Biotechnology and Genetic Engineering”

Course Handbook of the Bachelor Degree in

,,Biotechnology and Genetic Engineering”

Last Updated: 1/3/2019

Prepared, compiled and edited by: Departmental Accreditation Committee

TABLES OF CONTENT

University Compulsory Courses (25 Credit Hours, 30 ECTS) Page

Arabic Language (ARB101) 1 Social Responsibility (HSS110) 3 Entrepreneurship & Innovation (HSS119) 5 General Skills (HSS129) 8 Military Sciences (MS100) 11 English Language (LG112) 14

Faculty of Science Compulsory Courses (19 Credit Hours, 39 ECTS) Page Calculus for Biological Sciences (MATH102A) 17 Mathematical Applications of Biological Sciences (MATH103) 18 Elements of Statistics (MATH131) 20 General Physics (1) (PHY101A) 23 General Physics (2) (PHY102A) 25 General Physics Laboratory (PHY107) 27 Programming in C++ (CS115) 30

Biotechnology & Genetic Engineering Compulsory Courses Page (75 Credit Hours, 147 ECTS) Introduction to Hematology (LM251) 32 General Chemistry (1) (CHEM101) 35 General Chemistry (2) (CHEM102) 38 General Chemistry Laboratory (CHEM107) 41 Organic Chemistry (CHEM217) 43 Analytical Chemistry (CHEM233) 46 Analytical Chemistry Laboratory (CHEM234) 49 Biochemistry (CHEM262) 51 Biochemistry Laboratory (CHEM266) 54 General Biology (1) (BIO101) 56 General Biology (2) (BIO102) 59 General Biology Laboratory (BIO107) 62 General Microbiology (BIO231) 66 General Microbiology Laboratory (BIO232) 69

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TABLES OF CONTENT (continued)

Biotechnology & Genetic Engineering Compulsory Courses Page (74 Credit Hours, 147 ECTS) Cell Biology (BIO251) 71 Immunology & Serology (BIO333) 75 Immunology Laboratory (BIO336) 78 Molecular Genetics (BIO341) 81 Molecular Genetic Laboratory (BIO344) 84 Basic Biotechnology (BT232) 87 Bioinformatics (BT301) 90 Tissue Culture and Hybridoma Technology (BT363) 94 Field Training (BT399) 97 Animal Biotechnology (BT411) 99 Plant Biotechnology (BT421) 102 Microbial Biotechnology (BT431) 107 Human Genetics (BT441) 110 Molecular Biology (1) (BT451) 113 Molecular Biology Laboratory (BT453) 117 Molecular Biology (2) (BT454) 120 Cytogenetics (BT456) 123 Seminar (BT491) 126 Research Project (BT493) 128

Biotechnology & Genetic Engineering Elective Courses Page Clinical Biochemistry (LM321) 132 Diagnostic Bacteriology (BIO334) 136 Developmental Biology (BIO411) 140 Scientific Writing and Presentation (BT391) 144 Microbial Genetics (BT432) 148 Pharmaceutical Biotechnology (437) 153 Protein Biotechnology (BT452) 156 Selected Topics in Biotechnology (A) (BT492A) 160 Laboratory Management (BT495) 163 Ethical Aspects of Biotechnology (BT496) 165

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Course: Arabic Language (ARB101)

Semester: 1st Semester Course Coordinator: Variable Lecturer: Variable Language: Arabic Assignment in Curriculum Compulsory Course can be taken any semester Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 42 Exams: 4 32 Sum: 46 74

Total Sum: 120 hours

Credits 4 ECTS Prerequisites according to None examination regulations: Recommendations:

Course Description: This three credit hours course aims to study short texts from the Holy Quran, the Prophet’s Tradition, and verse and prose literature. This course also aims to analyze the aesthetic aspects of such texts in order to augment student’s connection to their mother tongue language and expose students to its literature, vocabulary, characteristics, and structure.

هذا المساق يغطي جانب نظري من اللغه وخصص له ثالث ساعات معتمده. يقوم على تناول نصوص قصيره من القران الكريم والحديث الشريف وكذلك االدب شعره ونثره وعلى الوقوف عند الجوانب الجماليه لهذه النصوص وذلك لتوثيق صله الطالب بلغته وتمكينه من االطالع على جوانب ادبها والتعرف الى خصائصها وحسن توظيف مفرداتها وتراكيبها وادراك طرق تنميتها والنهوض بها

• التأسيس إلدراك النصوص األدبية وفهمها وادراكها Learning outcomes • تجديد بعض المصطلحات النقدية والنحوية واللغوية من ضمن المنهاج • أن يصبح الطالب قادرا على تفسيربعض الظواهر األدبية والبالغية والنحوية • ن يدرك الطالب سعة اللغة العربية وقدرتها على استيعاب المصطلحات والمفردات الجديدة • تقان فن الكتابة والتعبيربنوعيه الكتابي والشفوي

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• سورة هود :تفسير وتحليل :Summary of indicative content • تطبيقات على سورة هود :االستيعاب والمناقشة ، التطبيقات اللغوية • قصيدة ذو االصبع العدواني في الفخر والعتاب : تفسير وتحليل • تطبيقات على قصيدة ذو االصبع العدواني : االستيعاب والمناقشة ، والتطبيقات اللغوية • المقامة البغدادية : تفسير وتحلی • تطبيقات على المقامة البغدادية: االستيعاب والمناقشة • قصيدة المتنبي على قدر أهل العزم : تفسير وتحليل • تطبيقات على قصيدة المتنبي: االستيعاب والمناقشة والتطبيقات اللغوی • من كتاب كليلة ودمنة "القط والفأر" : تفسير وتحليل • تطبيقات على نص كليلة ودمنة : االستيعاب والمناقشة والتطبيقات اللغوية • قصيدة في السوق القديم للسياب : تفسير وتحليل • تطبيقات على قصيدة في السوق القديم : األسئلة واالستيعابوالتطبيقات اللغوية • مقال لجبران خليل جبران "أحب من الناس العامل ": تفسير وتحليل • تطبيقات على مقالة جبران: المناقشة واالستيعاب ، والتطبيقات اللغوية • مراجعة عامة وشاملة

Assessment: The final mark of the course consists of: Computer-based exams: a. First exam (30% of the final mark): composed of multiple- choice questions. b. Second exam (30% of the final mark): composed of multiple-choice questions. c. Final exam (40% of the final mark): composed of multiple- choice questions.

Teaching style: Power point presentations will constitute mainly the lectures

Indicative Bibliography/Sources: Arabic Language 7th edition. Authored by several Arabic Teachers from the department of Humanities at JUST

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Course: Social Responsibility (HSS110) Semester: 1st Semester Course Coordinator: Department of Humanities Lecturer: Variable Language: Arabic Assignment in Curriculum Compulsory Course taken any semester Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 42 Assignments: 0 10 Exams: 4 22 Sum: 46 74

Total Sum: 120 hours

Credits 4 ECTS Prerequisites according to None examination regulations: Recommendations: None Course Description This course aims to define the concepts of homeland and citizenship to promote the notion of loyalty and belonging, and to stand on the role of the Hashemite family in the development of state facilities and the establishment of comprehensive national renaissance. It also introduces university environment and the draft of university code of conduct to guide students, especially in their first year, to discuss university violence, its causes, and appropriate treatment methods. In addition, it aims to instill the principle of moderation, acceptance of different opinions, rejection of violence, extremism and exaggeration in all its forms, and reinforce the embodiment of the principle of initiative in voluntary work and partnership with the community to activate the partnership between the university and the community and its positive impact on both sides.

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Learning outcomes: Having finished the course, students will be able to: 1. Define the concept of homeland and to completely understand their duties/responsibilities as well as their rights 2. Fully understand the role of Hashemite’s in developing modern Jordan 3. Understand the University Code of Conduct and the pertaining ethical issues 4. Accept the others opinion and live in harmony with the diversity and ethnicity of the university students 5. Reject violence and extremism in all its forms 6. Understand the social and moral benefits of voluntary work

Summary indicative content: • The course is given as a collection of lectures, group work and workshops that cover the following topics; • National education, homeland and loyalty: this chapter helps students understand the concept of the homeland and loyalty as part of the national education theme. • Loyalty and belonging; Discussion of the meaning of loyalty to the homeland • History and the geography of Jordan: Discussion of the history of Jordan, its geography and natural resources • The role of Hashemite’s in developing Jordan • The Political system in Jordan • University Environment and Student Counseling • Scribble of the university behavior and university violence • Health services and the healthy health practices • Scientific Research curriculum • Concepts of Voluntary work

Assessment: The final mark of the course consists of: 1. Written exams: a. Midterm exam (40% of the final mark): composed of multiple-choice questions. b. Final exam (40% of the final mark): composed of multiple- choice questions 2. Activities: a. Class participation (10% of the total mark) b. Projects related to environment preservation (10%)

Teaching style: Lectures: Projector, e-learning, power point presentations and whiteboard

Indicative Bibliography/Sources: National Education, authored by many department faculty. The Science of Social criminology authored by many of the teachers in the Department of Humanities at JUST

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Course: Entrepreneurship & Innovation (HSS119)

Semester: 1st Semester Course Coordinator: Dr Mutawakil Ubaidat Lecturer: Dr Mutawakil Ubaidat & others Language: Arabic and English Assignment in Curriculum Compulsory Course can be taken any semester Course Units/Credit hours Lecture: 2 credit hours Students workload: Contact hours Private study Lecture: 28 56 Assignments: 0 10 Exams & Quizzes: 6 20 Sum 34 86

Total Sum: 120 hours

Credits 4 ECTS Prerequisites according to None examination regulations: Recommendations: None Course Description: This course is an introductory course to entrepreneurship and creativity. Definition and challenges of entrepreneurship, creative thinking to do productive work projects, the link between creative ideas and available opportunities, feasibility studies, writing proposals, funding of projects, introduction of business profile, comparative measures of performance, analysis of business information, new opportunities, business objectives, evaluation of management and personnel, maintaining and strengthening existing business, overcoming weakness, operational plans, impact and management of change.

Learning outcomes: The outcomes of this course are divided into six major outcomes that are covered by the material and lecture notes. Students at the end of the class should be able: 1. To determine if entrepreneurship is an appropriate career choice for them 2. To learn ways of creativity enhancement 3. To learn how to protect intellectual property: patent, trademark, copyright 4. To learn the steps of a new business planning process 5. To learn how to conduct a feasibility analysis to determine the viability of a business concept and construct a business model

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accordingly 6. To learn writing a business plan

Summary of indicative content: The world of the entrepreneur, entrepreneurial activity across the globe, characteristics of entrepreneurs, most important qualities of an entrepreneur, benefits of entrepreneurship

Drawbacks of entrepreneurship, feeding the entrepreneurial fire, the cultural diversity of entrepreneurship

The power of small businesses, avoiding the pitfalls of small business failure, assignment 1, creativity, innovation, and entrepreneurship, creativity: essential for survival

Creative thinking, right-brained-thinkers' skills, barriers to creativity

Enhancing organizational creativity, enhancing organizational creativity

The creative process, techniques for improving the creative process

Intellectual property protection; paten, trade mark, copyright, assignment 2 Chapter 2

Conducting a feasibility analysis and designing a business model; new business planning process

Idea assessment, elements of feasibility analysis, industry/market feasibility analysis

Porter’s five forces model

Product or service feasibility analysis, financial feasibility analysis

Entrepreneur feasibility, developing and testing a business model, assignment3

Crafting a business plan, goals and benefits of a business plan, the three tests of a business plan: reality, competitive, and value tests

Elements of the business plan, the :5 Cs" of credit, assignment 4

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Assessment: The final mark of the course consists of: 1. Computer-based exams: a. Midterm exam (30% of the final mark): composed of multiple-choice questions. b. Final exam (40% of the final mark): composed of multiple- choice questions 2. Assignments and projects (20%): At least 4 assignments will be given during the course 3. Paper-based quizzes (10%): At least 5 quizes will be given during the course

Teaching style: • Students work individually on instructional materials, such as recorded lectures and power point presentations that will be uploaded on the e-learning system.

• In-class sessions will be dedicated for students’ inquiries and discussions. Furthermore, they will help students who are struggling with the instructional materials to progress.

• Students have to attend online classes through the e-learning system and will have to answer a set of questions after each session they attended.

Indicative Bibliography/Sources: Handouts distributed by course instructors

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Course: General Skills (HSS129)

Semester: Semester Course Coordinator: Dr. Nisreen Azar Lecturer: Dr. Nisreen Azar Language: English Assignment in Curriculum Compulsory Course in the 1st Semester of the second year Course Units/Credit hours Lecture: 2 credit hours Students workload: Contact hours Private study Lecture: 28 28 Exams & Quizzes: 4 30 Sum 32 58

Total Sum: 90 hours

Credits 3 ECTS Prerequisites according to English (ENG112) examination regulations: Recommendations: Passing English 112 Course Description:

Learning outcomes: The students who take this course are expected to: 1. Define verbal and nonverbal communication 2. Demonstrate proper techniques when communicating in writing and demonstrate skills for improving conversational skills 3. Describe how to receive and deliver constructive criticism as well 4. Identify barriers of communication 5. Demonstrate techniques for the improvement of team work and group communication with the use of active communication skills to absorb cultural differences 6. Make better decisions and build critical thinking skills 7. Increase engagement in communities as well as increase self-confidence

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Summary of indicative content: Week 1: the importance of communication is stressed in this introductory lecture so that students can build up on their understanding of this concept

Weeks 2&3: an introduction to communication; functions of communication, communication model, verbal and none verbal communication.

Week 4, 5 and 6: In this week, the qualities and the effective technical writing will be discussed. Students will write with the assistance or their teacher a technical report

Weeks 7&8: students will be introduced to writing ideal resumes and will be taught the techniques for a creative job hunt.

Week 9; students will learn the process of decision making and problem-solving skills

Week 10: students will practice communication skills in terms of speaking and listening. Each student will have to speak loudly and others have to listen and criticize.

Week11; students will be taught the essence of team working and action planning techniques.

Weak 12; The teacher will review all these techniques and skills with the students prior to the final assessment.

Assessment: The final mark of the course consists of: 1. Computer-based exams: a. Midterm exam (45% of the final mark): composed of multiple-choice questions. b. Final exam (40% of the final mark): composed of multiple- choice questions 2. Paper-based quizzes (15%): At least 5 quizzes will be given during the course

Teaching style: This is a blended course in which a portion of traditional face- to- face instruction is replaced by online learning.

Students work individually on instructional materials, such as recorded lectures and power point presentations that will be uploaded on the e-learning system.

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In-class sessions will be dedicated for students’ inquiries and discussions. Furthermore, they will help students who are struggling with the instructional materials to progress.

Students have to work on online videos and electronic material that are uploaded on JUST E-Learning and will have to answer a set of questions after each session they attended.

Indicative Bibliography/Sources: Bauer, T, Carpenter, M. and Erdogan, B.2012. Management Principles. Unnamed Publishers.

