturers:
Jeziki / Languages:
Predavanja / Lectures:
slovenščina, angleščina / Slovenian, English
Vaje / Tutorial:
Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti:
Prerequisites:

Poznavanje osnov biokemije, molekularne in celične biologije ter poznavanje osnov analitskih metod s področja.

Basic knowledge of biochemistry and molecular and cell biology, as well as basic knowledge of analytical methods from the field.

Vsebina:
Content (Syllabus outline):

Uvod v proteolizo: osnove proteolize in njena vloga pri fizioloških procesih:
- klasifikacija proteoliznih encimov
- priprava, izolacija in karakterizacija proteoliznih encimov: priprava s pomočjo rekombinantne DNA tehnologije v primerjavi z izolacijo iz naravnih virov, analitske in preparativne metode, katalitske aktivnosti
- analitske nanometode pri identifikaciji proteinov in peptidov
- struktura in mehanizem delovanja proteinaz
- inhibitorji proteoliznih encimov: naravni in sintetski inhibitorji
- intracelularna in ekstracelularna proteoliza, preprečevanje nezaželene proteolize
- vloga proteoliznih encimov pri boleznih: rak, nevrodegeneracija, kardiovaskularna obolenja, vneta obolenja, ...

Introduction to proteolysis: basics of proteolysis and its role in physiology
- Classification of proteolytic enzymes
- Preparation, purification and characterization of proteolytic enzymes: recombinant production vs. purification from natural sources, analytical and preparative methods, catalytic activities, …
- Analytical nanomethods for the identification of proteins and peptides
- Structure and mechanism of action of proteases
- Protease inhibitors: natural and synthetic
- Intracellular and extracellular proteolysis, the prevention of unwanted proteolysis
- Role of the proteolytic enzymes in disease: cancer, neurodegeneration, cardiovascular diseases, inflammation, …

Temeljna literatura in viri / Readings:

A. J. Barrett, N. D. Rawlings, J. F. Woessner: Handbook of Proteolytic Enzymes, 3rd Edition, Elsevier, Academic Press, 2012.
R. Beynon, J. S. Bond: Proteolytic Enzymes, 2nd Edition, Oxford Univ. Press, 2001.
Turk B., Turk D., Turk V. (2012) Protease signalling: the cutting edge. EMBO J. 31:1630-43.
Turk V., Stoka V., Vasiljeva O., Renko M,. Sun T., Turk B., Turk D. (2012) Cysteine cathepsins: from structure, function and regulation to new frontiers. Biochim Biophys Acta. 1824:68-88.

Tekoča relevantna literatura iz problematike. / Relevant current articles from the field (Nature, Science, Cell,
Nature Reviews, …).

Cilji in kompetence:
Objectives and competences:

Seznaniti študente s procesom proteolize, ki ima ključno vlogo pri razgradnji proteinov v normalnih in patoloških stanjih. Poudarek bo dan na poznavanju posameznih razredov proteoliznih encimov, njihovi karakterizaciji, strukturi in bioloških lastnosti.

Splošne kompetence:
- obvladanje raziskovalnih metod in postopkov, razvoj kritične in samokritične presoje,
- sposobnost uporabe znanja v praksi,
- razvoj komunikacijskih sposobnosti in spretnosti, posebej komunikacije v mednarodnem okolju,
- kooperativnost, delo v skupini in tudi v mednarodnem okolju.

Predmetnospecifične kompetence:
Študent se bo seznanil s teoretičnimi osnovami problematike proteolize in njenim pomenom za aplikacije v biomedicinskih raziskavah.
Pri svojem delu bo uporabljal najnovejšo tujo strokovno literaturo, kar bo izboljšalo njegove sposobnosti uporabe tujega jezika in kritičnega pogleda na objavljeno raziskovalno delo.
Priprava na pripravo projektov s področja proteolize v povezavi z biomedicino.

