Zachodniopomorski Uniwersytet Technologiczny w Szczecinie

Wydział Biotechnologii i Hodowli Zwierząt - Biotechnology (S2)
specjalność: Biotechnology in animal production and environmental protection

Sylabus przedmiotu Molecular modelling of enzymes:

Informacje podstawowe

Kierunek studiów Biotechnology
Forma studiów studia stacjonarne Poziom drugiego stopnia
Tytuł zawodowy absolwenta magister inżynier
Obszary studiów charakterystyki PRK, kompetencje inżynierskie PRK
Profil ogólnoakademicki
Moduł
Przedmiot Molecular modelling of enzymes
Specjalność Biotechnology in animal production and environmental protection
Jednostka prowadząca Katedra Mikrobiologii i Biotechnologii
Nauczyciel odpowiedzialny Radosław Drozd <Radoslaw.Drozd@zut.edu.pl>
Inni nauczyciele
ECTS (planowane) 3,0 ECTS (formy) 3,0
Forma zaliczenia zaliczenie Język angielski
Blok obieralny 5 Grupa obieralna 2

Formy dydaktyczne

Forma dydaktycznaKODSemestrGodzinyECTSWagaZaliczenie
ćwiczenia audytoryjneA2 15 1,50,41zaliczenie
wykładyW2 15 1,50,59zaliczenie

Wymagania wstępne

KODWymaganie wstępne
W-1The elementary knowledge of genetics, molecular genetics, cell biology and evolution.
W-2The intermadiate levele of knowledge of organic and inorganic chemistry, biochemistry, biophysics, English at intermediate level

Cele przedmiotu

KODCel modułu/przedmiotu
C-1Developing skills of selection of appropriate bioinformatics tools to solve and analyze the structure of proteins
C-2Mastering the ability to combine and correct interpretation of information relating to various levels of organization of protein structures

Treści programowe z podziałem na formy zajęć

KODTreść programowaGodziny
ćwiczenia audytoryjne
T-A-1The introduction to proteins molecular structure part II2
T-A-2The introduction to proteins molecular structure part II2
T-A-3The in silico methods of proteins structure II and III level determination2
T-A-4The in silico methods of oligomeric enzymes structure determination2
T-A-5The methods for the effective ligands design for the enzymes activity modulation part I2
T-A-6The methods for the effective ligands design for the enzymes activity modulation part II2
T-A-7The Molecular Dynamic simulation methods as tools for testing in-silico changed structure of enzymes. part I2
T-A-8The Molecular Dynamic simulation methods as tools for testing in-silico changed structure of enzymes. part II1
15
wykłady
T-W-1Methods for the data mining for protein structure on their I level. Prediction of catalytic and structural properties enzymes. part I2
T-W-2Methods for the data mining for protein structure on their I level. Prediction of catalytic and structural properties enzymes. part II2
T-W-3Methods for prediction localisation of enzymes catalytic sites2
T-W-4Methods for characterisaation catalytic sites properities.2
T-W-5Modeling of the catalytic properities of enzymes - pH optima2
T-W-6Molecular docking as tool for design a accurate enzymes inhibitors. Part I2
T-W-7Molecular docking as tool for design a accurate enzymes inhibitors. Part II2
T-W-8Methods of enzyme analysis results visualisation by using molecular modeling software1
15

Obciążenie pracą studenta - formy aktywności

KODForma aktywnościGodziny
ćwiczenia audytoryjne
A-A-1Participation in the classes.15
A-A-2Individual study of training materials7
A-A-3Preparation for passing the tutorial content.7
A-A-4consultations16
45
wykłady
A-W-1Participation in lectures.15
A-W-2Independent study of lecture materials and recommended literature.10
A-W-3Consultation5
A-W-4Preparation for passing the lecture content.8
A-W-5Passing the lecture content.5
A-W-6Discussing lecture content2
45

Metody nauczania / narzędzia dydaktyczne

KODMetoda nauczania / narzędzie dydaktyczne
M-1Information lectures
M-2explanation or clarification
M-3description

Sposoby oceny

KODSposób oceny
S-1Ocena podsumowująca: test
S-2Ocena formująca: multimedia presentation