Beebe, A,S., Beebe, J,S and Redmond, M. 2008. Interpersonal Communication, Relating to Others. London: Pearson.

Behera, A. K. and Tripathy, B. K.2009. Barriers to Effective Communication and How to overcome them. Academe

Cheesebro, T., O’Connor, L. and Rios, F. 2007. Communication Skills: Preparing for Career Success. London: Pearson.

Gerson, S. 2006.Writing That Works. The USA: Kansas Curriculum Center.

McPheat, S.2012. Advanced Communication Skills. Frederiksberg: Ventus Publishing APS.

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Course: Military Sciences (MS100) Semester: 1st Semester Course Coordinator: Military science department Lecturer: Variable Language: Arabic Assignment in Curriculum Compulsory Course taken any semester Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 39 48 Visits 3 6 Exams: 4 20 Sum 46 74

Total Sum: 120 hours

Credits 4 ECTS Prerequisites according to None examination regulations: Recommendations: None Course Description Military science and citizenship study material is considered as an organic extension of the education and teaching philosophy as it is a dimension of the national strategy of the Jordanian higher education, which takes into consideration the comprehensive national security concept in its traditional and social meaning. It deepens the loyalty values in the homeland’s land, people, regime institutions and military and security agencies that leads toward qualifying students to undertake their future roles as a loyal citizen and glorifying and sustaining the national feeling, loyalty, to be proud of the Jordanian fixed values and to trust the military and security systems until they achieve the positive change which sustain the security and stability of the country. In addition, it provides students with the basic information regarding building and developing the Hashemite kingdom of Jordan, its armed forces, its security agencies and showing its abilities in protecting the nation high interests. |Moreover, this course has a role in developing and serving local Arabic and international communities as well as the comprehensive security awareness in the operational and psychological fields, the danger of drug, terrorism and the meanings of loyalty and citizenship and to prepare and mobilize the national resources.

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Learning outcomes: Having finished the course, students will be able to:

1. Demonstrate knowledge on the establishment of the Jordan and its armed forces, in addition to acquainting knowledge on the different types of weapons they possess 2. Demonstrate knowledge on the rules of the Jordan Military in keeping peace around the world, and possessing knowledge on neighboring countries and the strength of their military forces 3. Demonstrate understanding of the Jordan Military forces in stabilizing the country from inside and help in building the country’s capacity. 4. Demonstrate understanding of the rule of citizens in keeping the country safe, clean and people live in harmony.

Summary indicative content: Part I: Establishment and development of the Hashemite Kingdome of Jordan and Jordan armed forces-Arab military • Establishment and development of the Hashemite Kingdome of Jordan • Establishment and development of Jordan armed forces • Maneuver weapons • Super weapons • Services unites • Royal Jordanian armed forces

Part II: Roles of Jordan armed forces –Arab army (JAF) • National and humanitarian rules • Great Arab revolt • Israeli-Arab wars • JAFs role in peace keeping missions

Part III: JAFs National Role • JAFs role in national comprehensive development • Military woman role in JAF • Economic social association of retired servicemen and veterans • King Abdullah II design and development bureau (KADDB)

Part IV: Security Agencies development • Public security directorate • General intelligence department • Gendarmerie Forces • Civil defense

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Part V: Citizenship and challenges Citizenship • Citizenship concept • Loyalty • Al-Hashimieens philosophy in the country management • King Abdullah II bin Al Hussein’s supervision toward civil society building • Jordan national identity • Jordan national security concept • Mobilizing national resources Challenges • Hyperbolism and extremism • Communal violence • Drugs

Assessment: The final mark of the course consists of: 1. Written exams: a. Midterm exam (30% of the final mark): composed of multiple-choice questions. b. Final exam (40% of the final mark): composed of multiple- choice questions. 2. Visits and extracurricular activities (30%)

Teaching style: Lectures: Projector, e-learning, power point presentations and white board

Indicative Bibliography/Sources: Class notes written and organized by Military department

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Course: English Language (LG112)

Semester: 2nd Semester Course Coordinator: Muneera Jaradat, Nisreen Azar, Asma, Al-Ghazu Language: English Assignment in Curriculum Compulsory Course in 2nd semester of the first year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 0 120 Exams 4 26 Sum 4 146

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to English language 099 examination regulations: Course Description This course is a general upper intermediate English course that aims at improving the four skills of language – listening, speaking, reading and writing. The first two skills – listening and speaking – are to be developed by the learners through being exposed to the language of lecturing. The skill of reading will be enhanced through the various presented reading skills. Also, the grammar and vocabulary sections target improving intact writing, the speaking fluency, the linguistic repertoire as well as the reading power.

Summary indicative content: Reading: (introduction), skimming Grammar: present simple & continuous, state verbs Vocabulary: parts of speech

Reading: scanning Grammar: past simple & continuous, used to Vocabulary: phrasal verbs

Reading: how skimming can serve scanning Grammar: present perfect, present perfect and past simple, present perfect continuous

Vocabulary: collocations, qualities of mind Reading: guessing the meaning of unknown words from the context

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Grammar: present perfect & present perfect continuous, past perfect, past perfect continuous Vocabulary: make/ do/ have/ take (collocations)

Reading: signal words of addition, signal words of change Grammar: time words for perfect tenses Vocabulary: participial adjectives, extreme adjectives

Reading: signal words of cause and effect Grammar: future simple, continuous, perfect, and perfect continuous Vocabulary: synonyms, antonyms, quantifiers

Reading: text mapping; Grammar: passive voice Vocabulary: have & have got

Reading: mapping longer passages Grammar: causative passive Vocabulary: hyponymy, meronymy

Reading: graphic aids, line graphs & bar graphs Grammar: definite and non-definite articles Vocabulary: collocations with get

Reading: graphic aids, pie charts & tables Grammar: zero article Vocabulary: collocations with mind

Reading: inferring; Vocabulary: idioms; Reading: paraphrasing

Reading: summarizing, clustering and review

Assessment: The final mark of the course consists of: 1. Written exams: a. First exam (25% of the final mark): composed of essay and multiple-choice questions. b. Second exam (25% of the final mark): composed of essay and multiple-choice questions. c. Final exam (40% of the final mark): composed of essay and multiple-choice questions. 2. Participation (10%)

Teaching style: 53 videos followed by exercises all online on Edraak platform, discussion forum on the platform

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Course: Calculus for Biological Sciences (MATH102A)

Semester: 1st Semester Course Coordinator: Dr Amer Darweesh Lecturer: Dr Amer Darweesh Language: English Assignment in Curriculum Compulsory course in the first year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 42 Exercise 0 70 Exams: 4 22 Sum 46 134

Total Sum: 180 hours

Credits 6 ECTS Prerequisites according to None examination regulations: Recommendations: None Course Description This hour course introduces students to exponential and logarithmic functions, trigonometric functions, techniques of integration and integral and its application Learning outcomes: By the end of the course, students should be able to: 1. Analyze linear functions and inequalities an draw them. 2. Manipulate limits of functions. 3. Apply the derivatives and use them in some applications. 4. Perform integration via the methods of substitution and by parts. 5. Find volumes generated by revolving areas under curves.

Summary of indicative content: 1.1 Real Number System; 1.2 Sets and their Representations

1.3 Functions; 1.4 Linear Functions; 1.5 Linear Inequalities; 1.6 Other Simple Functions; 1.7 More on Functions; 1.7 More on Functions: Composite Functions; 1.8 Limits as x Goes to Infinity

2.1 Increments and Rates; 2.2 Limits; 2.3 More on Limits; 2.4 Continuous Functions; 2.5 The Derivative; 2.6 Derivative of Power Functions; 2.7 Product and Quotient Rules; 2.8 Derivatives of Composite Functions; 2.9 Higher.

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3.1 Exponential Functions; 3.2 Inverse Functions and Logarithms; 3.4 Natural Logarithms and Exponential

5.2 Trigonometric Functions; 5.3 Derivatives of Trigonometric Functions.

6.1 Anti-derivatives; 6.2 Method of substitution; 6.4 Method of Partial Fractions; 6.6 Integration by Parts.

7.3 Definite Integrals; 7.4 More on areas; 7.5 Volumes of Revolutions.

Assessment: The final mark of the course consists of: 1. First written exam (30%) 2. Second written exam (30%) 3. Final written exam (40%)

Teaching style: Students mainly will be lectured using chalk board and students can benefit from the office for math counseling that was opened in the math department for helping students registered for their courses

Indicative Bibliography/Sources: Mathematics for the Biological science, J.C. Arya and R. W. Lardner, first edition, Prentic-Hill

References and Supplement Materials: 1. Calculus for the Life Sciences by R. N. Greenwell et al, Pearson; 2 ed., 2014. 2. Calculus with Applications for the Life Sciences 1st Edition, by R. N. Greenwell et al, Pearson; 2 ed., 2002. 3. Calculus for the Life Sciences by M. L. Bittinger et al, Pearson; 1 ed., 2008.

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Course: Mathematical Applications of Biological Sciences (MATH103)

Semester: 1st Semester Course Coordinator: Dr. Kamel Bashaireh Lecturer: Dr. Kamel Bashaireh Language: English Assignment in Curriculum Compulsory course in the first year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 42 Exercise 0 70 Exams: 4 22 Sum 46 134

Total Sum: 180 hours

Credits 6 ECTS Prerequisites according to None examination regulations: Recommendations: Passing the calculus course in the first semester of the first year Course Description: This 3-credit hour course is designed to introduce students to the application of mathematical modelling in the analysis of biological systems including populations of molecules, cells and organisms. In addition, the course will discuss how mathematics, statistics and computing can be used in an integrated way to analyze biological systems. The course is also designed to develop students' skills in algebraic manipulation, the calculus of linear differential equations, mathematical modelling, matrix algebra, probability and statistical methods.

Learning outcomes: By the end of the course, students should be able to: 1. Interpret differential equation models for populations, relating the expression appearing in the model to processes that affect the population. 2. Formulate and analyze ordinary differential equation (ODE) models for the population of a single species, finding equilibrium populations 3. Analyze ODE models for the populations 4. Recognize fitting models. 5. Analyze simplex method to solve some linear programming problems. 6. Understand basic of finance.

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Summary of indicative content: Introduction which will include a general review of calculus and its importance in life

First order differential equations, which will include the separable.

Linear equations and the Bernoulli concept

The exact differential equations

Modelling with ODEs with an example of this concept will be the population growth (logistics)

Modeling of the Population Growth (Harvesting)

Graphical Model fitting

Least squares, and modeling using difference equations

Linear regression and its applications in biological sciences

Normal distribution and its significance in biological research and results presentation

Inequalities and linear programming; introduction to matrices

Inequalities in one and two variables

Diet problems and models for weight gain prediction

Mathematics of finance; simple and compound interests.

Assessment: The final mark of the course consists of: 1. Written exams: a. First exam (25% of the final mark) b. Second exam (25% of the final mark) c. Final exam (40% of the final mark) 2. Assignments (10%): a. Students will be given 3-5 assignments

Teaching style: Students mainly will be lectured using chalk board and assignments and quizzes will be given to the students to help them understand and solve real problems they might encounter while in school

Indicative Bibliography/Sources: Textbook: Mathematical Biology, by Murray, James D

Reference: Lee A. Segel, Modeling dynamic phenomena in molecular and cellular biology (Cambridge University Press, 1984)

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Course: Elements of Statistics (MATH131)

Semester: 1st Semester Course Coordinator: Dr. Mohammad Shakhatreh Lecturer: Dr. Mohammad Shakhatreh Language: English Assignment in Curriculum Compulsory course in the first year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 42 Exercise 0 70 Exams: 4 22 Sum 46 134

Total Sum: 180 hours

Credits 6 ECTS Prerequisites according to None examination regulations: Recommendations: Passing the mathematics courses in the first academic year Course Description: Presentation and description of statistical data. Probability: concept of probability, probability rules. Random variables and probability distributions, expectation, Binomial distribution, Poisson distribution, Normal distribution. Sampling distributions, t-distribution, CLT. Estimation, point and interval estimation for normal population mean and the difference of two population means. Testing hypotheses, the z-test, the t-test, testing the difference between two means (small and large sample sizes), paired t-test. Correlation and simple linear regression, estimation and testing, residuals analysis

Learning outcomes: By the end of the course, students should be able to: 1. Represent given data graphically and compute and interpret descriptive statistics. 2. Compute and interpret probabilities and conditional probabilities. 3. Identify the types of random variables involved in a given problem and calculate relevant probabilities for binomial and normal distributions. 4. Compute point and interval estimates of the population means and proportions. 5. Sample size determination for estimating the population mean and proportion.

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6. Understand, apply and compute in one- and two- sample testing problems for mean (s), paired t-test and testing proportion(s) . 7. Fit simple linear regression model and perform model diagnostics

Summary of indicative content: Basic Concepts Types of data, sampling methods, defining descriptive and inferential statistics.

Descriptive Statistics Graphical summary, measures of center, measures of dispersion.

Probability Counting techniques, definition, axioms, rules of probability, conditional probability and independence.

Random Variables Discrete and continuous distributions, mean and variance.

Binomial, Hypergeometric, and uniform distributions.

Normal distribution.

Sampling distribution of the sample mean and CLT.

Estimation Estimation of the population mean and variance. Estimation for the normal distribution. Estimation of the population proportion.

Estimation Interval estimation. Sample size determination.

Hypothesis Testing Basic concepts, types of error, testing hypothesis for the population mean and variance. Testing hypothesis for the equality of two population means. Paired t-test.

Hypothesis Testing Testing hypothesis for the population proportion. Two population proportions.

Regression and Correlation Scatter Plot, Linear Relationship, Pearson correlation coefficient. Estimating of the model parameters.

Regression Testing hypothesis and model diagnostics.

Tests Based on Count Data. Contingency Tables and Goodness of Fit.

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Assessment: The final mark of the course consists of: 1. Written exams: a. First exam (30% of the final mark) b. Second exam (30% of the final mark) c. Final exam (40% of the final mark)

Indicative Bibliography/Sources: Textbook: Introduction to Statistics, J. S. Milton and J. J. Meteer, First Edition, D. C. Health and Company, 1986.

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Course: General Physics (1) (PHY101A)

Semester: 1st Semester Course Coordinator: Dr. Akram Al-Rosan Lecturer: Dr. Akram Al-Rosan Language: English Assignment in Curriculum Compulsory course in the first semester of the first year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 42 Exercise 0 70 Exams: 4 22 Sum 46 134

Total Sum: 180 hours

Credits 6 ECTS Prerequisites according to None examination regulations: Recommendations: None Course Description: This course covers mechanics: movement of objects, mechanical properties of solid objects, temperature and thermodynamics, fluids, vibrations and waves

Learning outcomes: By the end of the course, students should be able to: 1. Understanding and solving problems in motion in on and two dimensions 2. Understanding and solving problems in Newton's laws 3. Understanding and solving problems in mechanical energy 4. Understanding and solving problems in temperature and heat 5. Understanding and solving problems in fluid mechanics 6. Understanding and solving problems in vibrations and waves

Summary of indicative content: Motion in one dimension and vectors

Motion in two dimensions, Newton’s laws of motion

Friction, Work & Energy, Rotational motion

Equilibrium, Mechanical properties of solids.