The aim is to acquaint students with the process of proteolysis which has a key role in the degradation of proteins in normal and pathological states. Emphasis will be placed on the knowledge of individual classes of proteolytic enzymes, their characterization, structure and biological properties.

General Competences:
- the student will master research methods and procedures and develop skills for critical assessment of his activities,
- the student will be able to put his knowledge into practice,
- the student will develop communications skills to present research achievement in the international environment,
- training for team work including the work in international environment.

Course Specific Competences:
Student will learn theoretical background of proteolysis and its relevance for application in biomedical research.
During his study he will use the newest scientific literature, which will improve his foreign language skills and his ability to critically view the published research.
Preparation for implementation into project preparation from the field of proteolysis linked to biomedicine.

Predvideni študijski rezultati:
Intendeded learning outcomes:

Poznavanje in razumevanje pojmov iz celične in molekularne biologije s poudarkom na proteolizi.

Študent se seznani z različnimi razredi proteaz in njihovim mehanizmom delovanja.

Študent se seznani z načini regulacije proteaz s poudarkom na inhibitorjih.

Poznavanje in razumevanje osnov nekaterih bolezni s poudarkom na raku in nevrodegenerativnih obolenjih ter vloge proteaz.

Razumevanje in pregled različnih analitskih metod ter njihovih zmožnosti in omejitev.

Knowledge and understanding of the basic phenomena in cell and molecular biology with emphasis on proteolysis.

Student gets acquainted with different classes of proteases and their mechanism of action.

Student gets acquainted with different means of protease regulation with emphasis on inhibitors.

Knowledge and understanding of the basics of selected diseases with emphasis on cancer and neurodegeneration and the role of proteases.

Understanding and overview of analytical methods, their capabilities and limitations.

Metode poučevanja in učenja:
Learning and teaching methods:

Predavanja. seminarji, konzultacije, individualno delo.

Lectures, seminar work, consultations, individual work.

Načini ocenjevanja:
Delež v % / Weight in %
Assesment:
Seminar
50 %
Seminar
Ustni izpit
50 %
Oral exam
Reference nosilca / Lecturer's references:
1. KORDIŠ, Dušan, TURK, Vito. Origin and early diversification of the papain family of cysteine peptidases. International journal of molecular sciences. 2023, vol. 24, no. 14, str. 11761-1- 11761-17. ISSN 1422-0067. DOI: 10.3390/ijms241411761
2. MIKHAYLOV, Georgy, MIKAC, Urška, BUTINAR, Miha, TURK, Vito, TURK, Boris, PSAKHIE, Sergey, VASILJEVA, Olga. Theranostic applications of an ultra-sensitive T1 and T2 magnetic resonance contrast agent based on Cobalt ferrite spinel nanoparticles. Cancers. 2022, vol. 14, no. 16, str. 4026-1-4026-14. ISSN 2072-6694. DOI: 10.3390/cancers14164026
3. DOLENC, Iztok, KLEMENČIČ, Ivica, TURK, Dušan, TALER-VERČIČ, Ajda, TURK, Boris, TURK, Vito, STOKA, Veronika. Human cathepsin X/Z is a biologically active homodimer. Biochimica et biophysica acta. Proteins and proteomics. 2021, vol. 1869, iss. 2, str. 1-10, ilustr. ISSN 1878-1454
4. NI, Junjun, WU, Zhou, STOKA, Veronika, MENG, Jie, HAYASHI, Yoshinori, PETERS, Christoph, QING, Hong, TURK, Vito, NAKANISHI, Hiroshi. Increased expression and altered subcellular distribution of cathepsin B in microglia induce cognitive impairment through oxidative stress and inflammatory response in mice. Aging cell. 2019, vol. 18, no. 1, str. e12856-1-e12856-13. ISSN 1474-9718. DOI: 10.1111/acel.12856
5. TURK, Vito, STOKA, Veronika, TURK, Dušan. Cystatins: biochemical and structural properties, and medical relevance. Frontiers in bioscience, ISSN 1093-9946, 2008, vol. 13, no. 13, str. 5406-5420.