Zachodniopomorski Uniwersytet Technologiczny w Szczecinie

Administracja Centralna Uczelni - Wymiana międzynarodowa (S1)

Sylabus przedmiotu Proteomics:

Informacje podstawowe

Kierunek studiów Wymiana międzynarodowa
Forma studiów studia stacjonarne Poziom pierwszego stopnia
Tytuł zawodowy absolwenta
Obszary studiów —
Profil
Moduł —
Przedmiot Proteomics
Specjalność przedmiot wspólny
Jednostka prowadząca Katedra Fizjologii, Cytobiologii i Proteomiki
Nauczyciel odpowiedzialny Agnieszka Herosimczyk <Agnieszka.Herosimczyk@zut.edu.pl>
Inni nauczyciele Alicja Dratwa-Chałupnik <Alicja.Dratwa-Chalupnik@zut.edu.pl>, Agnieszka Herosimczyk <Agnieszka.Herosimczyk@zut.edu.pl>, Adam Lepczyński <Adam.Lepczynski@zut.edu.pl>, Katarzyna Michałek <Katarzyna.Michalek@zut.edu.pl>, Małgorzata Ożgo <Malgorzata.Ozgo@zut.edu.pl>
ECTS (planowane) 3,0 ECTS (formy) 3,0
Forma zaliczenia zaliczenie Język angielski
Blok obieralny — Grupa obieralna —

Formy dydaktyczne

Forma dydaktycznaKODSemestrGodzinyECTSWagaZaliczenie
laboratoriaL1 15 1,50,49zaliczenie
wykładyW1 15 1,50,51zaliczenie

Wymagania wstępne

KODWymaganie wstępne
W-1Basic of the cell biology and the protein biochemistry.

Cele przedmiotu

KODCel modułu/przedmiotu
C-1Theoretical and practical knowledge of gel-based and chromatographic protein separation techniques.
C-2The ability of the participants to use advanced bioinformatic tools to analyse proteomic data (1-D and 2-D gels, mass spectra).
C-3Practical use of MALDI-TOF MS (matrix-assisted laser desorption/ionisation time of flight mass spectrometer) for protein identification.

Treści programowe z podziałem na formy zajęć

KODTreść programowaGodziny
laboratoria
T-L-1Sample preparation techniques for proteomic analysis.2
T-L-2Protein separation using two-dimensional electrophoresis (2-DE).2
T-L-3Protein separation using SDS-PAGE (1-DE).2
T-L-4Protein gel staining methods.2
T-L-5Identification of proteins using mass spectrometer MALTI-TOF.3
T-L-6Identification of proteins using Western-blot technique.2
T-L-71-DE and 2-DE gel image acquisition and bioinformatic analysis.2
15
wykłady
T-W-1Introduction to proteomics. Biological significance of post-transcriptional and post-translational protein modifications. Proteome organization. The general principles of proteomic analysis.2
T-W-2Gel-based protein separation techniques. The components of resolving gel matrix. Sodium-dodecyl polyacrylamide gel electrophoresis (SDS-PAGE), the principle and application of native PAGE electrophoresis. Two dimensional electrophoresis (2-DE) – the principle of the method, sample preparation for 2-DE, IPG strips, isoelectric focusing.2
T-W-3Protein detection methods: coomassie stain, silver stain, negative ion staining (copper, zinc), autoradiography, fluorography, fluorescent staining. Two-dimensional difference in gel electrophoresis (2D-DIGE) – the principle and application of the method. Image acquisition and analysis of 1-D and 2-D gels. 1-D and 2-D gels analysis softwares.2
T-W-4Application of mass spectrometry (MS) for protein identification. Ionization methods in mass spectrometry. Types of mass analyzers. Peptide mass fingerprinting (PMF).2
T-W-5Chromatographic methods for protein separation. Liquid chromatography (LC). Two-dimensional liquid chromatography (2-D LC). The proteomic strategies based on liquid chromatography: LC-MS, LC-MS/MS, multidimensional LC-MS/MS. Affinity chromatography (AC).2
T-W-6Identification of proteins using Western-blot technique. Sample preparation. Methods of protein transfer. Incubation with antibodies. Visualisation.3
T-W-7Branches of proteomics: structural, functional and clinical.2
15

Obciążenie pracą studenta - formy aktywności

KODForma aktywnościGodziny
laboratoria
A-L-1Participation in laboratories.15
A-L-2Self work with publications.8
A-L-3Laboratory project preparation.10
A-L-4Consultations5
38
wykłady
A-W-1Participation in lectures.15
A-W-2Study of the recommended scientific literature.10
A-W-3Preparing for the writing test.10
A-W-4Consultations3
38

Metody nauczania / narzędzia dydaktyczne

KODMetoda nauczania / narzędzie dydaktyczne
M-1Theoretical lectures.
M-2Discussion during laboratory classes.
M-3Project preparation.