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Temperature and Heat, Laws of Thermodynamics Fluid mechanics

Vibrations

Waves

Assessment: The final mark of the course consists of: 1. Written exams: a. First exam (30% of the final mark): composed of multiple- choice questions. b. Second exam (30% of the final mark): composed of multiple- choice questions. c. Final exam (40% of the final mark): composed of multiple- choice questions.

Teaching style: Students mainly will be lectured using whiteboard and assignments will be given to the students to help them understand and solve real problems they might encounter while in school

Indicative Bibliography/Sources: Textbook: Physics for Biology and Pre-Medical Students, Burns & MacDonald. Addison-Wesley.

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Course: General Physics (2) (PHY102A)

Semester: 2nd Semester Course Coordinator: Dr. Akram Al-Rosan Lecturer: Dr. Akram Al-Rosan Language: English Assignment in Curriculum Compulsory course in the second semester of the first year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 42 Exercise 0 70 Exams: 4 22 Sum 46 134

Total Sum: 180 hours

Credits 6 ECTS Prerequisites according to None examination regulations: Recommendations: Passing the general Physics (1) course Course Description: This course covers topics in static electricity, electric current and circuits, magnetism, optics and optical instruments, modern physics, radiation and radiation protection

Learning outcomes: The student should be able to understand and solve problems in the following: 1. Static electricity 2. Circuits 3. magnetism 4. Optics 5. Optical instruments 6. Modern physics 7. Radiation and radiation protection

Summary of indicative content: Electric force Electric field and potential Capacitors Electric current, Ohm's law, resistance Kirchhoff's law, power, RC-circuit Nerve conduction

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Magnetic field, magnetic force, magnetic dipoles Sources of magnetic field, magnetic moment Faraday's law, generators Transformers and magnetic materials Light, reflection, refraction Mirrors, lenses Optical instruments, defects Wave and particle properties of light, wave properties of matter Radiation, radiation protection

Teaching style: Students mainly will be lectured using whiteboard and assignments will be given to the students to help them understand and solve real problems they might encounter while in school

Indicative Bibliography/Sources: Textbook: Physics, Kane & Sternheim. Wiley, New York, USA.

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Course: General Physics Laboratory (PHY107)

Semester: 2nd Semester Course Coordinator: Dr. Hasan Al-Khateeb Lecturer: Dr. Hasan Al-Khateeb and others Language: English Assignment in Curriculum Compulsory course in the second semester of the first year Course Units/Credit hours Lecture: 1 credit hour Students workload: Contact hours Private study Lab session: 30 30 Reports 0 10 Exams & Quizzes 3 17 Sum 33 57

Total Sum: 90 hours

Credits 3 ECTS Prerequisites according to None examination regulations: Recommendations: Passing the General Physics (1) course Course Description: This laboratory has 10 experiments that emphasize the experimental techniques and procedures in writing formal reports. These experiments reinforce and extend the work of the lectures of physics course Phys. 101 & physics 102. They emphasize on different topics in mechanics and electricity and magnetism as shown in details in the table below

Learning outcomes: The student should be able to: 1. Strengthen the students understanding of the basic physical concepts, measurements, motion, energy, electricity and magnetism. 2. Develop the students’ skills in collecting and analyzing the data and formulating meaningful conclusions based on this data. 3. Describe and calculate uncertainty of the measured values. 4. Enhance ability of students to communicate results and ideas through writing scientific reports and drawing figures. 5. Practice skills at working cooperatively within a group to achieve solutions to given problems.

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Summary of indicative content: Measurements and Error To learn how to use measurement tools such as Vernier caliper, micrometer and balance. Determination of the density of cylindrical metal.

Projectile motion To study the motion of a particle with constant acceleration in two dimensions such as projectile motion.

Newton’s Second Law To verify Newton’s second law.

Rotational motion To understand the rotational motion of a rigid body. Determination of the moment of the inertia of a rotating system.

Conservation of energy To verify the principle of conservation of mechanical energy for two conservative systems: a) Mass-Cart system. b) Mass-Spring system.

Ohm’s Law To test the validity of Ohm’s law. To construct series and parallel circuits. To measure an unknown resistance. To measure the equivalent resistance of series, and parallel combinations of resistors.

Potentiometer Investigation of the principle of the potentiometer. To measure the electromotive force of an unknown cell.

Galvanometer To convert a galvanometer into a DC ammeter having a specified full-scale range. To convert a galvanometer into a DC voltmeter having a specified full-scale range.

RC Circuits Investigation of the charging and the discharging characteristics of a capacitor in the RC circuits.

Wheatstone Bridge Resistors To learn to use Wheatstone bridge for precision measurements of resistance.

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Assessment: The final mark of the course consists of: 1. Written final exams (40%): composed of multiple-choice questions. 2. Quizzes and participation (20%): composed of essay questions 3. Lab reports (40%): Students will write a report for each experiment.

Teaching style: Lab session: demonstration, e-learning and whiteboard

Exercise: Examples and solved problems of course activities will be announced

Indicative Bibliography/Sources: Textbook: Physics for Scientists and Engineers, Serway and Jewett, 9th edition.

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Course: PROGRAMMING IN C++ (CS115)

Semester: 1st / 2nd Semester Course Coordinator: Mr. Abedl-Rahman Almodawar Lecturer: Mr. Abedl-Rahman Almodawar and others Language: English Assignment in Curriculum Compulsory course can be taken any semester Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 42 Exercise 0 70 Exams: 4 22 Sum 46 134

Total Sum: 180 hours

Credits 6 ECTS Prerequisites according to None examination regulations: Recommendations: None Course Description: This course introduces the student to object-oriented programming through a study of the concepts of program specification and design, algorithm development, and coding and testing using a modern software development environment. Students learn how to write programs in an object-oriented high-level programming language. Topics covered include fundamentals of algorithms, problem solving, programming concepts, methods, control structures, arrays, and strings. Throughout the semester, problem- solving skills will be stressed and applied to solving computing problems.

Learning outcomes: 1. The student will learn how to use arithmetic operators and Input/Output methods within C++ code. 2. The student will learn how to use selection statements such as if, if-else and switch within C++ code. 3. The student will learn how to use looping statements such as while, for and do-while within C++ code. 4. The student will learn how to use several predefined functions (built-in functions) within C++ code. 5. The student will learn how to use functions within C++ code. 6. The student will learn how to declare arrays and process its

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elements within C++ code

Summary of indicative content: An Overview of Computers and Programming Languages

Basic Elements of C++

Control Structures I (Selection)

Control Structures II (Repetition)

User-Defined Functions I

User-Defined Functions II

Arrays

Assessment: The final mark of the course consists of: 1. Written exams: a. First exam (20% of the final mark): b. Second exam (20% of the final mark) c. Final exam (40% of the final mark)

Teaching style: Students mainly will be lectured using whiteboard and assignments will be given to the students to help them understand and solve real problems they might encounter while in school

Indicative Bibliography/Sources: Textbook: C++ Programming: From Problem Analysis to Program Design. D. S. Malik, 5th Edition

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Course: Introduction to Hematology (LM251) Semester: 1st / 2nd Semester Course Coordinator: Dr. Mohammad A. Audeh Lecturer: Dr. Mohammad A. Audeh Language: English Assignment in Curriculum Compulsory Course in the second year Course Units/Credit hours Lecture: 2 credit hours Practical: 1 credit hour

Students workload: Contact hours Private study Lecture: 28 56 Practical 39 13 Exams: 4 40 Sum: 71 109

Total Sum: 180 hours

Credits 6 ECTS Prerequisites according to General Biology (2) examination regulations: Recommendations: Passing the general biology courses in the first year Course Description Hematology LM250/1 is introduced with the study blood and its components specifically the formed cellular elements including erythrocytes, leukocytes and thrombocytes. A detailed description of these elements will be provided with a major prospect on their generation, structure, function and metabolism. A considerable portion of the course will be directed to provide the students with an intensive specialized knowledge of the laboratory procedures for enumeration, examination and identification.

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Learning outcomes: Having finished the course, students will be able to: 1. Explain hematopoiesis process, hematopoiesis ontogeny and its regulatory mechanisms 2. Describe the structure, function, metabolism and the life cycle of cellular blood elements: erythrocytes, leukocytes and thrombocytes 3. Experience and be familiar with the routine and specialized laboratory techniques for the evaluation of blood cells 4. Interpret and analyze obtained results from hematological techniques and implement these for quality control and quality assurance measures 5. Define hemeostatic system as a host defense mechanism and understand its regulation

Summary indicative content: Hematopoiesis: Overview

Erythrocytes Structure and Function, Hemoglobin, Hemoglobin, Iron Homeostasis, Erythropoiesis and Its regulation, Destruction, analysis and red cell indices, Blood Film Examination, CBC correlation with BFE, Special Assays

Leukocytes Classification and Structure, Function, CBC and Differential, Morphological Examination, Immunohistochemistry, Platelets Structure and Function

Hemostasis Megakaryopoiesis, Coagulation System, -Coagulation and Fibrinolysis, Routine examination, Evaluation

Flow Cytometry: Principles and Applications

Quality Control and Quality Assurance

Assessment: The final mark of the course consists of: 1. Written exams: a. First exam (30% of the final mark): composed of multiple- choice questions. b. Second exam (30% of the final mark): composed of multiple-choice questions c. Final exam (40% of the final mark): composed of multiple- choice questions

Teaching style: Lectures: Projector, e-learning, power point presentations and whiteboard

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Indicative Bibliography/Sources: Hematology: Clinical principles and applications. Bernadette F. Rodak, George A. Fritsma and Kathryn Doig. Saunders Elsevier. 2012. 4th edition

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Course: General Chemistry (1) (CHEM101) Semester: 1st Semester Course Coordinator: Dr. Mohammad M. Fares Lecturer: Dr. Mohammad M. Fares Language: English Assignment in Curriculum Compulsory Course in 1st Semester of the first year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 63 Book exercises 0 14 Exams & Quizzes: 4 27 Sum 46 104

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to None examination regulations: Recommendations: None Course Description This course targets to teach students the basic principles of general chemistry. The first part of the course will cover the fundamental aspects of matter and measurements, stoichiometry, and electronic structure of atoms. The second part will cover the periodic table properties, chemical bonding and molecular geometry. The final part will cover the properties of gases and liquids together intermolecular forces. The course will be illustrated with many examples for each chemical aspect along with applications in modern and contemporary life technology.

Learning outcomes: Having finished the course lectures, students will be able to: 1. Understand the matter and measurements, stoichiometry, and electronic structure of atoms. 2. Recognize the periodic table properties, chemical bonding and molecular geometry 3D structure of molecules. 3. Study the properties of gases and liquids and its relation to intermolecular forces.

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Summary indicative content: Introduction: Matter and Measurement Classifications of Matter, Properties of Matter, Units of Measurements, Uncertainty in Measurements, Dimensional Analysis

Stoichiometry: Calculations with Chemical Formulas and Equations Chemical Equations, Some simple patterns of Chemical Reactivity, Formula Weights, Avogadro's Number and the Mole, Quantitative Information from Balanced Equation, Limiting Reactant

Aqueous Reactions and Solution Stoichiometry Concentrations of Solutions, Solution Stoichiometry and Chemical analysis, Electronic Structure of Atom, The Wave Nature of Light, Quantized Energy and Photons, Line Spectra and the Bohr Model, The Wave behavior of Matter, Quantum Mechanics and Atomic Orbitals, Representations of Orbitals, Many-Electron Atoms, Electron Configurations, Electron Configurations and the Periodic Table

Periodic Properties of the Elements Development of the Periodic Table, Effective Nuclear Charge, Sizes of Atoms and Ions, Ionization Energy, Electron Affinities, Metals, Nonmetals and Metalloids

Basic Concepts of Chemical Bonding Lewis symbols and the Octet Rule, Ionic Bonding, Covalent Bonding, Bond Polarity and Electronegativity, Drawing Lewis Structures, Resonance Structures, Exceptions to the Octet Rule, Strengths of Covalent Bonds

Molecular Geometry and Bonding Theories Molecular Shapes, The VSEPR Model, Molecular Shape and Molecular Polarity, Covalent Bonding and Orbital Overlap, Hybrid Orbitals, Multiple Bonds, Molecular Orbitals, Period 2 Diatomic Molecules

Characteristics of Gases Pressure, The Gas Law, The Ideal-Gas Equation, Applications of the Ideal-Gas Equation, Gas Mixtures and Partial Pressures, The Kinetic-Molecular Theory of Gases, Molecular Effusion and Diffusion

Liquids and Intermolecular Force A Molecular Comparison of Gases, Liquids and Solids, Intermolecular Forces, Select Properties of Liquids, Phase Changes, Vapor Pressure

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Assessment: The final mark of the course consists of: Computer-based exams: a. First exam (30% of the final mark): composed of multiple- choice questions. b. Second exam (30% of the final mark): composed of multiple- choice questions. c. Final exam (40% of the final mark): composed of multiple- choice questions.

Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard

Indicative Bibliography/Sources: CHEMISTRY: The Central Science 12th Edition by Brown, LeMay, Bursten, Murphy and Woodward 2012

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Course: General Chemistry (2) (CHEM102) Semester: 2nd Semester Course Coordinator: Dr. Salem Barakat Lecturer(s): Dr. Salem Barakat, Dr. Ahmad Gharaebeh Language: English Assignment in Curriculum Compulsory Course in 2nd Semester of the first year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 63 Book exercises 0 14 Exams & Quizzes: 4 27 Sum 46 104

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to General Chemistry (1) examination regulations: Recommendations: Passing the general chemistry course in the first semester of the first academic year

Course Description This course aims to teach students the basic principles of general chemistry. The first part of the course will cover the fundamental aspects of thermochemistry, the nature of energy, enthalpies and the laws of chemical thermodynamics. The second part will cover the properties of solutions, the chemical kinetics and the third part of the course will cover chemical equilibrium, acids base equilibria, additional aspects of aqueous equilibria and electrochemistry to familiarize the students the main concepts of advance course of general chemistry knowledge. The course will be frequently illustrated will examples linked to other scientific disciplines, in particular to the field of life material sciences..

Learning outcomes: Having finished the course lectures, students will be able to: 1. Understand the concepts of general chemistry for main basic chemistry. 2. Understand how to prepare chemical solution from stock solutions. 3. Manipulate the basic understanding of topics in application.