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-O5.2_W03
Student has knowledge about the organization and structural relationships of proteins. He knows bioinformatic methods and tools for the analysis of protein structures. Has knowledge about the possibilities and consequences of manipulation in protein structures.
BTap_2A_W01C-1, C-2T-A-1, T-A-3, T-A-4, T-A-5M-1, M-2, M-3S-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-O5.2_U01
Correctly applying a bioinformatic tools to 3D enzymes structure solving
BTap_2A_U05C-1, C-2T-W-1, T-W-2, T-W-3, T-W-4M-3S-2

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-O5.2_K02
Understands the consequences of modifying protein structures on the functioning of living organisms
BTap_2A_K02C-1, C-2T-A-1, T-A-3, T-A-4, T-A-5M-1, M-2, M-3S-2

Kryterium oceny - wiedza

Efekt uczenia sięOcenaKryterium oceny
BT_2A_BTZ-A-O5.2_W03
Student has knowledge about the organization and structural relationships of proteins. He knows bioinformatic methods and tools for the analysis of protein structures. Has knowledge about the possibilities and consequences of manipulation in protein structures.
2,0
3,0Preparation of a multimedia presentation, participation in 90% of auditory classes, Correct answer to 60% of test questions - exam
3,5
4,0
4,5
5,0

Kryterium oceny - umiejętności

Efekt uczenia sięOcenaKryterium oceny
BT_2A_BTZ-A-O5.2_U01
Correctly applying a bioinformatic tools to 3D enzymes structure solving
2,0
3,0Preparation of a multimedia presentation, participation in 90% of auditory classes,
3,5
4,0
4,5
5,0

Kryterium oceny - inne kompetencje społeczne i personalne

Efekt uczenia sięOcenaKryterium oceny
BT_2A_BTZ-A-O5.2_K02
Understands the consequences of modifying protein structures on the functioning of living organisms
2,0
3,0Preparation of a multimedia presentation, participation in 90% of auditory classes,
3,5
4,0
4,5
5,0

Literatura podstawowa

  1. K. I. Ramachandran, Gopakumar Deepa, Krishnan Namboori, Computational Chemistry and Molecular Modeling: Principles and Applications, Springer, Berlin Heidelberg, 2008
  2. Paul G. Higgs, Teresa K. Attwood, Bioinformatics and Molecular Evolution, Wiley-Blackwell, USA, 2005, I
  3. Huzefa Rangwala, George Karypis (Ed.), Introduction to Protein Structure Prediction: Methods and Algorithms, Wiley, USA, 2011, I
  4. Andrzej Koliński red., Multiscale Approaches to Protein Modeling, Springer, 2010, I

Literatura dodatkowa

  1. Alan Cooper, Biophysical Chemistry, RSC, 2010, II

Treści programowe - ćwiczenia audytoryjne

KODTreść programowaGodziny
T-A-1The introduction to proteins molecular structure part II2
T-A-2The introduction to proteins molecular structure part II2
T-A-3The in silico methods of proteins structure II and III level determination2
T-A-4The in silico methods of oligomeric enzymes structure determination2
T-A-5The methods for the effective ligands design for the enzymes activity modulation part I2
T-A-6The methods for the effective ligands design for the enzymes activity modulation part II2
T-A-7The Molecular Dynamic simulation methods as tools for testing in-silico changed structure of enzymes. part I2
T-A-8The Molecular Dynamic simulation methods as tools for testing in-silico changed structure of enzymes. part II1
15

Treści programowe - wykłady

KODTreść programowaGodziny
T-W-1Methods for the data mining for protein structure on their I level. Prediction of catalytic and structural properties enzymes. part I2
T-W-2Methods for the data mining for protein structure on their I level. Prediction of catalytic and structural properties enzymes. part II2
T-W-3Methods for prediction localisation of enzymes catalytic sites2
T-W-4Methods for characterisaation catalytic sites properities.2
T-W-5Modeling of the catalytic properities of enzymes - pH optima2
T-W-6Molecular docking as tool for design a accurate enzymes inhibitors. Part I2
T-W-7Molecular docking as tool for design a accurate enzymes inhibitors. Part II2
T-W-8Methods of enzyme analysis results visualisation by using molecular modeling software1
15

