Genetics and Bioengineering
Bachelor	TR-NQF-HE: Level 6	QF-EHEA: First Cycle	EQF-LLL: Level 6

General course introduction information

Course Code:

GBM202

Course Name:

Bioengineering Laboratory

Course Semester:

Fall

Course Credits:

Theoretical	Practical	Credit	ECTS
0	4	2	4

Language of instruction:

Course Requisites:

Does the Course Require Work Experience?:

Type of course:

Compulsory

Course Level:

Bachelor

TR-NQF-HE:6. Master`s Degree

QF-EHEA:First Cycle

EQF-LLL:6. Master`s Degree

Mode of Delivery:

Face to face

Course Coordinator :

Dr.Öğr.Üyesi METİN YAZAR

Course Lecturer(s):

Dr.Öğr.Üyesi METİN YAZAR

Course Assistants:

Course Objective and Content

Course Objectives:

At the end of this course the student will be able to:

• Learn the safety and general rules of a laboratory, how to use basic laboratory instruments
• Learn how to use basic measurement device, and make calculations with them
• Prepare basic buffers, mediums and mixes about biological samples
• Learn bacterial growth, staining, imaging
• Describe molecular tools such as PCR, isolation, ligation etc. and learn how to use them

Course Content:

• Describe measurement uncertainty
• Define using microscopy
• Describe The Growth Mediums and The Buffers
• Describe The Growth Mediums and The Buffers
• Describe The Serial Dilution
• Describe The Bacterial Cell Culture Methods
• Define Gram Staining Methods
• Describe The Bacterial Growth
• Define the Effects on Bacterial Growth as UV and High Temperature
• Describe DNA Isolation From Bacterial Cells
• Describe DNA Isolation From Blood
• Describe polymerase chain reaction (PCR) technique
• Describe agarose gel electrophoresis technique
• Describe plasmid isolation from microorganism
• Describe restriction, digestion and ligation process
• Describing real-time quantitative PCR technique (qRT-PCR)
• Describe protein polyacrylamide gel electrophoresis

Learning Outcomes

The students who have succeeded in this course;

Learning Outcomes

1 - Knowledge
Theoretical - Conceptual
1) Learn the safety and general rules of a laboratory, how to use basic laboratory instruments
2) Learn how to use basic measurement device, and make calculations with them
3) Prepare basic buffers, mediums and mixes about biological samples
4) Learn bacterial growth, staining, imaging
5) Describe molecular tools such as PCR, isolation, ligation etc. and learn how to use them
2 - Skills
Cognitive - Practical
3 - Competences
Communication and Social Competence
Learning Competence
Field Specific Competence
Competence to Work Independently and Take Responsibility

Lesson Plan

Week	Subject	Related Preparation
1)	• Syllabus • Introduction of bioengineering laboratory • Discussing laboratory safety rules • Describing using basic laboratory instruments • Describing how to take notes in laboratories • Describing scientific reports and preparing scientific reports
2)	• Describing measurement with balances and microbalances • Calculations of measurement uncertainty of balances
3)	• Defining how to use a microscope with pre-stained slides • Preparing epithelial sample from mouth and staining it with thryphan blue for microscope examination
4)	• Describe the mediums and the buffers • Concentration calculations • Preparing TBE buffer • Preparing LB and LB-Agar
5)	• Calculations of different dilutions of bacterial culture • Describing different bacterial cell culture methods • Colony counting with pre-cultured bacterial cells • Gram staining with pre-cultured bacterial cells • Imaging of gram staining
6)	• Treating bacterial cells with UV and high temperature; keeping a group as control • Repeating UV-Spectrophotometer Method • Drawing bacterial growth curve for preset 3 groups of bacterial cell cultures
7)	• Midterm Exam
8)	• Describing basic steps of DNA isolation from bacterial cell culture • Describing basic steps of DNA isolation from blood
9)	• Defining each PCR component function in PCR amplification • Describing how to prepare PCR mix • Primer dilution • Discussion of importance of specific primer selection in PCR amplification
10)	• Preparations of PCR products for agarose gel electrophoresis • Preparations of agarose gel • Explain the role of loading dye and DNA marker • Loading and running of PCR products in agarose gel electrophoresis • Evaluating the results of agarose gel electrophoresis in UV light. • Evaluating DNA size and weight from agarose gel electrophoresis results
11)	• Explain the plasmid structure • Plasmid isolation components • Plasmid purification
12)	• Describe restriction enzymes • Describing digestion process • Defining ligases and ligation process • Controlling ligation products with agarose gel electrophoresis
13)	• Describe imaging techniques in qRT-PCR-probes and dyes • Defining each qPCR component function in qPCR amplification • Describing how to prepare qPCR mix • Plotting a standard curve and normalization of the results • Interpretations of the qPCR results
14)	• Denaturation of the protein • Preparation of polyacrylamide gel • Loading and running the protein in electrophoresis • Evaluating the weight of the protein with imaging the gel
15)	• Final Exam

