Faculty of engineering and natural sciences department of genetics and bioengineering first cycle study program specification



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Course Code: GBE 337

Course Name: BIOMECHANICS

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2 + 2

Total Hours: 30 + 30

Course Description

This course is combining basics of mechanics with classical topics in biomechanics. The first half of the semester is offering topics such as movement, force, energy, and work, Newton’s laws, and pendulum. The second part of the course (after the mid-term exam) is dealing with the application of principles of mechanics as they refer to the movement of human body. Body systems are discussed from this point of view, followed by mechanics of upper and lower extremities. This course is taken concurrently with a lab course.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:

  • Introduction to the mechanics of rigid bodies and its application to biological systems.

  • Explaining physical parameters in mechanics.

  • Introduction to biomechanics of biological bodies.

  • Giving an outline of new technologies in biomechanics.

Course Content

(weekly plan)



Week 1: Introduction to mechanics

Week 2: Motion in mechanics; straight-line and rotational motion

Week 3: Force and force fields

Week 4: Work, energy, and power

Week 5: Newton’s laws

Week 6: Kinetic and potential energy; impulse, momentum, and angular momentum

Week 7: Fluids. Pendulums

Week 8: MID-TERM EXAM WEEK

Week 9: Introduction to biomechanics: Application of mechanics to biological bodies

Week 10: Skeletal and muscular systems; Levers and joints

Week 11: Neurological system

Week 12: Mechanics of upper extremities: Shoulder, elbow, and wrist

Week 13: Mechanics of lower extremities: Hip and knee

Week 14: Mechanics of lower extremities: Ankle, foot, and trunk

Week 15: New technology in biomechanics



Week 16: FINAL EXAM WEEK
LABORATORY CONTENT

Week 1-11: The laboratory course is designed so that the students repeat the concepts thought during the lectures in form of numerical problems in the first part of the semester. The second part of the course is mainly focused on reading scientific articles related to biomechanics, that is, human movement.

Teaching Methods

Description

  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Tutorials

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

After completion of this course, students should be able to:

  1. Describe the mechanics of rigid bodies and its application to biological systems

  2. Outline the significance of biomechanics with regards to biological bodies and systems

  3. Name new technologies in biomechanics

  4. Explain the basic physical parameters in mechanics

  5. Assess numerical problems regarding biomechanics

  6. Critically discuss scientific articles related to biomechanics and human movement

Prerequisite Course(s)

(if any)


None.

Language of Instruction

English

Mandatory Literature

Beer, F., Johnston, E. R., & Mazurek, D. (2012). Vector mechanics for engineers: Statics, 10th ed. New York, NY, USA: McGraw-Hill Science

Recommended Literature

Chandran, K. B. (1992). Cardiovascular Biomechanics, 1st ed. New York, NY, USA: New York University Press

ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project

1

14

14

Seminar / Presentation

1

18

18

Total Workload

125

ECTS Credit (Total Workload / 25)

5




Course Code: GBE 339

Course Name: RECOMBINANT DNA TECHNOLOGY

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2+2

Total Hours: 30+30

Course Description

The course deals with procedures that have been developed to successfully conduct DNA recombination and produce chimeric DNA, which includes DNA isolation, restriction digestion, DNA ligation, selection and screening, etc. An important part of the course is ethics related to recombinant DNA technology. Lab course offers series of experiments that are supposed to show students experimental workflow in a characteristic DNA recombination protocol.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:

  • Demonstrating practical experience of selected molecular biology techniques.

  • Demonstrating basic techniques involved in recombinant DNA manipulations including DNA restriction, ligation, transformation and selection of recombinant plasmid.

  • Demonstrating the principle of PCR and its applications (e.g. Analysis of DNA repeats to estimate its frequency in the population).