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Summary indicative content: Thermochemistry The Nature of Energy, The First Law of Thermodynamics, Enthalpy, Enthalpies of Reaction, Calorimetry, Hess's Law, Enthalpies of Formation

Chemical Thermodynamics Spontaneous Processes, Entropy and The Second Law of Thermodynamics, The Molecular Interpretation of Entropy, Entropy Changes in Chemical Reactions, Gibbs Free Energy, Free Energy and Temperature, Free Energy and The Equilibrium Constant

Properties of Solutions The Solution Process, Saturated Solutions and Solubility, Factors Affecting Solubility, Ways of Expressing Concentration, Colligative Properties, Chemical Kinetics, Factors That Affect Reaction Rates, Reaction Rates, The Rate Law: The Effect of Concentration on Rate, The Change of Concentration with Time, Temperature and Rate, Reaction Mechanisms, Catalysis

Chemical Equilibrium The Concept of Equilibrium, The Equilibrium Constant, Interpreting and Working with Equilibrium Constants, Heterogeneous Equilibria, Calculating Equilibrium Constants, Applications of Equilibrium Constants, Le Chatelier's Principle

Acids-Base Equilibria Acids and Bases: A Brief Review, Bronsted-Lowry Acids and Bases, The Autoionization of Water, The pH Scale, Strong Acids and Bases, Weak Acids, Weak Bases, Relationship Between Ka and Kb, Acid-Base Properties of Salt Solutions, Acid-Base Behavior and Chemical Structure, Lewis Acids and Bases

Additional Aspects of Aqueous Equilibria The Common-Ion Effect, Buffered Solutions

Electrochemistry Oxidation States and Oxidation-Reduction Reactions, Balancing Oxidation-Reduction Equation, Voltaic Cells, Cell EMF under Standard Conditions, Free Energy and Redox Reactions, Cell EMF under Nonstandard Conditions

Assessment: The final mark of the course consists of: Computer-based exams: a. First exam (30% of the final mark): composed of multiple- choice questions. b. Second exam (30% of the final mark): composed of multiple- choice questions. c. Final exam (40% of the final mark): composed of multiple-

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choice questions.

Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard

Exercise: Examples and solved problems of course activities will be announced

Indicative Bibliography/Sources: CHEMISTRY: The Central Science 12th Edition by Brown, LeMay, Bursten, Murphy and Woodward 2012

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Course: General Chemistry Laboratory (CHEM107) Semester: 2nd Semester Course Coordinator: Mr. Ibrahim Jawarneh Lecturer(s): Mr. Ibrahim Jawarneh and others Language: English Assignment in Curriculum Compulsory Course in 2nd Semester of the first year Course Units/Credit hours Lab session: 1 credit hour Students workload: Contact hours Private study Lab session: 33 33 Lab reports 0 11 Exams & Quizzes: 3 20 Sum 36 54

Total Sum: 90 hours

Credits 3 ECTS Prerequisites according to General Chemistry (1) examination regulations: Recommendations: Passing the general chemistry course in the first semester of the first academic year

Learning outcomes: Having finished the course lab sessions, students will be able to: 1. Develop reasoning and problem – solving skills including the ability to identify 2. Pertinent variables, recognize qualitative terndes in data , determine what , if any quantitative trends in data , determine what , if any , quantitative relationships exist , and test the validity of conclusions. 3. Master the basic laboratory skills need to enter advanced chemistry courses.

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4. Correlate the day–to–day observation with chemistry experiment. 5. Exhibit a basic knowledge of physical properties of chemical reactions.

Summary indicative content: 1. Laboratory Safety 2. Density 3. Physical Separation of mixture 4. Limiting Reactant 5. Chemicals in everyday life 6. Colligative Properties 7. Calorimetry 8. Acid–base titration 9. Determination of a rate law 10. Quantitative yield of redox reaction 11. Quantitative analysis of Cations

Assessment: The final mark of the course consists of: Computer-based exams: a. Midterm exam (40% of the final mark): composed of multiple-choice questions. b. Final exam (40% of the final mark): composed of multiple- choice questions. Lab reports: c. Reports (20% of the final mark): Description, results and conclusions about lab experiments

Teaching style: Lab session: demonstration, e-learning and whiteboard

Exercise: Examples and solved problems of course activities will be announced

Indicative Bibliography/Sources: CHEMISTRY: The Central Science 12th Edition by Brown, LeMay, Bursten, Murphy and Woodward 2012

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Course: Organic Chemistry (CHEM217) Semester: 1st Semester Course Coordinator: Dr. Mousa Al-Smadi Lecturer(s): Dr. Mousa Al-Smadi, Raed Al-Zoubi, Dr. Ahmad Ajlouni Language: English Assignment in Curriculum Compulsory Course in 1st Semester of the second year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 63 Book exercises 0 14 Exams & Quizzes: 4 27 Sum 46 104

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to General Chemistry (2) examination regulations: Recommendations: Passing the general chemistry courses in the first academic year

Course Description This course aims to teach students the basic principles of organic chemistry. The first part of the course will cover the fundamental aspects of structural organic chemistry to familiarize the students the main families of organic chemistry functions as well as the 3D structure of organic molecules. The basics of reactivity will also be covered using the mechanisms. The course will be frequently illustrated will examples linked to other scientific disciplines, in particular to the field of life sciences

Learning outcomes: Having finished the course lectures, students will be able to: 1. Understand the structural organic chemistry for main families of organic chemistry. 2. Understand the 3D structure of organic molecules. 3. Manipulate the basic of reactivity and the mechanisms 4. Manipulate the functional groups transformations.

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Summary indicative content: Bonding and Isomerism How electrons are arranged in atoms, Ionic and covalent bonds, Valence and hybridization, Isomerism, Writing structural formula, Resonance

Alkanes and Cycloalkanes and Geometric isomerism The structure of Alkanes, IUPAC Rules for naming Alkanes, Alkyl and Halogen substituents, Conformation and geometric isomerism, Cycloalkanes and Isomerisim, Reactions of Alkanes.

Alkenes and Alkynes Definition and classification, Nomenclature, Geometric Isomerism in Alkenes, Addition and substitution reactions, Polar addition reactions (addition of Halogens and water), Addition of unsymmetric reagents to unsymm. Alkenes (Markonikovs’ Rule and Hydroboration reaction), Reaction equilibrium and reaction rates, Addition of hydrogen, Addition to conjugated system, Oxidation of Alkenes, Addition reactions to alkynes, Acidity of alkynes

Aromatic compounds Some Facts About Benzene, Structure of Benzene. Orbital Model for Benzene & Resonance, Nomenclature of Aromatic compounds, Electrophilic Aromatic substitution reactions, Ring activating and deactivating substituents

Stereoisomerism Chirality and Enantiomers, Stereogenic Centers; the Stereogenic Carbon Atom, Configuration and the R-S Convention, The E-Z Convention for cis-trans Isomers, Polarized Light and Optical Activity, Properties of Enantiomers, Diastereomers and Meso compounds, Stereochemistry and chemical reactions, Organic Halogen Compounds, Nucleophilic Substitution, SN2 Mechanism, SN1 Mechanism, Dehydrohalogenation: E1 and E2, Substitution and Elimination in competition

Alcohols, Phenols, and Thiols Nomenclature of Alcohols & its Classification, Nomenclature of Phenols, Hydrogen Bonding in Alcohols and Phenols, Acidity and Basicity Reviewed. The Acidity & Basicity of Alcohols and Phenols., Dehydration of Alcohols to Alkenes, The Reaction of Alcohols with Hydrogen Halides, Oxidation of Alcohols to Aldehydes, Ketones, and Carboxylic Acids, Aromatic Substitution in Phenols, Thiols, the Sulfur Analogs of Alcohols and Phenols

Ethers and Epoxides Nomenclature of ethers and properties, The Grignard Reagent, Preparation and cleavage of ethers, Epoxides

Aldehydes and Ketones Nomenclature of Aldehydes and Ketones, Synthesis of Aldehydes

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and Ketones, Addition of Alcohol, Addition of water, Addition of Grignard Reagent, Addition of hydrogen cyanide, Addition of Nitrogen nucleophile, Reduction of carbonyl compounds, Oxidation of carbonyl compounds

Carboxylic Acids and their Derivatives Nomenclature and Physical Properties, Acidity and acidity constant, Effect of structure on Acidity, Preparation of Acids, Carboxylic acid derivatives, Preparation and Reactions of Esters, Preparation and Reactions of Acyl Halides, Preparation and Reactions of Acid Anhydrides, Urea and Amides

Amines and Related Nitrogen compounds Classification and structure of Amines, Nomenclature and preparation of Amines, Preparation of Amines, The basicity of Amines, Reaction of Amines with strong acids, Aromatic diazonium compounds, Diazo coupling

Assessment: The final mark of the course consists of: Computer-based exams: a. First exam (30% of the final mark): composed of multiple- choice questions. b. Second exam (30% of the final mark): composed of multiple- choice questions. c. Final exam (40% of the final mark): composed of multiple- choice questions.

Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard

Exercise: Examples and solved problems of course activities will be announced

Indicative Bibliography/Sources: Organic Chemistry (12th Edition), Authors: Harold Hart, Leslie Craine, David Hart and C. Hadad. Houghton Mifflin Company, Boston U.S.A. 2007

Organic Chemistry, 8th ed., By Solomons.(2004) Organic Chemistry, J. McMurry (2004)

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Course: Analytical Chemistry (CHEM233) Semester: 2nd Semester Course Coordinator: Dr. Yahya R. Tahboub Lecturer(s): Dr. Yahya R. Tahboub, Dr. Salem Barakat, Dr. Mahmoud Hamori Language: English Assignment in Curriculum Compulsory Course in 2nd Semester of the second year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 40 60 Book exercises 0 14 Exams & Quizzes: 6 40 Sum 46 104

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to General Chemistry (2) examination regulations: Recommendations: Passing the general chemistry courses in the first academic year

Course Description This course aims to teach students the basic principles of analytical chemistry. The first part of the course will cover statistical aspects of analytical chemistry including errors and validation of analytical results. The second part will deal with preparation of reagents and standards, equilibrium considerations and analyte matrix interactions. The third part will cover classical methods of analysis including gravimetric methods and volumetric (titrimetric) methods. The course will be frequently illustrated with case studies and practical examples linked to other scientific disciplines, in particular to the fields of environmental, pharmaceutical and forensic sciences.

Learning outcomes: Having finished the course lectures, students will be able to: 1. Understand preparation of solutions and expression of analytical results 2. Understand the statistical evaluation of analytical data. 3. Understand equilibrium considerations for analytical reactions including activity and systematic treatment of equilibrium. 4. Understand precipitation equilibrium and its applications on gravimetric and titrimetric methods. 5. Understand aqueous equilibrium and its applications on acid- base titrations including mono and diprotic.

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6. Apply classical methods for determination of analytes on real samples including environmental and pharmaceutical.

Summary indicative content: Analytical Process The analytical Chemist job, General steps in a chemical analysis

Chemical Measurements SI units, Preparation of solutions, Stoichiometric calculations

Experimental Error Significant figures, of errors, Manipulation of uncertainties of results Statistics, Gaussian distribution, Confidence intervals, of analytical result, Rejection of a replicate

Chemical Equilibria Equilibrium constant, Precipitation equilibria

Activity and Systematic Treatment of Equilibria Ionic strength and activity coefficients, Systematic treatment of equilibria

Gravimetric Analysis and Precipitation Titration Gravimetric analysis, Analytical precipitation, Precipitation titrations

Monoprotic Acid-Base Equilibria pH (Chapter 6), Strong acids and bases, Weak acids and bases, Weak acid equilibria, Weak base equilibria, Buffers

Polyprotic Acid-Base Equilibria Diprotic acids and bases, Diprotic buffers, Polyprotic acids and bases, Fractional composition equations

Acid-Base Titrations Titration of strong base with strong acid, Titration of weak base with strong acid, Titration of weak acid with strong base, of diprotic acid with strong base, Titration of dibasic salt with strong acid, Finding end point with indicators, Applications on acid-base titrations (mixtures, Kjeldal nitrogen analysis)

Complexation Titrations with EDTA Metal chelate complexes, EDTA, EDTA titration curves, Metal ion indicators, titration techniques

Fundamentals of Electrochemistry Basic concepts, cells, Standard potentials, Nernst equation

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Redox Titrations The shape of redox

Assessment: The final mark of the course consists of: Computer-based exams: a. First exam (25% of the final mark): composed of multiple- choice questions. b. Second exam (25% of the final mark): composed of multiple- choice questions. c. Final exam (40% of the final mark): composed of multiple- choice questions. Paper-based assessment: a. Quizzes (10% of the final mark): composed of multiple-choice questions. At least 5 quizzes will be given during the course

Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard

Exercise: Examples and solved problems of course activities will be announced

Indicative Bibliography/Sources: Textbook: Quantitative Chemical Analysis (8th Edition), Authors: Daniel C. Harris W. H. Freeman Company, New York U.S.A. 2010

References and Supplement Materials: 1. Fundamentals of Analytical Chemistry 9th edition, Skoog, West, Crouch & Hollar (2014) 2. Analytical Chemistry 7th edition, Christian, Dagupta & Chung (2017)

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Course: Analytical Chemistry Lab (CHEM234) Semester: 2nd Semester Course Coordinator: Mr. Ayman Amrat Lecturer(s): Mr. Ayman Amrat Language: English Assignment in Curriculum Compulsory Course in 2nd Semester of the second year Course Units/Credit hours Lecture: 1 credit hour Students workload: Contact hours Private study Lecture: 33 84 Book exercises 0 24 Exams & Quizzes: 4 26 Sum 46 134

Total Sum: 90 hours

Credits 3 ECTS Prerequisites according to General Chemistry Lab examination regulations: Recommendations: Passing the general chemistry courses in the first semester of the first academic year

Course Description This course aims to teach students the basic principles of analytical chemistry. The first part of the course will cover the preparation of reagent, statistical evaluation of replicated data measurements and study the validity of results. Analysis of unknowns will also be covered using different analytical qualitative and quantitative methods. The course will be frequently illustrated examples linked to other scientific disciplines, in particular to medicine, pharmaceutical, and agricultural sciences

Learning outcomes: Having finished the course lab sessions, students will be able to: 1. Develop the experimental skills including the ability to use balances, glassware, and chemicals required. 2. Learn the basics and applications of classical methods for qualitative and quantitative analysis (gravimetric and titrimetric) 3. Able to apply statistical methods for analyzing experimental data and test the validity of results and make reasonable conclusions about these results.