Sposoby oceny

KODSposób oceny
S-1Ocena formująca: Project presentation in the writing form.
S-2Ocena podsumowująca: Writing test.

Zamierzone efekty uczenia się - wiedza

Zamierzone efekty uczenia sięOdniesienie do efektów kształcenia dla kierunku studiówOdniesienie do efektów zdefiniowanych dla obszaru kształceniaCel przedmiotuTreści programoweMetody nauczaniaSposób oceny
WM-WBiHZ_1-_??_W01
Student can enumerate and describe commonly used techniques used in the study of proteins.		——C-1, C-2T-W-4, T-W-1, T-W-3, T-W-5, T-W-2, T-W-7, T-W-6M-1S-2

Zamierzone efekty uczenia się - umiejętności

Zamierzone efekty uczenia sięOdniesienie do efektów kształcenia dla kierunku studiówOdniesienie do efektów zdefiniowanych dla obszaru kształceniaCel przedmiotuTreści programoweMetody nauczaniaSposób oceny
WM-WBiHZ_1-_??_U01
Student is able to use commonly known proteomic techniques such as: 1-DE, 2-DE, MALDI-TOF MS and Western-blot.		——C-1, C-3T-L-1, T-L-2, T-L-3, T-L-4, T-L-5, T-L-6, T-L-7M-2, M-3S-1

Zamierzone efekty uczenia się - inne kompetencje społeczne i personalne

Zamierzone efekty uczenia sięOdniesienie do efektów kształcenia dla kierunku studiówOdniesienie do efektów zdefiniowanych dla obszaru kształceniaCel przedmiotuTreści programoweMetody nauczaniaSposób oceny
WM-WBiHZ_1-_??_K01
Student is aware that there is a number of methods to analyse the different levels of protein changes in response to various physiological/patophysiological stimmuli in the biological material.		——C-1, C-2, C-3T-L-1, T-L-2, T-L-3, T-L-4, T-L-5, T-L-6, T-L-7, T-W-4, T-W-1, T-W-3, T-W-5, T-W-2, T-W-7, T-W-6M-1, M-2, M-3S-1, S-2

Kryterium oceny - wiedza

Efekt uczenia sięOcenaKryterium oceny
WM-WBiHZ_1-_??_W01
Student can enumerate and describe commonly used techniques used in the study of proteins.		2,0
3,0- student has a basic knowledge in the frame of the material program - student exerts low attitude to knowledge - in the frame of expressing knowledge student makes a lot of mistakes
3,5
4,0
4,5
5,0

Kryterium oceny - umiejętności

Efekt uczenia sięOcenaKryterium oceny
WM-WBiHZ_1-_??_U01
Student is able to use commonly known proteomic techniques such as: 1-DE, 2-DE, MALDI-TOF MS and Western-blot.		2,0
3,0Student, with a help of a teacher is able to meet the challenges of preparing an appropriate laboratory protocol.
3,5
4,0
4,5
5,0

Kryterium oceny - inne kompetencje społeczne i personalne

Efekt uczenia sięOcenaKryterium oceny
WM-WBiHZ_1-_??_K01
Student is aware that there is a number of methods to analyse the different levels of protein changes in response to various physiological/patophysiological stimmuli in the biological material.		2,0
3,0Student shows a moderate interest in participating in a verbal discussion with the teacher and colleagues during the classes.
3,5
4,0
4,5
5,0

Literatura podstawowa

  1. Sheehan D., Tyther R. (Ed.)., Two-dimensional electrophoresis protocols., Humana Press, New York, 2009
  2. Garfin D., Ahuja S. (Ed.), Handbook of isoelectric focusing and proteomics., Elsevier Academic Press, Amsterdam, 2005
  3. Heftmann E. (Ed.)., Chromatography, sixth edition., Elsevier Academic Press, Amsterdam, 2004
  4. Walker J.M. (Ed.), second edition., The proteomics protocols handbook., Humana Press, New Jersey, 2002
  5. Rabilloud T. (Ed.), Proteome research: two-dimensional gel electrophoresis and identification methods., Springer, Berlin, 2000
  6. Hames B.D. (Ed.), third edition., Gel electrophoresis of proteins: a practical approach., Oxford University Press, England, 1998