Formy aktywności - ćwiczenia audytoryjne

KODForma aktywnościGodziny
A-A-1Participation in the classes.15
A-A-2Individual study of training materials7
A-A-3Preparation for passing the tutorial content.7
A-A-4consultations16
45
(*) 1 punkt ECTS, odpowiada około 30 godzinom aktywności studenta

Formy aktywności - wykłady

KODForma aktywnościGodziny
A-W-1Participation in lectures.15
A-W-2Independent study of lecture materials and recommended literature.10
A-W-3Consultation5
A-W-4Preparation for passing the lecture content.8
A-W-5Passing the lecture content.5
A-W-6Discussing lecture content2
45
(*) 1 punkt ECTS, odpowiada około 30 godzinom aktywności studenta
PoleKODZnaczenie kodu
Zamierzone efekty uczenia sięBT_2A_BTZ-A-O5.2_W03Student has knowledge about the organization and structural relationships of proteins. He knows bioinformatic methods and tools for the analysis of protein structures. Has knowledge about the possibilities and consequences of manipulation in protein structures.
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
Cel przedmiotuC-1Developing skills of selection of appropriate bioinformatics tools to solve and analyze the structure of proteins
C-2Mastering the ability to combine and correct interpretation of information relating to various levels of organization of protein structures
Treści programoweT-A-1The introduction to proteins molecular structure part II
T-A-3The in silico methods of proteins structure II and III level determination
T-A-4The in silico methods of oligomeric enzymes structure determination
T-A-5The methods for the effective ligands design for the enzymes activity modulation part I
Metody nauczaniaM-1Information lectures
M-2explanation or clarification
M-3description
Sposób ocenyS-2Ocena formująca: multimedia presentation
Kryteria ocenyOcenaKryterium oceny
2,0
3,0Preparation of a multimedia presentation, participation in 90% of auditory classes, Correct answer to 60% of test questions - exam
3,5
4,0
4,5
5,0
PoleKODZnaczenie kodu
Zamierzone efekty uczenia sięBT_2A_BTZ-A-O5.2_U01Correctly applying a bioinformatic tools to 3D enzymes structure solving
Odniesienie do efektów kształcenia dla kierunku studiówBTap_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-1Developing skills of selection of appropriate bioinformatics tools to solve and analyze the structure of proteins
C-2Mastering the ability to combine and correct interpretation of information relating to various levels of organization of protein structures
Treści programoweT-W-1Methods for the data mining for protein structure on their I level. Prediction of catalytic and structural properties enzymes. part I
T-W-2Methods for the data mining for protein structure on their I level. Prediction of catalytic and structural properties enzymes. part II
T-W-3Methods for prediction localisation of enzymes catalytic sites
T-W-4Methods for characterisaation catalytic sites properities.
Metody nauczaniaM-3description
Sposób ocenyS-2Ocena formująca: multimedia presentation
Kryteria ocenyOcenaKryterium oceny
2,0
3,0Preparation of a multimedia presentation, participation in 90% of auditory classes,
3,5
4,0
4,5
5,0
PoleKODZnaczenie kodu
Zamierzone efekty uczenia sięBT_2A_BTZ-A-O5.2_K02Understands the consequences of modifying protein structures on the functioning of living organisms
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
Cel przedmiotuC-1Developing skills of selection of appropriate bioinformatics tools to solve and analyze the structure of proteins
C-2Mastering the ability to combine and correct interpretation of information relating to various levels of organization of protein structures
Treści programoweT-A-1The introduction to proteins molecular structure part II
T-A-3The in silico methods of proteins structure II and III level determination
T-A-4The in silico methods of oligomeric enzymes structure determination
T-A-5The methods for the effective ligands design for the enzymes activity modulation part I
Metody nauczaniaM-1Information lectures
M-2explanation or clarification
M-3description
Sposób ocenyS-2Ocena formująca: multimedia presentation
Kryteria ocenyOcenaKryterium oceny
2,0
3,0Preparation of a multimedia presentation, participation in 90% of auditory classes,
3,5
4,0
4,5
5,0