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Summary indicative content: 1. Preparation of Analytical Reagents and Calibration standards 2. Statistical evaluation of analytical results 3. Gravimetric determination of sulfate 4. Application of acid-base titration 1: Assay of strong acids, acidity of vinegar and alkalinity of water 5. Application of acid-base titration 2: Assay of sodium carbonate in soda ash and determination of total alkalinity of water 6. Back titration 7. Potentiometric titration of mixtures of carbonates, bicarbonates and hydroxides 8. Determination of chloride by precipitation titration 9. Determination of calcium, magnesium and total hardness of water by complexation titration 10. Oxidation reduction Titrations 11. Iodimetric titration of ascorbic acid in vitamin tablets

Assessment: The final mark of the course consists of: Computer-based exams: a. Midterm exam (40% of the final mark): composed of multiple-choice questions. b. Final exam (40% of the final mark): composed of multiple- choice questions. Lab reports: a. Reports (20% of the final mark): Description, results and conclusions about lab experiments

Teaching style: Lab session: demonstration, e-learning and whiteboard

Exercise: Examples and solved problems of course activities will be announced

Indicative Bibliography/Sources: 1. Quantitative Chemical Analysis (8th Edition), Authors: Daniel C. Harris W. H. Freeman Company, New York U.S.A. 2010 2. Fundamentals of Analytical Chemistry 9th edition, Skoog, West, Crouch & Hollar (2014) 3. Analytical Chemistry 7th edition, Christian, Dagupta & Chung (2017)

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Course: Biochemistry (CHEM262) Semester: 2nd Semester Course Coordinator: Dr. Barakat Shabsoug Lecturer(s): Dr. Barakat Shabsoug, Dr Ayat Bani Irshaid, Dr. Amjad mahasneh Language: English Assignment in Curriculum Compulsory Course in 2nd Semester of the second year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 63 Exams: 4 41 Sum 46 104

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to Organic Chemistry and General Chemistry (2) examination regulations: Recommendations: Passing the organic and general chemistry courses in the first & second academic year

Course Description This course deals with structure and properties of biomolecules, such as amino acids, proteins, carbohydrates, lipids, and nucleic acids. The focus of this course will be on the relationship between protein structure and its biological function, generation and storage of metabolic energy, main metabolic pathways and their key steps. In addition, the role of phospholipids in determining the properties of biological membranes and their function will be discussed.

Learning outcomes: Having finished the course lectures, students will be able to: 1. Know the language of biochemistry. 2. Understand the structure and function of biomolecules. 3. Acquire knowledge and understanding of the concepts in this course. 4. Develop critical thinking skills. 5. Project a clear and repeated emphasis on major themes especially those relating to evolution, thermodynamics and regulation. 6. Sustain the student's interest by developing topics in a logical and stepwise manner.

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Summary indicative content: Aqueous Chemistry Water Molecules Form Hydrogen Bonds, The Hydrophobic Effect, Acid-Base Chemistry, Tools and Techniques: Buffers

Protein Structure Proteins Are Chains of Amino Acids, Structure: The Conformation of the Peptide Group, Tertiary Structure and Protein Stability, Quaternary Structure

Protein Structure Myoglobin and Hemoglobin: Oxygen-Binding Proteins, Structural Proteins, Actin, Tubulin, Keratin, Collagen is a triple helix

How Enzymes Work? What is an enzyme?, The Chemistry of Catalysis, The Unique Properties of Enzyme Catalysts, Some Additional Features of Enzymes

Enzyme Kinetics and Inhibition Introduction to Enzyme Kinetics, Derivation and Meaning of the Michaels-Menten Equation, Enzyme Inhibition

Lipids Membranes Lipids, The Lipid Bilayer, Membrane Proteins, The Fluid Mosaic Model

Membrane Transport The Thermodynamics of Membrane Transport, Passive Transport, Active Transport

Carbohydrates Monosaccharides, Polysaccharides, Glycoproteins

Metabolism and Bioenergetics Food and Fuel, Metabolic Pathways, Free Energy Changes and Metabolic Reactions

Glucose Metabolism Storage Mechanisms and Control in Carbohydrate Metabolism, How glycogen is produced and degraded, Gluconeogenesis produces glucose from pyruvate, Control of carbohydrate metabolism, Glucose is sometimes diverted through the pentose phosphate pathway

The Citric Acid Cycle The central role of the citric acid cycle in metabolism, overall pathway of the citric acid cycle, is pyruvate converted to acetyl-

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CoA?, The individual reactions of the citric acid cycle, Energetic and control of the citric acid cycle, The glyoxylate cycle, link to oxygen

Electron Transport and Oxidative Phosphorylation The role of electron transport in metabolism, The reduction potentials in the electron transport chain, of electron transport complexes, connection between electron transport and phosphorylation, mechanism of coupling in oxidative phosphorylation, Respiratory inhibitors used to study electron transport, The ATP yield from complete oxidation of glucose

Lipid Metabolism Lipids are involved in the generation and storage of energy, of lipids, energy yield from the oxidation of fatty acids, Catabolism of unsaturated fatty acids and odd-carbon fatty acids, Ketone bodies, Fatty-acid biosynthesis, Cholesterol biosynthesis (In brief)

The Metabolism of Nitrogen Nitrogen metabolism: an overview, fixation, Amino acid biosynthesis, amino acids, Amino acid catabolism, Purine and pyrimidine catabolism

Assessment: The final mark of the course consists of: Computer-based exams: a. First exam (30% of the final mark): composed of multiple- choice questions. b. Second exam (30% of the final mark): composed of multiple- choice questions. c. Final exam (40% of the final mark): composed of multiple- choice questions.

Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard

Exercise: Examples and solved problems of course activities will be announced

Indicative Bibliography/Sources: Textbook: ESSENTIAL BIOCHEMISTRY, C.W. Pratt and K. Cornely (20014), Third Edition. Publisher: John Wiley and Sons, Inc., USA

References and Supplement Materials: 1. BIOCHEMISTRY, M.K. Campbell and S. O. Farrell (2012), 7th Edition. Publisher: Thomson Learning, Inc., USA. 2. 2.Principles of Biochemistry, 4rd ed., by Lehninger, Nelson, & Cox (2004).

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Course: Biochemistry Laboratory (CHEM266) Semester: 2nd Semester Course Coordinator: Mr. Adeeb Al-Faqeeh Lecturer(s): Mr. Adeeb Al-Faqeeh and others Language: English Assignment in Curriculum Compulsory Course in 2nd Semester of the second year Course Units/Credit hours Lab session: 1 credit hour Students workload: Contact hours Private study Lab session: 33 84 Book exercises 0 24 Exams & Quizzes: 4 26 Sum 46 134

Total Sum: 90 hours

Credits 3 ECTS Prerequisites according to Biochemistry examination regulations: Recommendations: Passing the chemistry courses in first and second academic years

Course Description This course aims to teach students the principles of safety and hazards in biochemistry laboratories. The first five experiments of the course will cover the fundamental techniques and the advanced instruments used in the analysis and constructing important curves of amino acids and some other dyes. In the second five experiments the students will learn how to identify quantize and differentiate between different biochemical compounds. Learning outcomes: Having finished the course lab sessions, students will be able to: 1. Understand experiments and enhance their ability in thinking and research. 2. Manipulate all experimental data and curves construction. 3. Learn how to collect a human blood sample centrifuge and analyze the serum for Glucose, Albumin, and Cholesterol. 4. Learn how to test for Carbohydrate and their classification.

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Summary indicative content: 1. Titration curves of Amino Acids. 2. Absorbance curves of two colored compounds. 3. General properties of Amino Acids. 4. Separation of Amino acids by Paper chromatography and electrophoresis. 5. General properties of Proteins. 6. Quantitation of proteins. 7. Preparation of an enzyme extract Polyphenoloxidase (PPO). 8. General properties of Lipids. 9. Enzymatic colorimetric method (End Point). 10. General properties of Carbohydrates.

Assessment: The final mark of the course consists of: Computer-based exams: a. Midterm exam (40% of the final mark): composed of multiple-choice questions. b. Final exam (40% of the final mark): composed of multiple- choice questions. Lab reports: a. Reports (20% of the final mark): Description, results and conclusions about lab experiments

Teaching style: Lab session: demonstration, e-learning and whiteboard

Exercise: Examples and solved problems of course activities will be announced

Indicative Bibliography/Sources: 1. Essential Biochemistry, C.W. Pratt and K. Cornely (20014), Third Edition. Publisher: John Wiley and Sons, Inc., USA 2. Biochemistry, M.K. Campbell and S. O. Farrell (2012), 7th Edition. Publisher: Thomson Learning, Inc., USA. 3. Principles of Biochemistry, 4rd ed., by Lehninger, Nelson, & Cox (2004).

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Course: General Biology 1 (BIO101) Semester: 1st Semester Course Coordinator: Dr. Fawzi Al-Sheyab Lecturer: Dr. Fawzi Al-Sheyab Language: English Assignment in Curriculum Compulsory Course in 1st Semester of the first year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 84 Exams & Quizzes: 4 20 Sum 46 104

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to None examination regulations: Recommendations: None Course Description Biology 101 is dedicated to the study of the molecular and cellular basis of life. Topics include cell structure and physiology, information flow, metabolism, cellular reproduction, Mendelian and modern genetics. This course is designed for students planning to major in biotechnology, genetics or a related discipline

Learning outcomes: 1. Describe the basic properties of the major classes of biological molecules needed for life 2. Compare and contrast the structures, reproduction, and subcellular characteristics of prokaryotic and eukaryotic cells 3. Describe the structure of cell membranes and the movement of molecules across a membrane 4. Describe and explain the principles of Bioenergetics 5. Describe the importance of cell division in maintaining the continuity of life 6. Define and apply the principles of Mendelian genetics and its modern extensions to the unity and diversity of life. 7. Understand the molecular, structural and chromosomal basis of heredity..

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Summary indicative content: Biological Macromolecules and Lipids Macromolecules are polymers, built from monomers Carbohydrates serve as fuel and building material Lipids are a diverse group of hydrophobic molecules Proteins include a diversity of structures, resulting in a wide range of functions Nucleic acids store, transmit, and help express hereditary information Genomics and proteomics have transformed biological inquiry and applications

Cell Structure and Function Biologists use microscopes and the tools of biochemistry to study cells Eukaryotic cells have internal membranes that compartmentalize their functions The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes The endomembrane system regulates protein traffic and performs metabolic functions in the cell Mitochondria and chloroplasts change energy from one form to another The cytoskeleton is a network of fibers that organizes structures and activities in the cell Extracellular components and connections between cells help coordinate cellular activities

Cell Membranes Cellular membranes are fluid mosaics of lipids and proteins Membrane structure results in selective permeability Passive transport is diffusion of a substance across a membrane with no energy investment Active transport uses energy to move solutes against their gradients Bulk transport across the plasma membrane occurs by exocytosis and endocytosis

Cell Respiration Catabolic pathways yield energy by oxidizing organic fuels Glycolysis harvests chemical energy by oxidizing glucose to pyruvate After pyruvate is oxidized, the citric acid cycle completes the energy-yielding oxidation of organic molecules During oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis Fermentation and anaerobic respiration enable cells to produce ATP without the use of oxygen Glycolysis and the citric acid cycle connect to many other metabolic pathways

Photosynthetic Processes Photosynthesis converts light energy to the chemical energy of food The light reactions convert solar energy to the chemical energy of ATP and NADPH The Calvin cycle uses the chemical energy of ATP and NADPH to

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reduce CO2 to sugar 199

Mitosis Most cell division results in genetically identical daughter cells The mitotic phase alternates with interphase in the cell cycle The eukaryotic cell cycle is regulated by a molecular control system

Sexual Life Cycle and Meiosis Offspring acquire genes from parents by inheriting chromosomes Fertilization and meiosis alternate in sexual life cycles Meiosis reduces the number of chromosome sets from diploid to haploid Genetic variation produced in sexual life cycles contributes to evolution

Mendelian Genetics Mendel used the scientific approach to identify two laws of inheritance Probability laws govern Mendelian inheritance Inheritance patterns are often more complex than predicted by simple Mendelian genetics Many human traits follow Mendelian patterns of inheritance

Linkage and Chromosomes Morgan showed that Mendelian inheritance has its physical basis in the behavior of chromosomes: Scientific inquiry Sex-linked genes exhibit unique patterns of inheritance Linked genes tend to be inherited together because they are located near each other on the same chromosome Alterations of chromosome number or structure cause some genetic disorders

Nucleic Acids and Inheritance DNA is the genetic material Many proteins work together in DNA replication and repair A chromosome consists of a DNA molecule packed together with proteins

Assessment: The final mark of the course consists of:

1. Written exams:

a. First exam (30% of the final mark) composed of MCQ or short answer essay questions to the content of the lecture. b. Second exam (30% of the final mark): composed of MCQ or short answer essay questions to the content of the lecture. c. Final exam (40% of the final mark): composed of MCQ questions to the content of the lecture.

Teaching style: Lecture: Projector, e-learning, power point presentations and white board Indicative Bibliography/Sources: Biology: A global Approach, (11th Edition), Campell, Urry, Cain, Wasserman, Minorsky, Reece. Pearson Education Inc., 2018.

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Course: General Biology 2 (BIO102) Semester: 2nd Semester Course Coordinator: Dr. Asem Alkhateeb Lecturer: Dr. Asem Alkhateeb Language: English Assignment in Curriculum Compulsory Course in 2nd Semester of the first year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 84 Exams & Quizzes: 4 20 Sum 46 104

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to General Biology 101 examination regulations: Recommendations: Passing the General Biology (1) course in the first academic year

Course Description Biology 102 builds upon Biology 101 and the first part of the course introduces students to the concepts of molecular biology, information flow, evolution and DNA biotechnology. The second part of the course provides an introduction to viruses, prokaryotes, and human digestive, transport and immune systems.

Learning outcomes: 1. Demonstrate knowledge and comprehension of core concepts, which includes but is not limited to knowledge of cell biology, biochemistry, genetics, molecular biology, microbiology and immunology. 2. Exhibit basic laboratory skills necessary for the field of biotechnology and genetic engineering. 3. Utilize and apply knowledge of biotechnology in various applications like industry, medicine, agriculture and other related fields 4. Demonstrate effective reading, critical thinking, and problem- solving skills as well as exhibiting effective oral and written communication skills 5. Recognize and understand ethical and social implications of the use of biotechnology and genetic engineering. 6. Demonstrate knowledge of contemporary issues in biotechnology and genetic engineering.