Course Contents

(weekly plan)



Week 1: Introduction to the course

Week 2: The basic terminology of recombinant DNA technology

Week 3: Recombination vectors: Plasmids, viruses, competent cells

Week 4: Restriction digestion of DNA samples

Week 5: Chemical synthesis of a DNA sequence

Week 6: DNA ligation

Week 7: Introduction of chimeric DNA into the host organism

Week 8: MID-TERM EXAM WEEK

Week 9: Expression of recombinant DNA

Week 10: Selection and screening for recombined DNA

Week 11: Recombinant proteins

Week 12: Applications of recombinant DNA technology

Week 13: Ethical considerations in recombinant DNA technology

Week 14: Analysis of scientific articles

Week 15: Student presentations



Week 16: FINAL EXAM WEEK
LABORATORY CONTENTS

Week 1: Beginning of classes

Week 2, Lab 1: Introduction to lab course

Week 3, Lab 2: Ethical considerations in recombinant DNA technology

Week 4, Lab 3: Recombinant DNA technology in bacteria: An overview

Week 5, Lab 4: Preparation of vector DNA: Plasmid isolation

Week 6, Lab 5: Restriction digestion of DNA samples

Week 7, Lab 6: DNA ligation and introduction of novel DNA into the host cell



Week 8: MID-TERM EXAM WEEK

Week 9, Lab 7: Growing host cells

Week 10 Lab 8: Selection and screening for recombined DNA

Week 11, Lab 9: Usage of recombinant DNA

Week 12, Lab 10: Student presentations

Week 13, Lab 11: Student presentations



Week 14: Preparation for practical exam

Week 15: Practical exam from lab course

Week 16: FINAL EXAM WEEK

Teaching Methods

Description

  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Laboratory work

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

After completion of this course, students should be able to:

  1. Categorize molecular mechanisms underlying the PCR reaction

  2. Handle molecular cloning

  3. Prepare basic tools of engineering: restriction enzymes, ligation, etc.

  4. Operate PCR

  5. Perform bacterial transformation

Prerequisite Course(s)

(if any)


None

Language of Instruction

English

Mandatory Literature

Sandhu, S.S. (2010). Recombinant DNA Technology, 1st ed. New Delhi, India: International Publishing House

Recommended Literature

Chaudchuri, K. (2013). Recombinant DNA Technology, 1st ed. New Delhi, India: TERI

ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project




18

18

Seminar / Presentation




14

14

Total Workload

125

ECTS Credit (Total Workload / 25)

5



Course Code: GBE 340

Course Name: PLANT PATHOLOGY

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2+2

Total Hours: 30+30

Course Description

This course examines disease progression in plants on molecular and morphologic level. Also, symptoms of plant disease, as well as plant immune system are covered in the first part of the course. The second part of the course discusses biological agents causing plant diseases, such as bacteria, viruses, and fungi. Lab course is offering students an opportunity to experimentally examine disease progression when it is caused by different biological agents and to compare them.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:

  • Introduction to plant diseases caused by fungi, bacteria, viruses, nematodes and higher parasitic plants.

  • Explaining vectors as means of disease transmission.

  • Explaining genetics of plant diseases.

  • Giving an outline of plant defense mechanisms.

Course Contents

(weekly plan)



Week 1: Introduction: History of plant pathology and early significant plant diseases

Week 2: Parasitism and disease development. Pathogenesis

Week 3: Genetics of plant disease

Week 4: How pathogens attack plants

Week 5: How plants defend themselves against pathogens

Week 6: Environmental effects on the development of infectious plant disease

Week 7: Plant disease epidemiology

Week 8: MID-TERM EXAM WEEK

Week 9: Control of plant diseases

Week 10: Plant diseases caused by bacteria and mollicutes

Week 11: Plant diseases caused by viruses

Week 12: Plant diseases caused by fungi

Week 13: Plant diseases caused by protozoa

Week 14: Plant diseases caused by nematodes

Week 15: Plant diseases caused by parasitic plants



Week 16: FINAL EXAM WEEK
LABORATORY CONTENTS

Week 1-11: In the lab course, students will get a theoretical introduction into the symptoms and causative agents of plant diseases. Following that, they will grow plants and infect them with various causative agents. They will subsequently observe the development of disease symptoms on the plants, record the results, and discuss them together.