Sources

Course Notes / Textbooks:	Laboratory Manual
References:	Laboratory Manual

Course-Program Learning Outcome Relationship

Learning Outcomes	1	2	3	4	5
Program Outcomes
1) Sufficient knowledge in mathematics, science and engineering related to their branches; and the ability to apply theoretical and practical knowledge in these areas to model and solve engineering problems.
2) The ability to identify, formulate, and solve complex engineering problems; selecting and applying appropriate analysis and modeling methods for this purpose.
3) The ability to design a complex system, process, device or product under realistic constraints and conditions to meet specific requirements; the ability to apply modern design methods for this purpose. (Realistic constraints and conditions include such issues as economy, environmental issues, sustainability, manufacturability, ethics, health, safety, social and political issues, according to the nature of design.)
4) Ability to develop, select and use modern techniques and tools necessary for engineering applications; ability to use information technologies effectively.
5) Ability to design experiments, conduct experiments, collect data, analyze and interpret results to examine engineering problems or discipline-specific research topics.
6) The ability to work effectively in disciplinary and multidisciplinary teams; individual work skill.
7) Effective communication skills in Turkish oral and written communication; at least one foreign language knowledge; ability to write effective reports and understand written reports, to prepare design and production reports, to make effective presentations, to give and receive clear and understandable instructions.
8) Awareness of the need for lifelong learning; access to knowledge, ability to follow developments in science and technology, and constant self-renewal.
9) Conform to ethical principles, and standards of professional and ethical responsibility; be informed about the standards used in engineering applications.
10) Awareness of applications in business, such as project management, risk management and change management; awareness of entrepreneurship, and innovation; information about sustainable development.
11) Information about the universal and social health, environmental and safety effects of engineering applications and the ways in which contemporary problems are reflected in the engineering field; awareness of the legal consequences of engineering solutions.

Course - Learning Outcome Relationship

No Effect	1 Lowest	2 Low	3 Average	4 High	5 Highest

	Program Outcomes	Level of Contribution
1)	Sufficient knowledge in mathematics, science and engineering related to their branches; and the ability to apply theoretical and practical knowledge in these areas to model and solve engineering problems.	1
2)	The ability to identify, formulate, and solve complex engineering problems; selecting and applying appropriate analysis and modeling methods for this purpose.	1
3)	The ability to design a complex system, process, device or product under realistic constraints and conditions to meet specific requirements; the ability to apply modern design methods for this purpose. (Realistic constraints and conditions include such issues as economy, environmental issues, sustainability, manufacturability, ethics, health, safety, social and political issues, according to the nature of design.)	1
4)	Ability to develop, select and use modern techniques and tools necessary for engineering applications; ability to use information technologies effectively.	1
5)	Ability to design experiments, conduct experiments, collect data, analyze and interpret results to examine engineering problems or discipline-specific research topics.	1
6)	The ability to work effectively in disciplinary and multidisciplinary teams; individual work skill.	1
7)	Effective communication skills in Turkish oral and written communication; at least one foreign language knowledge; ability to write effective reports and understand written reports, to prepare design and production reports, to make effective presentations, to give and receive clear and understandable instructions.	1
8)	Awareness of the need for lifelong learning; access to knowledge, ability to follow developments in science and technology, and constant self-renewal.
9)	Conform to ethical principles, and standards of professional and ethical responsibility; be informed about the standards used in engineering applications.	1
10)	Awareness of applications in business, such as project management, risk management and change management; awareness of entrepreneurship, and innovation; information about sustainable development.
11)	Information about the universal and social health, environmental and safety effects of engineering applications and the ways in which contemporary problems are reflected in the engineering field; awareness of the legal consequences of engineering solutions.

Learning Activity and Teaching Methods

Expression
Brainstorming/ Six tihnking hats
Lesson
Lab
Q&A / Discussion
Application (Modelling, Design, Model, Simulation, Experiment etc.)

Assessment & Grading Methods and Criteria

Written Exam (Open-ended questions, multiple choice, true-false, matching, fill in the blanks, sequencing)
Application
Reporting

Assessment & Grading

Semester Requirements	Number of Activities	Level of Contribution
Laboratory	12	% 36
Midterms	1	% 24
Final	1	% 40
total		% 100
PERCENTAGE OF SEMESTER WORK		% 60
PERCENTAGE OF FINAL WORK		% 40
total		% 100

Workload and ECTS Credit Grading

Activities	Number of Activities	Duration (Hours)	Workload
Laboratory	15	4	60
Midterms	1	2	2
Paper Submission	12	2	24
Final	1	2	2
Total Workload			88