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Summary indicative content: • Gene Expression: From Gene to Protein • Genes specify proteins via transcription and translation • Transcription is the DNA-directed synthesis of RNA • Eukaryotic cells modify RNA after transcription • Translation is the RNA-directed synthesis of a polypeptide • Mutations of one or a few nucleotides can affect protein structure and function • Control of Gene Expression • Bacteria often respond to environmental change by regulating transcription • Eukaryotic gene expression is regulated at many stages • Noncoding RNAs play multiple roles in controlling gene expression • A program of differential gene expression leads to the different cell types in a multicellular organism • Cancer results from genetic changes that affect cell cycle control • DNA Technology • DNA sequencing and DNA cloning are valuable tools for genetic engineering and biological inquiry • Biologists use DNA technology to study gene expression and function • Cloned organisms and stem cells are useful for basic research and other applications • The practical applications of DNA-based biotechnology affect our lives in many ways • The Evolution of Genomes • The human genome project fostered development of faster, less expensive sequencing techniques • Scientists use bioinformatics to analyze genomes and their functions • Genomes vary in size, number of genes, and gene density • Multicellular eukaryotes have a lot of noncoding DNA and many multigene families • Duplication, rearrangement, and mutation of DNA contribute to genome evolution • Comparing genome sequences provides clues to evolution and development • Microevolution • Genetic variation makes evolution possible • The Hardy-Weinberg equation can be used to test whether a population is evolving • Natural selection, genetic drift, and gene flow can alter allele frequencies in a population • Natural selection is the only mechanism that consistently causes adaptive evolution • Introduction to viruses • A virus consists of a nucleic acid surrounded by a protein coat • Viruses replicate only in host cells • Viruses and prions are formidable pathogens in animals and plants • Prokaryotes • Structural and functional adaptations contribute to prokaryotic success • Rapid reproduction, mutation, and genetic recombination

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promote genetic diversity in prokaryotes • Diverse nutritional and metabolic adaptations have evolved in prokaryotes • Prokaryotes have radiated into a diverse set of lineages • Prokaryotes play crucial roles in the biosphere • Prokaryotes have both beneficial and harmful impacts on humans • Human digestive system • Organs specialized for sequential stages of food processing form the mammalian digestive system • Feedback circuits regulate digestion, energy storage, and appetite • Human transport system • Coordinated cycles of heart contraction drive double circulation in mammals • Patterns of blood pressure and flow reflect the structure and arrangement of blood vessels • Blood components function in exchange, transport and defense • Breathing ventilates lungs • Adaptations for gas exchange include pigments that bind and transport gases • Human Defenses Against Infection • In innate immunity, recognition and response rely on traits common to groups of pathogens • In adaptive immunity, receptors provide pathogen-specific recognition • Adaptive immunity defends against infection of body fluids and body cells • Disruptions in immune system function can elicit or exacerbate disease

Assessment: The final mark of the course consists of:

1. Written exams:

Teaching style: Lecture: Projector, e-learning, power point presentations and white board

Indicative Bibliography/Sources: Biology: A global Approach, (11th Edition), Campell, Urry, Cain, Wasserman, Minorsky, Reece. Pearson Education Inc., 2018.

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Course: General Biology Laboratory (BIO107) Semester: 2ed Semester Course Coordinator: Bayen Mahawreh Lecturer: TA’s Language: English Assignment in Curriculum Compulsory Course Course Units/Credit hours Lab session: 1 credit hour Students workload: Contact hours Private study Lab session: 26 13 Reports 0 8 Exams & Quizzes: 3 10 Sum 29 31

Total Sum: 60 hours

Credits 2 ECTS Prerequisites according to General Biology (2) examination regulations: Recommendations: Passing the general biology courses in the first academic year.

Course Description This course is designed to introduce students to the basic concept of biology as a discipline. An overview of the microscope, different cell types, essential molecules, cell divisions, anatomy of the plant and human body with a wide range of laboratory experiments related to these topics where students are required to experience their ability in doing experiments, synthesize results and draw conclusions from their own work.

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Learning outcomes: Having finished the course lectures and practical work, students will be able to: 1. Discuss the main concepts of biology. 2. Describe the structural and functional properties of different cell types among living organisms. 3. Explore many biological activities within living organisms such as, respiration, enzymatic reactions, molecules transporting and cell division with the concepts of genetics and inheritance. 4. Examine representative models and slides. 5. Perform experiments; dealing with laboratory materials, tools and instruments. 6. Ability to analyze and solve practical problems. 7. Ability to organize group work, implement team and communication skills.

Summary indicative content: • Lab Safety and Microscopy General guidelines, precautions and instructions, concepts of the microscope, microscope handling and caring, parts of the compound microscope, viewing prepared slides under the compound microscope, prepared and viewing wet mount slides, dissecting microscope, viewing object under the dissecting microscope.

• Cell Structure and Function Types of cells, prokaryotic and eukaryotic cells, main differences, structural compartments and their main function, studying a representative model of animal, plant, bacterial and paramecium cells, preparing wet mount slides of animal and plant cells.

• Macromolecules and Living Things Carbohydrates, fats and lipids, proteins, vitamin C, Benedict test for reducing sugar, Lougl’s for starch, Biuret test for peptide bonds, solubility test and vitamin C concentration.

• Enzyme Activity Enzymes function, enzyme action, enzyme model, factors affecting enzymes activity, Isolation of the catalase enzyme, enzyme activity as a function of substrate concentration, enzyme activity as a function of enzyme concentration, enzyme activity as a function of temperature, enzyme activity as a function of pH.

• Cellular Respiration and Fermentation Types of cellular respiration, sites and products of the respirations, carbon dioxide liberation, water liberation, heat of respiration, dehydrogenase activity, anerobic respiration of yeast cells.

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• Diffusion and Osmosis Molecules transporting pathways, diffusion direction, factors affecting diffusion, diffusion of gases, diffusion of molecules through a selective permeable membrane, osmosis, definition and direction, tonicity, osmatic behavior in animal and plants cells.

• Mitosis and Meiosis Purposes of cells division, the cell cycle, mitosis, stages of mitosis, main events of mitosis, cytokinesis, cell cycle in plant cells, meiosis, stages of meiosis I and II, main events of meiosis, differences of meiosis and mitosis, prepared slide of mitosis in plant cells.

• Human Genetics Main concepts in genetics, DNA structure, RNA structure, inheritance pathways in human, autosomal inheritance, sex-linked inheritance, sex affected traits, ABO blood grouping, determining your blood type.

• Plant tissues Plant tissues, meristematic tissues, permeant tissues, complex permeant tissues, viewing prepared slides of plant tissues.

• Plant Organs Vegetative organs, root anatomy, stem anatomy, the woody dicot stem anatomy, leaf anatomy, reproductive organs of the plant, the flower parts, viewing prepared slides of the plant organs.

• Animal Tissues Animal tissue types, epithelial tissue, connective tissue, muscular tissue, nervous tissue, viewing prepared slides of animal tissues.

• Animal Organs Human skin, intestine, kidney, liver, spinal cord, trachea, viewing prepared slides of animal organs.

• Animal Systems Human system overview, cardiovascular system, digestive system, reproductive system, muscular system, respiratory system, nervous system, skeletal system, urinary system, sense organs.

Reports: • Solving problems and questions about the conducted experiments.

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Assessment: The final mark of the course consists of: 1. Computer-based exams: a. Midterm exam (40% of the final mark): composed of multiple-choice questions on the content of the lectures and practical works. b. Final exam (40% of the final mark): composed of multiple- choice questions on the content of the lectures and practical work. 2. Quizzes (10% of the final mark): 6 quizzes composed of multiple-choice, true/false or fill in the blank questions. 3. Reports (10% of the final mark): 12 reports with certain requirements related to each experiment filled with the results of the practical work.

Teaching style: Lecture: Power point presentations and whiteboard. Practical work: Demonstration of the experiments by the lecturer and presenting objects and materials for the students.

Indicative Bibliography/Sources: Manual of General Biology. Department of Biotechnology and Genetics Engineering, 2016- 2017.

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Course: General Microbiology (BIO231)

Semester: 2nd Semester Course Coordinator: Dr. Abdullkarim Al Sallal Lecturer: Dr. Abdullkarim Al Sallal and Dr Ziad Jaradat Language: English Assignment in Curriculum Compulsory Course in 1st Semester of the second year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 84 Exams 4 20 Sum 46 104

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to General Biology 1 & 2 examination regulations: Recommendations: Passing the general biology courses in the first academic year Course Description Introduction to the microbial world. Diversity of prokaryotes, their development, structure and function. Prokaryotic metabolism, nutrition, growth and control. Major classes of bacteria as well as Viruses and fungi are thoroughly discussed. Host-pathogen relationship and antimicrobial chemotherapy are also be addressed.

Learning outcomes: Having finished the course and successfully passed the exams the students should be able; 1. Describe the surface structure as well as the internal structure of bacterial cells and their functions 2. Describe the nutritional and physical requirements for bacterial growth and the effect of environment on bacteria and explain the dynamics of the growth of a bacterial population and how this growth can be measured 3. Describe the principals involved in killing bacteria, and be able to decide on the use of physical and chemical methods including antimicrobial chemotherapeutic agents used to control microbial growth in industrial and medical settings 4. Express the fundamental concepts associated with viruses including a detailed understanding of viral classification and replication 5. Comprehend the modern scheme of bacterial classification using molecular microbiology methods and be familiar with

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major groups of bacteria and fungi and their importance in medical, environmental and food industry 6. Understand ways in which bacterial pathogens can be transmitted to humans, and the factors that influence transmission of pathogens and the occurrence of infectious diseases. This includes the concepts of virulence and virulence factors, opportunistic pathogens, and predisposing factors to disease. 7. Summary indicative content: Lecture • Bacterial cell structure; the chapter explains the structure of all bacterial organelles and their function. • Microbial growth; the chapter deals with all aspects of the microbial growth and the growth curve. The closed and open systems of the growth are discussed. All types of microbial media are explained in details. • Control of Microorganisms in the Environment; the chapter deals with physical, chemical, mechanical and biological methods of controlling the microbes in the environment. • Antimicrobial chemotherapy; the chapter deals with controlling microbes in the human body and tissues using different types and groups of natural and synthetic antibiotics • Viruses and other acellular infectious agents; this chapter deals with the classification of the different types of viruses including human, animal and bacterial viruses. The chapter also deals with the acellular infectious agents such as the virusoides and prions. • Microbial Taxonomy; the chapter explains the process of microbial taxonomy and its three components; the classification, nomenclature and identification. The taxonomic ranks are discussed as well as the phonetic and genetic methods of classification are addressed. • Bacteria- the Poteobacteria: the chapter discusses different types of bacteria based on the new classification schemes. It discusses the 5 types of the protebacteria, alpha, beta, gamma, delta and epsilon. The focus in this chapter is given for bacteria that is important, industrially, or environmentally, or from health point of view with special consideration for enteric pathogens. • Bacterial, low GC gram positives; the chapter deals with gram positive bacteria that is important industrially as well as from a pathogenic point of view. Examples of pathogenic bacteria are discussed. • Bacteria the High GC gram positives; the chapter deals with major Gram-positive Bacteria that high in GC with a special focus on Actinomycetes and its beneficial role in decomposition, antibiotic production as well as some pathogenic aspects. • The Fungi (Eumycota); the chapter deals with the different groups of fungi that are important as pathogens, decomposers or even the edible ones. The life cycles of all fungi groups is discussed. • Pathogenicity and Infection; the chapter deals with the

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pathogenesis of the different microbes and the process of the microbial transmission and infection. The definition and calculations of the infectious doses as well as the lethal doses of the microbes are explained.

Assessment: The final mark of the course consists of: 1. Computer-based exams: d. First Midterm exam (30% of the total mark): composed of multiple-choice questions (MCQ) pertaining to the content of the lectures given in the first part of the course. e. Second midterm exams; (30%) of the total mark, composed of multiple-choice questions (MCQ) pertaining to the content of the lectures given in the second part of course. f. Final exam (40% of the total mark): composed of MCQ questions covering the whole course content.

Teaching style: Lecture: Projector, e-learning, power point presentations and white board

Indicative Bibliography/Sources: Prescott, L., Harely , J. P. and Klein. Tenth edition, 2017

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Course: General Microbiology Laboratory (BIO232)

Semester: 2nd Semester Course Coordinator: Mr. Bayen Mahawreh Lecturer: Mr. Bayen Mahawreh and others Language: English Assignment in Curriculum Compulsory Course in 2nd Semester of the second year Course Units/Credit hours Lab session: 1 credit hour Students workload: Contact hours Private study Lab session: 39 12 Reports 0 12 Exams & Quizzes: 4 23 Sum 43 47

Total Sum: 90 hours

Credits 3 ECTS Prerequisites according to General Biology 1 & 2 examination regulations: Recommendations: Passing the general biology courses in the first academic year Course Description This course focuses on developing laboratory skills in microbiology. It includes isolation, purification, cultivation, smear preparation, staining of the bacteria, performing tests to classify and identify the major groups of bacteria, and studying microbial growth control methods. Upon completion of this lab course, students will acquire basic microbiology techniques and principles. The students will get first-hand experience that will coincide with what is taught in the lecture portion of the class.

Learning outcomes: Having finished the course and successfully passed the exams the students should be able; 1. Demonstrate the ability to work with standard lab safety protocols and procedures and how to handle biologically hazardous material, needles and sharps 2. Correctly perform microbiologic lab skills and display a habit of good lab practices, which extends to relevant situations in the student’s homes. 3. Demonstrate appropriate laboratory skills and techniques related to the staining of bacteria and estimating the number of microorganisms in a sample 4. Demonstrate appropriate laboratory skills to isolate bacteria and testing antimicrobial activity of agents

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5. Explain principles of physical and chemical methods used in the control of microorganisms to prevent and control infectious diseases 6. Demonstrate appropriate laboratory skills related to the identification of bacteria using biochemical testing and metabolism 7. Learn how to make careful observations, collect and analyze data, and draw appropriate conclusions

Summary indicative content: • Regulation and management of microbiology lab. • The microscope and Microscopic examination of living bacterial Preparation • Bacterial staining • Bacterial staining: Gram staining • Bacterial staining: Acid fast staining • Culture transfer techniques • Techniques for isolation of pure cultures • Physical factors • Cultivation of Microorganisms • Biochemical activities of Microorganisms I • Cultivation and Enumeration of Bacteriophages

Teaching style: Lecture: Power point presentations and whiteboard.

Practical work: Demonstration by the lecturer.

Indicative Bibliography/Sources: Microbiology: A laboratory Manual. James Cappuccino and Natalia Sherman. 10th Edition

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Course: Cell Biology (BIO251)

Semester: 1st Semester Course Coordinator: Dr. Khaldon Bodoor Lecturer: Dr. Khaldon Bodoor Language: English Assignment in Curriculum Compulsory Course in 1st Semester of the second year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 40 80 Exams: 4 36 Sum 44 106

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to General Biology (2) examination regulations: Recommendations: Passing the general biology courses in the first academic year Passing the microbiology & biochemistry courses in the second academic year

Course Description This a single semester course in cell biology that focuses on fundamental cellular concepts such as the relationship between molecular organelle structure and function, the dynamic character of cellular organelles, the use of chemical energy in running cellular activities and ensuring accurate macromolecular biosynthesis, the observed unity and diversity at the macromolecular and cellular levels, and the mechanisms that regulate cellular activities. Additionally, students will be exposed to the experimental approach in cell biology to gain some knowledge of how we know what we know in cell biology.

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Learning outcomes: Having finished the course lectures, students will be able to: 1. Understand the basic properties of cells and describe and the structure and function of cellular organelles. 2. Describe the interactions between cells and their environments and understand the molecular basis of cellular signaling. 3. Understand the concept of cellular reproduction and the cellular basis of cancer. 4. Get a brief introduction to the tools and experiments related to cell biology. 5. Students should be able to discuss and analyze contemporary issue in cell biology.

