Zachodniopomorski Uniwersytet Technologiczny w Szczecinie

Wydział Biotechnologii i Hodowli Zwierząt - Biotechnologia (S2)

Sylabus przedmiotu Proteomics:

Informacje podstawowe

Kierunek studiów Biotechnologia
Forma studiów studia stacjonarne Poziom drugiego stopnia
Tytuł zawodowy absolwenta magister inżynier
Obszary studiów charakterystyki PRK, kompetencje inżynierskie PRK
Profil ogólnoakademicki
Moduł —
Przedmiot Proteomics
Specjalność Biotechnology in animal production and environmental protection
Jednostka prowadząca Katedra Fizjologii, Cytobiologii i Proteomiki
Nauczyciel odpowiedzialny Małgorzata Ożgo <Malgorzata.Ozgo@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>
ECTS (planowane) 3,0 ECTS (formy) 3,0
Forma zaliczenia zaliczenie Język angielski
Blok obieralny — Grupa obieralna —

Formy dydaktyczne

Forma dydaktycznaKODSemestrGodzinyECTSWagaZaliczenie
laboratoriaL2 20 1,50,41zaliczenie
wykładyW2 10 1,50,59zaliczenie

Wymagania wstępne

KODWymaganie wstępne
W-1Basic of the cell biology and the protein biochemistry.
W-2Basic knowledge of genetics.

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.3
T-L-2Protein separation using two-dimensional electrophoresis (2-DE).3
T-L-3Protein separation using SDS-PAGE (1-DE).3
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.3
T-L-71-DE and 2-DE gel image acquisition and bioinformatic analysis.3
20
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-5Identification of proteins using Western-blot technique. Sample preparation. Methods of protein transfer. Incubation with antibodies. Visualisation.2
10

Obciążenie pracą studenta - formy aktywności

KODForma aktywnościGodziny
laboratoria
A-L-1Participation in laboratories.20
A-L-2Self work with publications.12
A-L-3Laboratory project preparation.13
45
wykłady
A-W-1Participation in lectures.10
A-W-2Study of the recommended scientific literature.15
A-W-3Preparing for the writing test.20
45

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 kształceniaOdniesienie do efektów uczenia się prowadzących do uzyskania tytułu zawodowego inżynieraCel przedmiotuTreści programoweMetody nauczaniaSposób oceny
BT_2A_BTZ-A-C4_W01
Student can enumerate and describe commonly used techniques used in the study of proteins.		BTap_2A_W01, BTap_2A_W06, BTap_2A_W08, BTap_2A_W16——C-2, C-1T-W-2, T-W-1, T-W-4, T-W-3, T-W-5M-1, M-2S-2

Zamierzone efekty uczenia się - umiejętności

Zamierzone efekty uczenia sięOdniesienie do efektów kształcenia dla kierunku studiówOdniesienie do efektów zdefiniowanych dla obszaru kształceniaOdniesienie do efektów uczenia się prowadzących do uzyskania tytułu zawodowego inżynieraCel przedmiotuTreści programoweMetody nauczaniaSposób oceny
BT_2A_BTZ-A-C4_U01
Student is able to use commonly known proteomic techniques such as: 1-DE, 2-DE, MALDI-TOF MS and Western-blot.		BTap_2A_U02, BTap_2A_U07, BTap_2A_U05——C-3T-L-1, T-L-2, T-L-3, T-L-6, T-L-5, T-L-4, T-L-7M-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 kształceniaOdniesienie do efektów uczenia się prowadzących do uzyskania tytułu zawodowego inżynieraCel przedmiotuTreści programoweMetody nauczaniaSposób oceny
BT_2A_BTZ-A-C4_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.		BTap_2A_K02, BTap_2A_K01, BTap_2A_K05——C-3, C-2, C-1T-L-1, T-L-2, T-L-3, T-L-6, T-L-5, T-L-4, T-L-7, T-W-2, T-W-1, T-W-4, T-W-3, T-W-5M-1, M-3, M-2S-1, S-2

Kryterium oceny - wiedza

Efekt uczenia sięOcenaKryterium oceny
BT_2A_BTZ-A-C4_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
BT_2A_BTZ-A-C4_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
BT_2A_BTZ-A-C4_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.3
T-L-2Protein separation using two-dimensional electrophoresis (2-DE).3
T-L-3Protein separation using SDS-PAGE (1-DE).3
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.3
T-L-71-DE and 2-DE gel image acquisition and bioinformatic analysis.3
20

