Istanbul Health and Technology University INFORMATION PACKAGE / COURSE CATALOGUE
| Molecular Biology and Genetics | |||||
| Bachelor | TR-NQF-HE: Level 6 | QF-EHEA: First Cycle | EQF-LLL: Level 6 | ||
Course General Introduction Information
| Course Code: | MBG214 | ||||
| Course Name: | BasiCalculations in Molecular Biology | ||||
| Course Semester: | Spring | ||||
| Course Credits: |
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| Language of instruction: | TR | ||||
| Course Requirement: | |||||
| Does the Course Require Work Experience?: | No | ||||
| Type of course: | Area Ellective | ||||
| Course Level: |
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| Mode of Delivery: | Face to face | ||||
| Course Coordinator : | Dr.Öğr.Üyesi SONER AKSU | ||||
| Course Lecturer(s): | Soner Aksu, PhD | ||||
| Course Assistants: |
Course Purpose and Content
| Course Objectives: | The aim of the Basic Computations in Molecular Biology course is to provide the students of the Department of Molecular Biology and Genetics with information about the basic computational methods used within the scope of experimental studies used in this field. In this way, it is aimed to have information about how the data obtained as a result of experimental studies are analysed, what are the important parameters calculated on the basis of the study and how these numerical values should be evaluated. |
| Course Content: | 1- Introduction and History History Measurement, Unit, SI Basic and Derived Units Osmosis, Diffusion, Concentration Examples with Solutions 2- Scientific Notation and Metrics: An Overview of Measurement in Biology Meaningful Steps Rounding to Significant Digits in Calculations Exponents and Scientific Notation Expression of Numbers in Scientific Demonstration Converting numbers from scientific notation to decimal notation Addition and Subtraction of Numbers Written in Scientific Notation Multiplication and Division of Numbers Written in Scientific Notation Metric Prefixes Conversion Factors and Simplification Conditions 3- Solutions, Mixtures and Media Dilution Concentration Percentage Solution Preparation and Dilution Mole and Molecular Weight Normality pH, pKa MIDTERM EXAM 4- Cell Growth Bacterial Growth Curve Adjusting Cell Concentration OD550 Linear Graph and Logarithmic Graph Drawing against Time Logarithmic Curve with Cell Concentration and Time Doubling Time Ripple Test Mutation Rate and Speed Haemocytometer 5- Bacteriophage Studies Multiplicity and Probability of Infection Measurement of Phage Titre Dilution 6- Determination of Nucleic Acid Amount, Synthesis and Transcription UV spectroscopy Determination of double stranded DNA concentration Determination of Single Strand DNA concentration Oligonucleotide quantification Determination of RNA concentration Molecular Weight, Molarity and Nucleic Acid length Limit of Detection and Limit of Quantity 7- PCR DNA template and Amplification Exponential Amplification Efficiency of PCR Amplicon and Primer Tm Calculations Primers and dNTPs Error Percentage of DNA polymerases |
Learning Outcomes
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The students who have succeeded in this course;
1) The concept of measurement and different measurement basic and derived units, general information about SI 2) Significant digits, scientific representation of numbers, exponents and operations with exponents, four operations with numbers converted to scientific representation, rounding 3) Concepts of concentration, dilution, dilution, concentration, amount of substance, molecular weight, 4) Mol, molarity, normality, pH, percentage concentration calculations, 5) Cell growth over time, calculation of cell concentration, doubling time, fluctuation variation, mutation rate and rate calculations, 6) Multiplicity of infection, phage titre calculations, moi and pfu concepts 7) Single and double stranded DNA and RNA concentration calculations, concentration and quality parameters, Beer's law, depletion coefficient and concentration relationship, OD and concentration relationship, 8) LOD and LOQ concepts and calculations 9) Concentration and quantity calculations for PCR chemicals 10) PCR efficiency and amplification relationship 11) Calculation of the amount of DNA polymerase error 12) Calculation of Amplicon and Primer Tm temperatures |
Course Flow Plan
| Week | Subject | Related Preparation |