Treści programowe - laboratoria

KODTreść programowaGodziny
T-L-1Sample preparation techniques for proteomic analysis.2
T-L-2Protein separation using two-dimensional electrophoresis (2-DE).2
T-L-3Protein separation using SDS-PAGE (1-DE).2
T-L-4Protein gel staining methods.2
T-L-5Identification of proteins using mass spectrometer MALTI-TOF.3
T-L-6Identification of proteins using Western-blot technique.2
T-L-71-DE and 2-DE gel image acquisition and bioinformatic analysis.2
15

Treści programowe - wykłady

KODTreść programowaGodziny
T-W-1Introduction to proteomics. Biological significance of post-transcriptional and post-translational protein modifications. Proteome organization. The general principles of proteomic analysis.2
T-W-2Gel-based protein separation techniques. The components of resolving gel matrix. Sodium-dodecyl polyacrylamide gel electrophoresis (SDS-PAGE), the principle and application of native PAGE electrophoresis. Two dimensional electrophoresis (2-DE) – the principle of the method, sample preparation for 2-DE, IPG strips, isoelectric focusing.2
T-W-3Protein detection methods: coomassie stain, silver stain, negative ion staining (copper, zinc), autoradiography, fluorography, fluorescent staining. Two-dimensional difference in gel electrophoresis (2D-DIGE) – the principle and application of the method. Image acquisition and analysis of 1-D and 2-D gels. 1-D and 2-D gels analysis softwares.2
T-W-4Application of mass spectrometry (MS) for protein identification. Ionization methods in mass spectrometry. Types of mass analyzers. Peptide mass fingerprinting (PMF).2
T-W-5Chromatographic methods for protein separation. Liquid chromatography (LC). Two-dimensional liquid chromatography (2-D LC). The proteomic strategies based on liquid chromatography: LC-MS, LC-MS/MS, multidimensional LC-MS/MS. Affinity chromatography (AC).2
T-W-6Identification of proteins using Western-blot technique. Sample preparation. Methods of protein transfer. Incubation with antibodies. Visualisation.3
T-W-7Branches of proteomics: structural, functional and clinical.2
15

Formy aktywności - laboratoria

KODForma aktywnościGodziny
A-L-1Participation in laboratories.15
A-L-2Self work with publications.8
A-L-3Laboratory project preparation.10
A-L-4Consultations5
38
(*) 1 punkt ECTS, odpowiada około 30 godzinom aktywności studenta