Summary indicative content: • A Preview of Cell Biology: Topics: Cells Are Highly Complex and Organized; Cells Possess a Genetic Program and the Means to Use It; Cells Are Capable of Producing More of Themselves; Cells Acquire and Utilize Energy; Cells Carry Out a Variety of Chemical Reactions; Cells Engage in Mechanical Activities; Cells Are Able to Respond to Stimuli; Cells Are Capable of Self-Regulation; Cells Evolve; Characteristics That Distinguish Prokaryotic and Eukaryotic Cells; Types of Prokaryotic Cells; Types of Eukaryotic Cells: Cell Specialization; The Sizes of Cells and Their Components. • • The Chemistry of the Cell: The Importance of Carbon; The Importance of Water; The Importance of Selectively Permeable Membranes; The Importance of Synthesis by Polymerization 56 Macromolecules Are Critical for Cellular Form and Function; The Importance of Self-Assembly; Noncovalent Bonds and Interactions. • • The Macromolecules of the Cell: Proteins structure and function; Nucleic Acids structure and function; Polysaccharides structure and function; Lipids structure and function.

• Cells and Organelles: Where Did the First Cells Come From; Properties and Strategies of Cells; The Eukaryotic Cell in Overview: Structure and Function; Viruses, Viroids, and Prions: Agents That Invade Cells. • • Membranes: Their Structure, Function, and Chemistry: The Functions of Membrane; Models of Membrane Structure: An Experimental Perspective; Membrane Lipids: The “Fluid” Part of the Model; Membrane Proteins: The “Mosaic” Part of the Model. • • Transport Across Membranes: Overcoming the Permeability Barrier: Cells and Transport Processes; Simple Diffusion: Unassisted Movement Down the Gradient; Facilitated Diffusion: Protein- Mediated Movement Down the Gradient; Active Transport: Protein-Mediated Movement Up the Gradient; Examples of Active Transport; The Energetics of Transport.

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• • The Endomembrane System: The Endoplasmic Reticulum; The Golgi Apparatus; The Nuclear Envelope; Roles of the ER and Golgi Apparatus in Protein Glycosylation; Roles of the ER and Golgi Apparatus in Protein Trafficking; Exocytosis and Endocytosis: Transporting Material Across the Plasma Membrane; Coated Vesicles in Cellular Transport Processes; Lysosomes and Cellular Digestion; The Plant Vacuole: A Multifunctional Organelle; Peroxisomes. • • Cytoskeletal Systems: Major Structural Elements of the Cytoskeleton; Microtubules; Microfilaments; Intermediate Filaments. • • Cellular Movement: Motility and Contractility: Microtubule-Based Movement Inside Cells: Kinesins and Dyneins; Microtubule-Based Cell Motility: Cilia and Flagella; Microfilament- Based Movement Inside Cells: Myosins; Microfilament-Based Motility: Muscle Cells in Action; Microfilament-Based Motility in Nonmuscle Cells. • • Beyond the Cell: Cell Adhesions, Cell Junctions, and Extracellular Structure: Cell-Cell Junctions; The Extracellular Matrix of Animal Cells; The Plant Cell Surface. • • Molecular Techniques for Cell Biology: Protein purification and characterization; Microscopy; Tissue culture; antibodies; DNA and RNA tools; In vitro and In vivo models and tools.

• Signal Transduction Mechanisms: I. Electrical and Synaptic Signaling in Neurons: Neurons and Membrane Potential; Electrical Excitability and the Action Potential; Synaptic Transmission and Signal Integration. • Signal Transduction Mechanisms: II. Messengers and Receptors: Chemical Signals and Cellular Receptor; G Protein–Coupled Receptors; Protein Kinase-Associated Receptors; Putting It All Together: Signal Integration; rmones and Other Long-Range Signals.

• The Cell Cycle and Mitosis: Overview of the Cell Cycle; Nuclear and Cell Division; Regulation of the Cell Cycle; Growth Factors and Cell Proliferation; Apoptosis. • • Cancer Cells: How Cancers Arise; How Cancers Spread; What Causes Cancer?; Oncogenes and Tumor Suppressor Genes; Diagnosis, Screening, and Treatment

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Assessment: The final mark of the course consists of: 1. Written exams: a. First and Second exam (50% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. b. Final exam (40% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. c. Quizzes (5% of the final mark): 10 quizzes composed of MCQ questions. 2. Presentation (5% of the final mark): students present about recent disease-related cell biology topics.

Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard Assignments: e-learning

Indicative Bibliography/Sources: Becker's World of the Cell. Jeff Hardin , Gregory Paul Bertoni and Lewis J. Kleinsmith. Ninth Edition. Publisher: Pearson USA

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Course: Immunology & Serology (BIO333)

Semester: 2nd Semester Course Coordinator: Dr. Nizar Abuharfeil Lecturer: Dr. Nizar Abuharfeil Language: English Assignment in Curriculum Compulsory Course in 1st semester of the second year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 63 Oral presentation: 2 9 Exams & Quizzes: 4 30 Sum 48 102

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to Microbiology & Biochemistry examination regulations: Recommendations: Passing the general biology courses in the first academic year Passing the microbiology & biochemistry courses in the second academic year

Course Description This course is designed to introduce students to the basic concept of Immunology as a discipline. This course will describe the immune systems of vertebrates that enable them to recognize and respond specifically to foreign substances. The molecular and cellular basis of immunity will be emphasized. The roles of antigens, antibodies and immunocompetent cells in pathogenesis and immunity to infectious diseases will be covered. Specific topics include antigens and antigenic determinants, antigen-antibody reactions, antibody structure and formation, anatomy and physiology of immunocompetent tissues, cellular immune responses, the complement system and other immune modulators, phagocytosis, monoclonal antibody formation, immunogenetics and the histocompatibility antigens, diseases of the immune system and immunopathology, tolerance, inflammation, allergies, and hypersensitivity reactions. The applications of immunology in the design of vaccines, immunotherapeutics, immunodiagnostics, and organ transplantation will be discussed, as will the uses of immunology in biological research.

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Learning outcomes: Having finished the course lectures, students will be able to: 1. Describe the basic principles of immunology including innate immunity, organs and tissues of immune system 2. Describe the immunochemistry and immunogenetics of B cells and antibodies. 3. Describe the steps of the immune response including development of B and T lymphocytes after antigen exposure 4. Describe the immunobiology of the immune system including hypersensitivity, immunodeficiency, autoimmune diseases and tumor immunology 5. Describe the immunity part of immune system including transplantation and vaccination

Summary indicative content: • Introduction and overview • Elements of innate immunity • Acquired immunity • Immunogenes and antigens • Antibody structure and function • The genetic basis of antibody structure • Biology of the B lymphocyte • Biology of T lymphocyte • The role of the major hisrocompatibility complex in the immune response • Activation and function of t and b cells • Cytokines • Autoimmunity • Complement • Tolerance • Hypersensitivity reactions: antibody-mediated (Type1) reactions • Immunodeficiency and other disorders of the immune system • Transplantation immunology • Tumor immunology • Resistance and immunization to infectious disease

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Assessment: The final mark of the course consists of: 1. Written exams: a. First and second exam (50% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. b. Final exam (40% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture.

2. Presentation (10% of the final mark): students present about recent advances in immunology from the available primary literature.

Teaching style: Lecture: Projector, e-learning, power point presentations and white board Assignments: e-learning

Indicative Bibliography/Sources: 1. Roit et al., (2017) Essential Immunology . Blackwell wiley 2. Roderick Nairn and Matthew Helbert, 2016. Immunology for medical students. Third edition, Mosby 3. Kenneth Murphy et al., 2016. Immunobiology, 9th edition, Garland science

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Course: Immunology Laboratory (BIO336)

Semester: 1st and 2nd Semesters Course Coordinator: Dr. Nizar Abuharfeil Lecturer: Dr. Nizar Abuharfeil Language: English Assignment in Curriculum Compulsory Course in 1st and 2nd Semester of the 2nd year Course Units/Credit hours Practical: 1 credit hour Students workload: Contact hours Private study Lab session: 33 33 Reports 0 9 Exams & Quizzes: 5 10 Sum 38 52

Total Sum: 90 hours

Credits 3 ECTS Prerequisites according to Immunology and serology examination regulations: Recommendations: Passing the immunology course or simultaneously in the second academic year

Course Description The purpose of the Immunology lab course is to provide a basic knowledge of the Experimental and serological applications of immunobiology for diagnosis of viral, bacterial and fungal diseases and for investigation of research problems

Learning outcomes: Having finished the course, students will be able to: 1. Describe the precipitation methods in antigen or antibody detection including primary and secondary immune response 2. Describe isolation of lymphocytes and Describe the clinical tests based on direst agglutination of antigen and antibody 3. Describe the clinical tests based on indirect agglutination of antigen and antibody 4. Describe the most sensitive immunoassays including ELISA, IFA and RIA

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Summary indicative content: Handling and injection of experimental animals Preparation of antigens using adjuvant Injection sites and doses

Isolation of lymphocytes and differential WBC count Ficoll-hypaque method, Blood film to examine the different WBC WBC count using hemocytometer

Mancini test The principle of single or radial immuodiffusion, Applications of SID

Immunodiffusion (Ouchterloney ) Define multivalent antigen. Define "identity", "partial identity", and "non-identity"

Immunoelectrophoresis The principle and application, Immunoelectrophoresis, also called gamma globulin electrophoresis, or Ig electrophoresis, is a method of determining the blood levels of three major Ig: IgM, IgG, and IgA.

Direct immunoagglutination: Rosebengal test, Widal test The principle, Define endpoint or titer. c. Evaluate serial dilutions, grading reactions. the significance, the specimen, false positive and false negative results

Indirect Immunoagglutination: RF, CRP, Pregnancy tests The principle, the significance, the specimen, false positive and false negative results

ELISA (hepatitis) Know the principle of ELISA The controls, the procedure and limitations

Immunofluorescence (ANA test) or MTT test The principle, the significance, the specimen, false positive and false negative results

Radioimmunoassay The principle, the significance, the specimen, false positive and false negative results

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Assessment: The final mark of the course consists of: 1. Written exams: a. Midterm exam (40% of the final mark): composed of MCQ and short answer essay questions. b. Final exam (40% of the final mark): composed of MCQ and short answer essay questions. 2. Lab evaluation: a. Lab report 10% b. Lab quizzes 10%

Teaching style: Introduction to each session: white board, Assignments: e-learning

Indicative Bibliography/Sources: 1. Frank C. Hay, Olwyn M.R. Westwood (2008). Practical immunology. 4th edition. Blackwell 2. Stevens. (2015). Practical immunology and serology. Davis company

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Course: Molecular Genetics (BIO341)

Semester: 1st Semester Course Coordinator: Dr. Osamah Batiha Lecturer: Dr. Osamah Batiha Language: English Assignment in Curriculum Compulsory Course in 1st Semester of the third year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 40 80 Assignment: 0 6 Exams & Quizzes: 4 20 Sum 44 106

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to General Biology 2 examination regulations: Recommendations: Passing the general biology course in the first academic year Course Description This course introduces you to the laws of heredity and the study of inherited traits. Topics include Mendelian and non-Mendelian inheritance, structure and function of chromosomes and genomes, biological variation resulting from recombination, mutation, and selection, and population genetics.

Learning outcomes: After completing this course, students should be able to: 1. Understand the basics of inheritance rules 2. Understand chromosome and gene structure and function 3. Apply probability rules to predict the risk of reoccurrence of genetic traits and diseases. 4. Understand how genetic and physical maps were constructed 5. Understand and apply genetic tools to test/discover a genetic problem

Summary indicative content: Lecture • Introduction to genetics and heredity • • Mendel’s principles of heredity Background: The Historical Puzzle of Inheritance, Genetic Analysis According to Mendel, Mendelian Inheritance in Humans

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• Extensions to Mendel’s laws Extensions to Mendel for Single-Gene Inheritance, Extensions to Mendel for Multifactorial Inheritance

• The chromosome theory of inheritance Chromosomes: The Carriers of Genes, Sex Chromosomes and Sex Determination, Mitosis: Cell Division That Preserves Chromosome Number, Meiosis: Cell Divisions That Halve Chromosome Number, Gametogenesis, Validation of the Chromosome Theory, Sex-Linked and Sexually Dimorphic Traits in Humans

• Linkage, recombination, and the mapping of genes on chromosomes Gene Linkage and Recombination, Recombination: A Result of Crossing-Over During Meiosis, Mapping: Locating Genes Along a Chromosome, The Chi-Square Test and Linkage Analysis, Tetrad Analysis in Fungi Mitotic Recombination and Genetic Mosaics

• DNA structure, replication, and recombination Experimental Evidence for DNA as the Genetic Material The Watson and Crick Double Helix Model of DNA, Genetic Information in Nucleotide Sequence, DNA Replication, Recombination at the DNA Level

• Mutations Mutations: Primary Tools of Genetic Analysis, Molecular Mechanisms of Mutation, What Mutations Tell Us About Gene Structure, What Mutations Tell Us About Gene Function

• Gene Expression The Genetic Code, Transcription: From DNA to RNA Translation: From mRNA to Protein, Differences in Gene Expression Between Prokaryotes and Eukaryotes, The Effects of Mutations on Gene Expression and Function

• Digital analysis of genomes Fragmenting DNA, Cloning DNA Fragments, Sequencing DNA, Sequencing Genomes, Finding the Genes in Genomes, Bioinformatics: Information Technology and Genomes

Assignments: • Solving problems about gene mapping.

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Assessment: The final mark of the course consists of: 1. Written exams: a. 1st exam (25% of the final mark): composed of MCQ, short answer essay questions and problem solving b. 2nd exam (25% of the final mark): composed of MCQ, short answer essay questions and problem solving c. Final exam (40% of the final mark): composed of MCQ, short answer essay questions and problem solving 2. Quizzes (10% of the final mark): 5 quizzes composed of MCQ questions. 3. Assignments: Problem solving questions about genetic mapping (2% of the final mark)

Teaching style: Lecture: Projector, e-learning, power point presentations and white board Assignments: e-learning

Indicative Bibliography/Sources: Genetics: from Genes to Genomes (6th Edition) by Hartwell, Hood, Goldberg, Reynolds, Silver, McGraw Hill

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Course: Molecular Genetics laboratory (BIO344)

Semester: 1st or 2nd Semester Course Coordinator: Dr. Osamah Batiha Lecturer: TA: Salsabeel Sabi Language: English Assignment in Curriculum Compulsory laboratory in the third year Course Units/Credit hours Lab session: 1 credit hour Students workload: Contact hours Private study Lab sessions: 36 24 Assignment 0 6 Exams 3 21 Sum 39 51

Total Sum: 90 hours

Credits 3 ECTS Prerequisites according to General Biology (2) examination regulations: Course Description Genetics laboratory (B344) is a practical guide for the basic genetics course. The experiments have been carefully chosen to suit the needs of students who are taking a basic genetics course.