| 1) | 1- Introduction and History History Measurement, Unit, SI Basic and Derived Units Osmosis, Diffusion, Concentration Examples with Solutions 2- Scientific Notation and Metrics: An Overview of Measurement in Biology Meaningful Steps Rounding to Significant Digits in Calculations Exponents and Scientific Notation Expression of Numbers in Scientific Demonstration Converting numbers from scientific notation to decimal notation Addition and Subtraction of Numbers Written in Scientific Notation Multiplication and Division of Numbers Written in Scientific Notation Metric Prefixes Conversion Factors and Simplification Conditions 3- Solutions, Mixtures and Media Dilution Concentration Percentage Solution Preparation and Dilution Mole and Molecular Weight Normality pH, pKa MIDTERM EXAM 4- Cell Growth Bacterial Growth Curve Adjusting Cell Concentration OD550 Linear Graph and Logarithmic Graph Drawing against Time Logarithmic Curve with Cell Concentration and Time Doubling Time Ripple Test Mutation Rate and Speed Haemocytometer 5- Bacteriophage Studies Multiplicity and Probability of Infection Measurement of Phage Titre Dilution 6- Determination of Nucleic Acid Amount, Synthesis and Transcription UV spectroscopy Determination of double stranded DNA concentration Determination of Single Strand DNA concentration Oligonucleotide quantification Determination of RNA concentration Molecular Weight, Molarity and Nucleic Acid length Limit of Detection and Limit of Quantity 7- PCR DNA template and Amplification Exponential Amplification Efficiency of PCR Amplicon and Primer Tm Calculations Primers and dNTPs Error Percentage of DNA polymerases | Lecture Notes and Presentations |
Sources
| Course Notes / Textbooks: | Frank H. Stephenson – Moleküler Biyoloji ve Biyoteknoloji İçin Matematiksel Hesaplamalar, 3. Baskı |
| References: | Frank H. Stephenson – Mathematical Calculations for Molecular Biology and Biotechnology, 3th Edition |
Course - Learning Outcome Relationship
| No Effect | 1 Lowest | 2 Medium | 3 Highest |
| Program Outcomes | Level of Contribution | |
| 1) | Having knowledge and understanding of Molecular Biology and Genetics subjects, established on competencies gained in previous education and supported by using course books containing latest information, application tools and other scientific literature. | 3 |
| 2) | Students can integrate knowledge and skills from molecular biology and genetics courses and can acquire further knowledge according to their own interests. | 3 |
| 3) | Students acquire practical skills in fundamental molecular biology and genetics techniques. | 3 |
| 4) | Ability of proposing solutions in unexpected, complicated situations on applications of Molecular Biology and Genetics by claiming responsibility individually or as a part of a team. | 1 |
| 5) | Competency in planning academic studies on Molecular Biology and Genetics and carrying out these studies individually or collectively. | 2 |
| 6) | Students can develop ability to analyse and interpret experimental data obtained in a laboratory setting statistically. | 3 |
| 7) | Sufficient foreign language knowledge for communication between colleagues and following literature on Molecular Biology and Genetics. | 1 |
| 8) | Students can use computational technologies to analyse scientific data and for information retrieval. | 1 |
| 9) | Being aware of the necessity of lifelong education, reaching information, following the advances in science and technology and constant struggle of renewing oneself. | 1 |
| 10) | Evaluating natural and social events with an environmental point of view and ability of informing and leading the public opinion | |
| 11) | Students acquire professional knowledge and skills to fulfil requirements of their future employers. | 3 |
| 12) | Having proper social, ethical and scientific values and the will to protect these values on studies about collection, evaluation, contemplation, publication and application of data regarding Molecular Biology and Genetics. | 1 |
| 13) | Students can understand and evaluate advantages and limitations of technological platforms in life sciences including genomics, genetic engineering and biotechnology. | 1 |
| 14) | Students would have consciousness on subjects such as the quality management, worker welfare and safety. |
Learning Activity and Teaching Methods
| Anlatım | |
| Course | |
| Homework | |
| Problem Çözme |
Measurement and Evaluation Methods and Criteria
| Yazılı Sınav (Açık uçlu sorular, çoktan seçmeli, doğru yanlış, eşleştirme, boşluk doldurma, sıralama) | |
| Homework | |
| Uygulama |
Assessment & Grading
| Semester Requirements | Number of Activities | Level of Contribution |
| Homework Assignments | 4 | % 30 |
| Midterms | 1 | % 20 |
| Final | 1 | % 50 |
| total | % 100 | |
| PERCENTAGE OF SEMESTER WORK | % 50 | |
| PERCENTAGE OF FINAL WORK | % 50 | |
| total | % 100 | |
İş Yükü ve AKTS Kredisi Hesaplaması
| Activities | Number of Activities | Aktiviteye Hazırlık | Aktivitede Harçanan Süre | Aktivite Gereksinimi İçin Süre | Workload | ||
| Course Hours | 14 | 2 | 28 | ||||
| Application | 14 | 1 | 14 | ||||
| Study Hours Out of Class | 10 | 3 | 30 | ||||
| Homework Assignments | 4 | 4 | 16 | ||||
| Midterms | 1 | 1.5 | 1.5 | ||||
| Final | 1 | 1.5 | 1.5 | ||||
| Total Workload | 91 | ||||||