Učni načrt predmeta

Predmet:
Izbrana poglavja iz sinteze proteinov
Course:
Advanced Topics in Protein Synthesis
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
Univerzitetna koda predmeta / University course code:
NANO3-803
Predavanja
Lectures		 Seminar
Seminar		 Vaje
Tutorial		 Klinične vaje
work		 Druge oblike
študija		 Samost. delo
Individ. work		 ECTS
15 15 15 10 5

*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. Nenad Ban
Sodelavci / Lecturers:
Jeziki / Languages:
Predavanja / Lectures:
angleščina / English
Vaje / Tutorial:
Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti:
Prerequisites:

Zaključen študij druge stopnje ali ekvivalenten univerzitetni študij. Osnovno poznavanje biologije, kemije s poudarkom na biokemiji, organski kemiji, molekularni biologiji na dodiplomskem nivoju.

Completed Bologna second level study program or an equivalent pre-Bologna university study program. Basic knowledge in biology, chemistry, and in particular biochemistry, organic chemistry, molecular biology at the undergraduate level.

Vsebina:
Content (Syllabus outline):

Strukture visoke resolucije male ribozomske podenote
- Zgradba male ribozomske podenote
- Interakcije med proteini in RNA
- Vloga in natančnost translacije – dekodiranje

Struktura visoke resolucije velike ribozomske podenote
- Zgradba velike ribozomske podenote
- Vloga ribozoma pri prenosu peptidne vezi
- Tunel v ribozomu in primer mehanizma delovanja antibiotika

Struktura visoke resolucije bakterijskega 70S ribozoma
- Konformacija mRNK
- Interakcije tRNK z ribozomom

Usmerjanje proteina med njegovo sintezo
- Prepoznavanje signalnega zaporedja
- Translokon – usmerjevalni kanal za proteine

Z ribozomom povezani čaperoni in ko-translacijsko zvijanje in procesiranje proteinov
- Sprožitveni faktor – z bakterijskim ribozomom povezani čaperon
- Peptidna deformilaza – mehanizem ko-translacijskega procesiranja nastajajoče verige

High resolution structure of the small ribosomal subunit
- Overall architecture
- Protein RNA interactions
- Role in translational fidelity - decoding

High resolution structure of the large ribosomal subunit
- Overall structure of the large ribosomal subunit
- The role of the ribosome in the peptidyl transferase reaction
- The tunnel of the ribosome and an example of antibiotic action

High resolution structure of the bacterial 70S ribosome
- Conformation of the mRNA
- Interactions of tRNAs with the ribosome

Co-translational protein targeting
- Signal recognition particle
- Translocon – protein conducting channel

Ribosome associated chaperones and co-translational protein folding and processing
- Trigger factor – bacterial ribosome associated chaperone
- Peptide deformylase – mechanism of co-translational nascent chain processing

Temeljna literatura in viri / Readings:

- Copies of lecture notes
- Kramer G, Boehringer D, Ban N, Bukau B. (2009) The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins. Nat Struct Mol Biol. 6:589-97.
- Schmeing, T.M., and Ramakrishnan, V. (2009). What recent ribosome structures have revealed about the mechanism of translation. Nature 461, 1234-1242.
- Klinge S, Voigts-Hoffmann F, Leibundgut M, Ban N. (2012) Atomic structures of the eukaryotic ribosome. Trends Biochem Sci. 2012 May;37(5):189-98.

Cilji in kompetence:
Objectives and competences:

Cilj predmeta je, da se študent seznani s trenutnim stanjem raziskav na področju proteinske sinteze na podlagi podane literature. Študenti naj bi nato napisali sestavek, v katerem predlagajo raziskovalni projekt, ki naj bi privedel do novih odkritij na tem področju. Po poslušanju predavanj bodo študenti predstavili svoj raziskovalni projekt.

Splošne kompetence:
- Študenti bodo usposobljeni za kritično spremljanje literature in povzemanje najbolj pomembnih podatkov, bistvenih za razumevanje publikacij.
- Pridobili bodo sposobnosti za znanstveno izražanje in diskusije.
- Pridobili bodo osnove nekaterih metod strukturne biologije (rentgenska kristalografija in elektronska mikroskopija).
- Možnost predstavitve in obrambe njihovih znanstvenih idej bo vzpodbudila njihovo neodvisno razmišljanje.