Teaching Methods

Description

  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Laboratory work

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

After completion of this course, students should be able to:

  1. Define pathogenesis

  2. Recall the basics of plant disease caused by viruses

  3. Classify plant viruses

  4. Recall basics of plant diseases caused by fungi

  5. Describe transmission of plant viruses through vectors

Prerequisite Course(s)

(if any)


None

Language of Instruction

English

Mandatory Literature

Schumann, G. L. & D’Arcy, C. J. (2009). Essential plant pathology, 2nd ed. St. Paul, MN, USA: American Phytopathological Society

Recommended Literature

Sambamurty, A.V.S.S. (2005). Textbook of Plant Pathology, 1st ed. New Delhi, India: IK International

ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project




14

14

Seminar / Presentation




18

18

Total Workload

125

ECTS Credit (Total Workload / 25)

5



Course Code: GBE 341

Course Name: BIOPHYSICS

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2+2

Total Hours: 30+30

Course Description

This course is focused on the application of physical principles in order to: (1) perform a detailed study of DNA structure and interactions within DNA building blocks, (2) understand the structure and formation of RNA and proteins, and (3) introduce processes occurring within the basic biological structures, such as biological membranes.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:

  • Introduction to physical principles in biophysical processes, biomedical engineering problems.

  • Showing the correlation between physics and biological sciences.

  • Revising the basics of DNA structure.

  • Explaining the impact of physical forces on DNA structure.

  • Providing an outline of RNA, protein, molecular and medical biophysics.

Course Contents

(weekly plan)



Week 1: Introduction to biophysics

Week 2: DNA structure

Week 3: Base-pair interactions and DNA melting

Week 4: Mechanics and statistical mechanics of DNA

Week 5: Electrostatics of DNA and DNA-DNA interactions

Week 6: DNA collapse and DNA mesophases

Week 7: DNA organization in chromatin and viruses

Week 8: MID-TERM EXAM WEEK

Week 9: Biophysics of RNA

Week 10: Biophysics of proteins

Week 11: Molecular biophysics

Week 12: Membrane biophysics

Week 13: Medical biophysics

Week 14: Biomechanics

Week 15: Methods in molecular biophysics



Week 16: FINAL EXAM
LABORATORY CONTENTS

Week 1-11: The laboratory course is designed so that the students prepare oral presentations and discuss scientific articles on topics covered during the lectures and improve their knowledge in that way.

Teaching Methods

Description

  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Tutorials

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

After completion of this course, students should be able to:

  • Recognize basic physical principles underlying biological processes

  • Relate physical principles to biophysical processes

  • Apply the knowledge of physical principles on engineering problems

  • Make DNA models

  • Deliver an effective presentation

Prerequisite Course(s)

(if any)


None

Language of Instruction

English

Mandatory Literature

Hobbie, R. K. & Roth, B. J. (2009). Intermediate Physics for Medicine and Biology, 4th ed. New York, NY, USA: Springer

Recommended Literature

Nelson, P. (2003). Biological Physics: Energy, Information, Life, 1st ed. New York, NY, USA: W. H. Freeman

Davidovits, P. (2001). Physics in Biology and Medicine. Waltham, MA, USA: Academic Press



ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project




14

14

Seminar / Presentation




18

18

Total Workload

125

ECTS Credit (Total Workload / 25)

5



Course Code: GBE 342

Course Name: ORGANIC CHEMISTRY II

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2+2

Total Hours: 30+30

Course Description

Organic chemistry of carbonyl compounds I, II, and III is presented through the main chemical reactions of each class of organic compounds. Organic chemistry of biomolecules such as amino acids, proteins, enzymes etc. is explained too. The course revolves around shared features and unifying concepts and it emphasizes principles that can be repeatedly applied. Learning on this way, students will see that organic chemistry is integral to biology as well as to their daily lives.


Course Objectives

The cognitive, affective and behavioral objectives of this course are following:

  • To teach about the application to scientific and commercial fields.

  • To understand the basics of organic chemistry needed for further studies.

  • To learn the basic structures of organic molecules.

Course Contents

(weekly plan)



Week 1: Carbonyl compounds I (carboxylic acids and carboxylic acid derivatives)

Week 2: Carbonyl compounds I (carboxylic acids and carboxylic acid derivatives)

Week 3: Carbonyl compounds II (aldehydes and ketones)

Week 4: Carbonyl compounds III, reactions at the -carbon

Week 5: Quiz I, Determining the structures of organic compounds

Week 6: Determining the structures of organic compounds

Week 7: Quiz II, Preparation for midterm

Week 8: MIDTERM WEEK

Week 9: The organic chemistry of carbohydrates

Week 10: The organic chemistry of amino acids, peptides, proteins

Week 11: Quiz III, The organic chemistry of enzymes and vitamins

Week 12: The organic chemistry of metabolic pathways

Week 13: The organic chemistry of lipids

Week 14: Quiz IV, The organic chemistry of the nucleic acids

Week 15: Preparation for final exam



Week 16: FINAL EXAM WEEK
LABORATORY CONTENTS

Week 1: Beginning of classes

Week 2, Lab 1: Introduction to Organic Chemistry II lab

Week 3, Lab 2: Analysis of biological macromolecules

Week 4, Lab 3: Titration curves of amino acids: Experimental

Week 5, Lab 4: Titration curves of amino acids: Result analysis

Week 6, Lab 5: Carbohydrate analysis: Estimation of glucose concentration in a samples; Detection of starch in a sample

