COURSE UNIT TITLE

: MACHINERY OF LIFE

DEGREE PROGRAMMES

Description of Individual Course Units

Course Unit Code Course Unit Title Type Of Course D U L ECTS
BST 6006 MACHINERY OF LIFE ELECTIVE 3 0 0 12

Offered By

Biomedicine and Health Technologies

Level of Course Unit

Third Cycle Programmes (Doctorate Degree)

Course Coordinator

ASSISTANT PROFESSOR EZGI KARACA EREK

Offered to

Biomedicine and Health Technologies

Course Objective

To gain a thorough understanding of the life machinery through the lenses of diverse biological approaches.

Learning Outcomes of the Course Unit

1   Thorough knowledge on molecular machines and their components
2   Familiarity with the three-dimensional structures of molecular machines
3   Being able understand and discuss functioning of various molecular machines
4   Being able understand and discuss the effect of oncogenic mutations on the functioning of molecular machines
5   Familiarity with the structure and function of extremophilic enzymes
6   Being able to understand and use computational design algorithms
7   Interpreting signaling machineries at the atomistic scale
8   Interpreting metabolism machineries at the atomistic scale
9   Being able to discuss the capabilities and limitations of current design strategies
10   Presentation of research findings

Mode of Delivery

Face -to- Face

Prerequisites and Co-requisites

None

Recomended Optional Programme Components

None

Course Contents

Week Subject Description
1 The Molecular World
2 Protein centered Molecular Machineries
3 Nucleic Acid centered Molecular Machineries
4 Glycans and Lipids
5 The Process of Living: Energy and Entropy
6 Examples of Integral Molecular Machines - I
7 Examples of Integral Molecular Machines - II
8 Midterm
9 Functioning of Signaling Machineries
10 Functioning of Metabolic Machineries
11 The Effect of Oncogenic Mutations in Molecular Machines
12 The world of extremophiles
13 Predicting, Engineering and Design of Biomolecular Complexes - I
14 Predicting, Engineering and Design of Biomolecular Complexes - II
15 Assignment Presentations
16 Final Exam

Recomended or Required Reading

Textbook(s)/References/Materials:
Machinery of Life, David Goodsell
Hardcover: 167 pages
Publisher: Copernicus; 2nd ed. 2009 edition (April 16, 2010)
Language: English
ISBN-10: 0387849246
ISBN-13: 978-0387849249

Introduction to Protein Structure, Carl Branden and John Tooze
Paperback: 424 pages
Publisher: Garland Science; 2 edition (January 3, 1999)
Language: English
ISBN-10: 9780815323051
ISBN-13: 978-0815323051

Lehninger Principles of Biochemistry
Hardcover: 1328 pages
Publisher: W.H. Freeman; Sixth edition (November 21, 2012)
Language: English
ISBN-10: 9781429234146
ISBN-13: 978-1429234146

Planned Learning Activities and Teaching Methods

Oral presentation, literature search and discussion

Assessment Methods

SORTING NUMBER SHORT CODE LONG CODE FORMULA
1 ASG ASSIGNMENT
2 MTE MIDTERM EXAM
3 FIN FINAL EXAM
4 FCG FINAL COURSE GRADE ASG * 0.30 + MTE * 0.30 + FIN * 0.40
5 RST RESIT
6 FCGR FINAL COURSE GRADE (RESIT) ASG * 0.30 + MTE * 0.30 + RST * 0.40


*** Resit Exam is Not Administered in Institutions Where Resit is not Applicable.

Further Notes About Assessment Methods

None

Assessment Criteria

To be announced.

Language of Instruction

English

Course Policies and Rules

To be announced.

Contact Details for the Lecturer(s)

ezgi.karaca@deu.edu.tr

Office Hours

To be announced.

Work Placement(s)

None

Workload Calculation

Activities Number Time (hours) Total Work Load (hours)
Lectures 14 3 42
Preparations before/after weekly lectures 14 8 112
Preparation for midterm exam 1 20 20
Preparation for final exam 1 25 25
Preparing assignments 2 35 70
Preparing presentations 1 30 30
Midterm 1 5 5
Final 1 5 5
TOTAL WORKLOAD (hours) 309

Contribution of Learning Outcomes to Programme Outcomes

PO/LOPO.1PO.2PO.3PO.4PO.5PO.6PO.7PO.8
LO.1555
LO.25555
LO.35555
LO.45555555
LO.55555555
LO.655555555
LO.755555555
LO.855555555
LO.955555555
LO.1055555555

CONTACT INFORMATION
Dokuz Eylül Üniversitesi Cumhuriyet Bulvarı No: 144 35210 Alsancak / İZMİR
Phone: +90(232) 412 12 12 - Fax: +90 (232) 464 81 35

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