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-5Identification of proteins using Western-blot technique. Sample preparation. Methods of protein transfer. Incubation with antibodies. Visualisation.2
10

Formy aktywności - laboratoria

KODForma aktywnościGodziny
A-L-1Participation in laboratories.20
A-L-2Self work with publications.12
A-L-3Laboratory project preparation.13
45
(*) 1 punkt ECTS, odpowiada około 30 godzinom aktywności studenta

Formy aktywności - wykłady

KODForma aktywnościGodziny
A-W-1Participation in lectures.10
A-W-2Study of the recommended scientific literature.15
A-W-3Preparing for the writing test.20
45
(*) 1 punkt ECTS, odpowiada około 30 godzinom aktywności studenta
PoleKODZnaczenie kodu
Zamierzone efekty uczenia sięBT_2A_BTZ-A-C4_W01Student can enumerate and describe commonly used techniques used in the study of proteins.
Odniesienie do efektów kształcenia dla kierunku studiówBTap_2A_W01has an extended knowledge in the field of biology, chemistry, mathematics, physics and related sciences adapted to the biotechnology field
BTap_2A_W06has detailed and ordered knowledge of the use of molecular, enzymatic and physiological processes of living organisms in biotechnology
BTap_2A_W08has knowledge of advanced laboratory methods, techniques and engineering tools allowing to perform technical tasks tailored to the biotechnology
BTap_2A_W16knows advanced bioinformatics techniques and is able to use them in the field of biotechnology
Cel przedmiotuC-2The ability of the participants to use advanced bioinformatic tools to analyse proteomic data (1-D and 2-D gels, mass spectra).
C-1Theoretical and practical knowledge of gel-based and chromatographic protein separation techniques.
Treści programoweT-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-1Introduction to proteomics. Biological significance of post-transcriptional and post-translational protein modifications. Proteome organization. The general principles of proteomic 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-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-5Identification 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.
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 sięBT_2A_BTZ-A-C4_U01Student is able to use commonly known proteomic techniques such as: 1-DE, 2-DE, MALDI-TOF MS and Western-blot.
Odniesienie do efektów kształcenia dla kierunku studiówBTap_2A_U02knows how to plan and analyze biotechnology research using bioinformatics tools
BTap_2A_U07analyzes the main metabolic pathways and mechanisms for their regulation based on knowledge of the structure and function of proteins, hormones and vitamins; can acquire and use enzymes
BTap_2A_U05can individually and in a group design and implement experimental process, including measurements, applicable in biotechnology; interprets the results obtained and draws conclusions; conducts discussions based on self-knowledge acquired using specialist language
Cel przedmiotuC-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-6Identification of proteins using Western-blot technique.
T-L-5Identification of proteins using mass spectrometer MALTI-TOF.
T-L-4Protein gel staining methods.
T-L-71-DE and 2-DE gel image acquisition and bioinformatic analysis.
Metody nauczaniaM-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 sięBT_2A_BTZ-A-C4_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.
Odniesienie do efektów kształcenia dla kierunku studiówBTap_2A_K02demonstrates understanding of biotechnological processes used in various areas of human activity; interprets and describes these processes using a scientific approach
BTap_2A_K01demonstrates the need to constantly improve general and directional knowledge; is aware of the purposefulness of raising the acquired knowledge both in professional activities and personal development
BTap_2A_K05shows discipline in individual work; willing to participate in group work; can creatively plan and implement own and team activities
Cel przedmiotuC-3Practical use of MALDI-TOF MS (matrix-assisted laser desorption/ionisation time of flight mass spectrometer) for protein identification.
C-2The ability of the participants to use advanced bioinformatic tools to analyse proteomic data (1-D and 2-D gels, mass spectra).
C-1Theoretical and practical knowledge of gel-based and chromatographic protein separation techniques.
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-6Identification of proteins using Western-blot technique.
T-L-5Identification of proteins using mass spectrometer MALTI-TOF.
T-L-4Protein gel staining methods.
T-L-71-DE and 2-DE gel image acquisition and bioinformatic analysis.
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-1Introduction to proteomics. Biological significance of post-transcriptional and post-translational protein modifications. Proteome organization. The general principles of proteomic 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-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-5Identification of proteins using Western-blot technique. Sample preparation. Methods of protein transfer. Incubation with antibodies. Visualisation.
Metody nauczaniaM-1Theoretical lectures.
M-3Project preparation.
M-2Discussion during laboratory classes.
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