Formy aktywności - wykłady

KODForma aktywnościGodziny
A-W-1Participation in lectures.15
A-W-2Study of the recommended scientific literature.10
A-W-3Preparing for the writing test.10
A-W-4Consultations3
38
(*) 1 punkt ECTS, odpowiada około 30 godzinom aktywności studenta
PoleKODZnaczenie kodu
Zamierzone efekty uczenia sięWM-WBiHZ_1-_??_W01Student can enumerate and describe commonly used techniques used in the study of proteins.
Cel przedmiotuC-1Theoretical and practical knowledge of gel-based and chromatographic protein separation techniques.
C-2The ability of the participants to use advanced bioinformatic tools to analyse proteomic data (1-D and 2-D gels, mass spectra).
Treści programoweT-W-4Application of mass spectrometry (MS) for protein identification. Ionization methods in mass spectrometry. Types of mass analyzers. Peptide mass fingerprinting (PMF).
T-W-1Introduction to proteomics. Biological significance of post-transcriptional and post-translational protein modifications. Proteome organization. The general principles of proteomic analysis.
T-W-3Protein detection methods: coomassie stain, silver stain, negative ion staining (copper, zinc), autoradiography, fluorography, fluorescent staining. Two-dimensional difference in gel electrophoresis (2D-DIGE) – the principle and application of the method. Image acquisition and analysis of 1-D and 2-D gels. 1-D and 2-D gels analysis softwares.
T-W-5Chromatographic methods for protein separation. Liquid chromatography (LC). Two-dimensional liquid chromatography (2-D LC). The proteomic strategies based on liquid chromatography: LC-MS, LC-MS/MS, multidimensional LC-MS/MS. Affinity chromatography (AC).
T-W-2Gel-based protein separation techniques. The components of resolving gel matrix. Sodium-dodecyl polyacrylamide gel electrophoresis (SDS-PAGE), the principle and application of native PAGE electrophoresis. Two dimensional electrophoresis (2-DE) – the principle of the method, sample preparation for 2-DE, IPG strips, isoelectric focusing.
T-W-7Branches of proteomics: structural, functional and clinical.
T-W-6Identification of proteins using Western-blot technique. Sample preparation. Methods of protein transfer. Incubation with antibodies. Visualisation.
Metody nauczaniaM-1Theoretical lectures.
Sposób ocenyS-2Ocena podsumowująca: Writing test.
Kryteria ocenyOcenaKryterium oceny
2,0
3,0- student has a basic knowledge in the frame of the material program - student exerts low attitude to knowledge - in the frame of expressing knowledge student makes a lot of mistakes
3,5
4,0
4,5
5,0
PoleKODZnaczenie kodu
Zamierzone efekty uczenia sięWM-WBiHZ_1-_??_U01Student is able to use commonly known proteomic techniques such as: 1-DE, 2-DE, MALDI-TOF MS and Western-blot.
Cel przedmiotuC-1Theoretical and practical knowledge of gel-based and chromatographic protein separation techniques.
C-3Practical use of MALDI-TOF MS (matrix-assisted laser desorption/ionisation time of flight mass spectrometer) for protein identification.
Treści programoweT-L-1Sample preparation techniques for proteomic analysis.
T-L-2Protein separation using two-dimensional electrophoresis (2-DE).
T-L-3Protein separation using SDS-PAGE (1-DE).
T-L-4Protein gel staining methods.
T-L-5Identification of proteins using mass spectrometer MALTI-TOF.
T-L-6Identification of proteins using Western-blot technique.
T-L-71-DE and 2-DE gel image acquisition and bioinformatic analysis.
Metody nauczaniaM-2Discussion during laboratory classes.
M-3Project preparation.
Sposób ocenyS-1Ocena formująca: Project presentation in the writing form.
Kryteria ocenyOcenaKryterium oceny
2,0
3,0Student, with a help of a teacher is able to meet the challenges of preparing an appropriate laboratory protocol.
3,5
4,0
4,5
5,0
PoleKODZnaczenie kodu
Zamierzone efekty uczenia sięWM-WBiHZ_1-_??_K01Student is aware that there is a number of methods to analyse the different levels of protein changes in response to various physiological/patophysiological stimmuli in the biological material.
Cel przedmiotuC-1Theoretical and practical knowledge of gel-based and chromatographic protein separation techniques.
C-2The ability of the participants to use advanced bioinformatic tools to analyse proteomic data (1-D and 2-D gels, mass spectra).
C-3Practical use of MALDI-TOF MS (matrix-assisted laser desorption/ionisation time of flight mass spectrometer) for protein identification.
Treści programoweT-L-1Sample preparation techniques for proteomic analysis.
T-L-2Protein separation using two-dimensional electrophoresis (2-DE).
T-L-3Protein separation using SDS-PAGE (1-DE).
T-L-4Protein gel staining methods.
T-L-5Identification of proteins using mass spectrometer MALTI-TOF.
T-L-6Identification of proteins using Western-blot technique.
T-L-71-DE and 2-DE gel image acquisition and bioinformatic analysis.
T-W-4Application of mass spectrometry (MS) for protein identification. Ionization methods in mass spectrometry. Types of mass analyzers. Peptide mass fingerprinting (PMF).
T-W-1Introduction to proteomics. Biological significance of post-transcriptional and post-translational protein modifications. Proteome organization. The general principles of proteomic analysis.
T-W-3Protein detection methods: coomassie stain, silver stain, negative ion staining (copper, zinc), autoradiography, fluorography, fluorescent staining. Two-dimensional difference in gel electrophoresis (2D-DIGE) – the principle and application of the method. Image acquisition and analysis of 1-D and 2-D gels. 1-D and 2-D gels analysis softwares.
T-W-5Chromatographic methods for protein separation. Liquid chromatography (LC). Two-dimensional liquid chromatography (2-D LC). The proteomic strategies based on liquid chromatography: LC-MS, LC-MS/MS, multidimensional LC-MS/MS. Affinity chromatography (AC).
T-W-2Gel-based protein separation techniques. The components of resolving gel matrix. Sodium-dodecyl polyacrylamide gel electrophoresis (SDS-PAGE), the principle and application of native PAGE electrophoresis. Two dimensional electrophoresis (2-DE) – the principle of the method, sample preparation for 2-DE, IPG strips, isoelectric focusing.
T-W-7Branches of proteomics: structural, functional and clinical.
T-W-6Identification of proteins using Western-blot technique. Sample preparation. Methods of protein transfer. Incubation with antibodies. Visualisation.
Metody nauczaniaM-1Theoretical lectures.
M-2Discussion during laboratory classes.
M-3Project preparation.
Sposób ocenyS-1Ocena formująca: Project presentation in the writing form.
S-2Ocena podsumowująca: Writing test.
Kryteria ocenyOcenaKryterium oceny
2,0
3,0Student shows a moderate interest in participating in a verbal discussion with the teacher and colleagues during the classes.
3,5
4,0
4,5
5,0