Predmetno specifične kompetence:
Študenti se bodo naučili kritične presoje literature s tega področja in spoznali prednosti in omejitve vrste metod strukturne biologije. Pouk, raziskovalni projekt in diskusije bodo v angleškem jeziku. To bo doprineslo k usposobljenosti študentov za izvajanje znanstveno raziskovalnega dela na mednarodnem nivoju.

The goal of the course is to familiarize the student with the current state of research in the field of protein synthesis using as a help a script that will be provided. The students are then supposed to prepare a paper in which they propose a research project that would have potential for new discoveries in the field. After hearing the lectures the students present and defend their research proposal paper.

General competences:
- Students will develop skills to evaluate the literature and extract the most important data for understanding of the subject.
- Students will also develop skills for scientific writing and for scientific discussions.
- Students will also learn the basics of some methods used in structural biology (x-ray crystallography and electron microscopy).
- Students will have an opportunity to present and defend their scientific ideas fostering independent thinking in science.

Course specific competences:
The student will learn to critically evaluate the literature in a particular field. They will also learn the advantages and the limitations of various methods in structural biology. The class, the research paper and the discussions will be held in English providing additional training and preparation for conducting science at an international level.

Predvideni študijski rezultati:
Intendeded learning outcomes:

Znanje in razumevanje:
Študenti se bodo usposobili za kritično razumevanje literature na področju strukturne biologije in proteinske sinteze. Pridobili bodo širok pregled polja in predstavili svoje razumevanje polja s pisanjem prispevka, v katerem bodo predlagali raziskovalni projekt, ki bi lahko doprinesel k nadaljnjemu razvoju področja.

Knowledge and Understanding:
The students will learn to evaluate scientific literature in the field of structural biology and protein synthesis. They will acquire broad overview of the field and attempt to provide a critical opinion by writing a paper that suggest future projects that would advance the field.

Metode poučevanja in učenja:
Learning and teaching methods:

Predavanja, seminar in diskusija

Lectures, seminar and discussion.

Načini ocenjevanja:
Delež v % / Weight in %
Assesment:
Ustni izpit
50
Oral exam
Predstavitev raziskovalnega projekta
50
Presentation of the research proposal paper
Reference nosilca / Lecturer's references:
1. Martin Saurer, Marc Leibundgut, Hima Priyanka Nadimpalli, Alain Scaiola, Tanja Schönhut, Richard G Lee, Stefan J Siira, Oliver Rackham, René Dreos, Tea Lenarčič, Eva Kummer, David Gatfield, Aleksandra Filipovska, Nenad Ban, Molecular basis of translation termination at noncanonical stop codons in human mitochondria, Science 380 (6644), 531-536
2. Mateusz Jaskolowski, Ahmad Jomaa, Martin Gamerdinger, Sandeep Shrestha, Marc Leibundgut, Elke Deuerling, Nenad Ban, Molecular basis of translation termination at noncanonical stop codons in human mitochondria, Science 380 (6644), 531-536
3. Mateusz Jaskolowski, Ahmad Jomaa, Martin Gamerdinger, Sandeep Shrestha, Marc Leibundgut, Elke Deuerling, Nenad Ban, Molecular basis of the TRAP complex function in ER protein biogenesis, Nature Structural & Molecular Biology, 1-8
4. Sebastian Oehler, Laura Lucaroni, Francesca Migliorini, Abdullah Elsayed, Luca Prati, Sara Puglioli, Mattia Matasci, Kristina Schira, Jörg Scheuermann, Denis Yudin, Min Jia, Nenad Ban, Dave Bushnell, Roger Kornberg, Samuele Cazzamalli, Dario Neri, Nicholas Favalli, Gabriele Bassi, A DNA-encoded chemical library based on chiral 4-amino-proline enables stereospecific isozyme-selective protein recognition, Nature Chemistry, 1-13
5. Ahmad Jomaa, Martin Gamerdinger, Hao-Hsuan Hsieh, Annalena Wallisch, Viswanathan Chandrasekaran, Zeynel Ulusoy, Alain Scaiola, Ramanujan S Hegde, Shu-ou Shan, Nenad Ban, Elke Deuerling, Mechanism of signal sequence handover from NAC to SRP on ribosomes during ER-protein targeting, Science 375 (6583), 839-844