Week 7, Lab 6: Estimation of saponification value of fats and oils

Week 8: MIDTERM WEEK

Week 9, Lab 7: Synthesis of a soap

Week 10 Lab 8: Quantitative analysis of vitamin C contained in foods

Week 11, Lab 9: Measurement of active ingredient in aspirin pills

Week 12, Lab 10: Water analysis

Week 13, Lab 11: Chemical properties of consumer products



Week 14, Lab 12: Preparation from practical exam

Week 15, Practical exam from lab course

Week 16: FINAL EXAM WEEK

Teaching Methods

Description

  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Guest instructors

  • Laboratory work

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

After completion of this course, students should be able to:

  • Aldehydes and ketones

  • Carboxylic acids

  • Determination of the structure of organic compounds

  • Organic chemistry of amines, proteins and peptides

  • Organic chemistry of carbohydrates, nucleic acids and lipids

Prerequisite Course(s)

(if any)


None

Language of Instruction

English

Mandatory Literature

Bruice, P.Y. (2006). Essential organic chemistry, Pearson Education, Inc.

Recommended Literature

None

ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project




14

14

Seminar / Presentation




18

18

Total Workload

125

ECTS Credit (Total Workload / 25)

5




Course Code: GBE 343

Course Name: VIROLOGY

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2+2

Total Hours: 30+30

Course Description

This course is aimed at providing students with an introduction to virology. Students will become familiar with history and scope, virus structure their multiplication and growth in laboratory conditions. Further on they will be familiarized with the effect of physical and chemical agents on viruses as well as their ecology. Basics of viral classification will be elaborated as well as some viral families and genera.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:

  • Introduction to virus structure

  • Understand the basics of viral taxonomy

  • Do experimental design and manipulation with viruses,

  • Conduct viral analysis and understand their possible application.

Course Contents

(weekly plan)



Week 1: History and development of virology

Week 2: Virus structure, chemical composition and basic characteristics

Week 3: Methods in virology I

Week 4: Methods in virology II

Week 5: Multiplication of viruses and their growth cycles

Week 6: Effect of physical and chemical agents on viruses and viral storage

Week 7: Virus genetics

Week 8: MIDTERM EXAM WEEK

Week 9: Vaccines,

Week 10: Viral classification

Week 11: Virus ecology, viroides and prions

Week 12: DNA viruses

Week 13: DNA viruses

Week 14: RNA viruses

Week 15: RNA viruses



Week 16: FINAL EXAM WEEK
LABORATORY CONTENTS

Week 1-14 Design and conduct an experiment, record the results and present them as a poster at the end of the lab session.

Teaching Methods

Description

  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Guest instructors

  • Research projects

  • Laboratory work

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

After completion of this course, students should be able to:

  • Recall and name basic virology laboratory techniques, as well as explain the foundations of virology

  • Demonstrate understanding of viral structure and replication cycles

  • Translate the knowledge from this course in future virology courses and/or having a good appreciation of concepts needed to make reasoned choices in their everyday lives

  • Interpret and explain how viruses survive where they do, how they are related, and how they interact with us

  • Operate with basic microbiological skills and successfully use them in the lab

Prerequisite Course(s)

(if any)


None

Language of Instruction

English

Mandatory Literature

  • Knipe, D. M., & Howley, P. M. (2001). Fundamental virology (No. Ed. 4). Lippincott Williams & Wilkins.

Recommended Literature

None

ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project




14

14

Seminar / Presentation




18

18

Total Workload

125

ECTS Credit (Total Workload / 25)

5


1BOS 101 Bosnian/Croatian/Serbian Language I/ TDE 101 Turkish Language I/ GRM 101 German Language I

2BOS 102 Bosnian/Croatian/Serbian Language II/ TDE 102 Turkish Language II/ GRM 102 German Language II

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