Learning outcomes: Upon completion of the course, students should: 1. Comprehensive understanding of the basis of Mendelian genetics. 2. The ability to handle and culture flies, and learn how to do crosses. 3. Comprehensive understanding of the basic molecular biology experiments and the ability to run these experiments. 4. Understanding the basis of genetic transformation and obtain the knowledge required to design a virtual lab experiment. 5. Comprehensive understanding of the basis of population genetics and mutations. 6. The ability to read and write a scientific report

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Summary indicative content: Labs Introduction and some definitions

Cell division (mitosis) in onion root tips Students learn about mitotic and meiotic cell divisions and how to examine cells under the microscope

Meeting the fruit fly (Drosophila genetics I ) Students learn how to distinguish the phenotypic characteristics of the Drosophila in addition for proper handling

Chi square analysis (Drosophila genetics II ) Students learn how to test experimentally specific genetic problem using the Chi square statistical test

Polytene chromosome Students learn how to prepare Drosophila polytene chromosome from the salivary glands

Fly transformation Students learn how transgenic flies are prepared and examine GFP transgene expressing flies

DNA extraction Students learn how to isolate DNA from tissues

Determination of DNA properties and content (Gel electrophoresis, Nanodrop, spectrophotometer) Students learn how to quantify and qualify DNA properties

Polymerase Chain Reaction (PCR) Students learn how to perform PCR in different applications

Population genetics Students learn how to determine if two populations are genetically stable using Hardy-Weinberg law

Physical mutations, Chemical mutations (Ames Test) Students learn how to test the mutagenicity of certain chemicals using Ames test

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Assessment: The final mark consists of: 1. Written exams: a. Midterm exam (35% of the final mark). The questions are in the form of short answer essay questions and MCQs covering the topics discussed in the labs. b. Final exam (40% of the final mark): The questions are in the form of short answer essay questions and MCQs covering the topics discussed in the labs.

2. Assignments and quizzes (25%): a. Quizzes (15%): tests students’ preparation and understanding of lab experiments. b. Assignments (10%): given during the lab to allow students interaction and group work.

Teaching style: Lab experiments: Whiteboard, lab demonstrations and e-learning Assignments: e-learning

Indicative Bibliography/Sources: Online uploaded lab description prepared by the TA and the coordinator

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Course: Basic Biotechnology (BT232) Semester: 1st Semester Course Coordinator: Dr. Qutaiba Ababneh Lecturer: Dr. Qutaiba Ababneh Language: English Assignment in Curriculum Compulsory Course in 1st Semester of the second year Course Units/Credit hours Lecture: 2 credit hours Students workload: Contact hours Private study Lecture: 26 52 Oral presentation: 2 6 Exercise 0 10 Exams & Quizzes: 4 20 Sum 32 88

Total Sum: 120 hours

Credits 4 ECTS Prerequisites according to General Biology 2 examination regulations: Recommendations: Passing the general biology course in the first academic year Course Description This course is designed to introduce students to the basic concept of Biochemistry as a discipline. An overview of the molecular and genetic principles and techniques and approaches used to manipulate living organisms and their products will be discussed. In addition, microbial, aquatic, agricultural, animal, forensic, medical and industrial applications of biotechnology will be presented. The course will also examine the ethical implications of biotechnology and introduce latest technologies and applications where appropriate

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Learning outcomes: Having finished the course lectures and presentations, students will be able to: 1. Discuss the history and major discoveries of biotechnology. 2. Describe the structural and functional properties of DNA, the process of gene expression, basic concepts in genetics and the role of DNA in inheritance. 3. Describe the principles of recombinant DNA technology and molecular biology techniques. 4. Explain the role of biotechnology in the fields of medicine, agriculture, forensic science, food production, diagnostics, and industry. 5. Examine ethical aspects of modern biotechnology 6. Explore recent advances in biotechnology and genetic.

Having finished the group assignments students will be able to analyze and solve practical biological problems. Also students will be able to organize group work, and implement team and communication skills

Summary indicative content: Lecture • History, discovery, types and workforce of biotechnology • Recombinant DNA Technology and DNA Cloning Restriction enzymes, types of DNA vectors, transformation of bacterial cells and antibiotic selection of recombinant bacteria, DNA libraries, Agarose gel electrophoresis, Restriction mapping and gene structure, DNA sequencing, Next-generation sequencing (NGS), fluorescence in situ hybridization, Southern blotting, Gene expression & Northern blot, genomics and bioinformatics, the human genome project. • Protein biotechnology Proteomics, protein structure and function, protein production in medical, food, textile, detergent industries and proteins for bioremediation. • Microbial Biotechnology The structure of microbes, microorganisms as tools in research, using microbes for everyday applications, vaccines, microbial genomes, biofuels, microbial diagnostics • Plant Biotechnology Methods of plant transgenics, practical application of plant biotechnology. • Animal Biotechnology Animals in research, cloning, transgenic animals, production of human antibodies in animals. • DNA fingerprinting & forensic analysis Preparing and using DNA fingerprint, DNA and the rules of evidence, familial relationships and DNA profiles, Nonhuman DNA analysis.

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• Bioremediation Fundamentals of cleanup reactions, bioremediation genomics, cleanup sites and strategies, applying genetically engineered strains to clean up the environment. • Medical Biotechnology Detecting and diagnosing human disease condition, medical products and applications of biotechnology, gene therapy, the potential of regenerative medicine.

Assignments: • Solving problems and questions about recombinant DNA technology. • Working and presenting primary literature from the field.

Assessment: The final mark of the course consists of: 1. Written exams: a. Midterm exam (30% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. b. Final exam (40% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. 2. Quizzes (15% of the final mark): 10 quizzes composed of MCQ questions. 3. Group Assignments: a. Problem set (7.5% of the final mark): composed of problems and questions about recombinant DNA techniques. b. Presentation (7.5% of the final mark): students present about recent biotechnology applications from the available primary literature.

Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard Assignments: e-learning

Indicative Bibliography/Sources: INTRODUCTION TO BIOTECHNOLGY, William J. Thieman and Michael A. Palladino, Third Edition. Publisher: Pearson USA

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Course: Bioinformatics (BT301)

Semester: 2nd Semester 2018-2019 Course Coordinator: Dr. Amjad Mahasneh Lecturer: Mrs. Wafa Garqaz Language: English Assignment in Curriculum Compulsory Course in 2nd Semester of the third year Course Units/Credit hours Lecture: 1 credit hours Students workload: Contact hours Private study Lecture: 26 26 Assignments: 0 12 Exams: 4 22 Sum 30 60

Total Sum: 90 hours

Credits 3 ECTS Prerequisites according to C++ Programming Language examination regulations: Recommendations: Course Description In this course, the students are exposed to a broad overview of bioinformatics with a significant problem-solving component, including hands-on practice using computational tools to solve a variety of biological problems. Topics include: database searching, sequence alignment, Sequence and Structure Databases, protein structure prediction, construction of phylogenetic trees, comparative and functional genomics.

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Learning outcomes: Having finished the course lectures and presentations, students will be able to: 1. Define what bioinformatics is and its importance in the sciences 2. Use bioinformatics software and tools to mine the databases to explore questions about molecular structure, function, and evolution 3. Illustrate how sequence alignments and database searching are used to gather data about gene sequences 4. Perform advanced BLAST searches 5. Differentiate between the types of phylogenetic analyses available and choose appropriate programs for specific questions 6. Design primers for PCR amplification 7. analysis DNA sequencing chromatograms 8. Explain relationships between known protein structures and predicted protein structures 9. Analyze and discuss the analytical results for a biological application

Having finished the assignments students will be able to analyze and solve practical biological problems.

Summary indicative content: The Beginning of Bioinformatics • Definition of Bioinformatics • Bioinformatics Software: Two Cultures o Web-Based Software o Command-Line Software • Goals of Bioinformatics Analysis

Searching Literature Using PubMed • Introduction of PubMed • Keys to successful searching

Building a search using PubMed tools • Access to Sequence Data and Related Information(Sequence Databases) • Sequence Data Formats • Primary Sequence Databases—GenBank, EMBL-Bank, and DDBJ • Sequence Accession Numbers and Redundancy in Primary Databases • Access to Information via Gene Resource at NCBI • Secondary Databases- (RefSeq) Database

Genomes and Gene browsers o Data Visualization in Genome Browsers o Ensemble Genome Browser o UCSC Genome Browser o NCBI’s Map Viewer o VEGA Genome Browser

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Pairwise Sequence Alignment o Dot plot o Global Sequence Alignment: Algorithm of Needleman and Wunsch o Local Sequence Alignment: Smith and Waterman Algorithm

Basic Local Alignment Search Tool (BLAST) • BLAST Search Steps • BLAST Algorithm Uses Local Alignment Search Strategy • BLAST Search Strategies

Multiple Sequence Alignments • Definition of Multiple Sequence Alignment • Typical Uses and Practical Strategies of Multiple Sequence Alignment • Databases of Multiple Sequence Alignments

Molecular Evolution and Phylogeny • Principles of Molecular Phylogeny and Evolution • Molecular Phylogeny: Properties of Trees • Type of Trees • Stages of Phylogenetic Analysis

Primer Analysis and SNP Genotyping • SNP databases • Primer design • RFLP design and analysis

DNA Sequencing • DNA Sequencing Technologies • Interpretation of Sequencing Chromatograms

Protein Analysis and Proteomics • Protein Databases • Techniques for Identifying Proteins • Finding Protein Domains and Motifs • Finding Physical Properties of Proteins

Proteomics and Protein Modeling • Protein Structure Prediction o Homology Modeling (Comparative Modeling) o Fold Recognition (Threading o Ab Initio Prediction (Template-Free Modeling)

Assignments: All homework assignments are to be individual efforts unless specifically told otherwise

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Assessment: The final mark of the course consists of: 1. Written exams: a. Midterm exam (30% of the final mark): composed of short answer essay questions and to the content of the lecture. b. Final exam (40% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. 2. Individual Assignments: a. Six assignments (30% of the final grade): composed of exercises and questions about the discussed topics.

Teaching style: Lecture: Projector, worksheet, e-learning, power point presentations and white board Assignments: e-learning inside the laboratory

Indicative Bibliography/Sources: 1. Bioinformatics and Functional Genomics by Jonathan Pevsner (3rd Edition, 2015) 2. Bioinformatics for Beginners by Supratim Choudhuri (1st Edition, 2014) 3. Other: Lectures notes, handouts and assignments

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Course: Tissue Culture and Hybridoma Technology (BT363)

Semester: 1st and 2nd Semester Course Coordinator: Dr. Nizar Abuharfeil Lecturer: Dr. Nizar Abuharfeil Language: English Assignment in Curriculum Compulsory Course in 1st Semester of the second year Course Units/Credit hours Lecture: 1 credit hour Lab session: 1 credit hour Students workload: Contact hours Private study Lecture: 15 30 lab 36 12 Exams & Quizzes: 6 6 Sum 44 52

Total Sum: 120 hours

Credits 4 ECTS Prerequisites according to Immunology and serology examination regulations: Recommendations: Passing the Immunology and microbiology courses in the second academic year

Course Description The course involves the administration of an Ag to a recipient mouse. This animal becomes the source of Ab-producing B cells. The B cells are mixed with a specifically selected Myeloma immortal cell line. The hybrids that survive still be a mixed population. A cloning protocol is then applied to separate the different hybridomas. Finally a large scale production will be applied Learning outcomes: Having finished he course lectures and lab sessions, students will be able to: 1. Describe the concept of monoclonal antibody production, immunization, screening 2. Describe the principles of tissue culture techniques 3. Describe the isolation of B cell, fusion with myeloma cells and cloning 4. Industrial scale production of monoclonal antibodies and characterization

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Summary indicative content: Lecture

Principle of monoclonal antibodies

Immunization Principles, handling of animals, preparation of antigens, routes of administration, adjuvants, in vivo and in vitro immunization

Screening tests: ELISA

Tissue culture technique Equipment requirements, Procedures, Cultural media Contamination, recognition, prevention and elimination

Myeloma cells Origin, viability test, storage of cells, maintenance of cells, freezing and thawing of cells, counting of cells

Preparation of Lymphocyte from spleen cells T cell depletion, negative and positive cell, elimination, EBV transformation

Fusion Criteria of PEG, fusion protocol

Hybrid selection and cloning Expansion of hybridoma, Addition of HT media, feeder cell layer

Propagation of selected clones in vivo and in vitro Mab purification, Different approaches for preparation of human Mab antibodies

Practical

1. Preparation of solutions 2. Immunization of mice 3. Testing of specific antibodies in the immunized animals by ELISA 4. Preparation of tissue culture media 5. Maintenance of myeloma cell line: counting, viability test, storage and freezing 6. Preparation of a spleen cell suspension 7. Fusion of myeloma with B lymphocytes, Selection with HAT media 8. Follow-up and screening of hybridoma cells 9. Expansion of hybridoma cells 10. Cloning of hybridoma cells (Limiting dilution) 11. Ascitic fluid preparation

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Assessment: The final mark of the course consists of: 1. Written exams: a. Midterm exam (40% of the final mark): composed of MCQ and short answer essay questions. b. Final exam (40% of the final mark): composed of MCQ and short answer essay questions. 2. Practical (20% of the final mark): a. 10% reports b. 10% quizzes

Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard Assignments: e-learning

Indicative Bibliography/Sources: 1. lei Zheng and Mohammad shameem (2015). Monoclonal antibodies. Future science Ltd. 2. MaherAlbitar (2007). Monoclonal antibodies. Humana press 3. Gary Howard and Matthew Kaser (2006). Making and using antibodies. A practical handbook. CRC 4. A practical guide to monoclonal antibodies. Eryl Liddell & A. Cryer (1995), John Wiley

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Course: Field Training (BT399) Semester: Summer Course Coordinator: Department Head Lecturer: Department Head and others Language: English/Arabic Assignment in Curriculum Compulsory Course in Summer Semester of the third year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Training: 180 30 Sum 180 30

Total Sum: 210 hours

Credits 7 ECTS Prerequisites according to Passing 90 credit hours examination regulations: Recommendations: Passing compulsory course in the first, second and third academic year

Course Description The students will experience working in a real laboratory settings. The department contacts certain private and public sectors in order to secure training positions in specialized areas such as: hospitals, forensic labs, food industries, environment labs control, private and governmental labs and research labs. The duration of such training will be 8 weeks. A faculty member is assigned to the students, visits them while training and arranges for lectures and seminars for them.

Learning outcomes: Having finished the course Lab training, students will be able to: 1. Apply theoretical knowledge in real life settings such as in hospitals, diagnostic labs, forensic labs, food industries and environment labs control. 2. Apply the laboratory skills they learnt at University in real setting and make necessary adjustments in laboratory protocols

Summary indicative content: Practical training in specialized places such as: hospitals, private and the government diagnostic labs, research centers, forensic labs, environmental labs, food and drug inspection labs, cancer centers

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Training places inside Jordan: Princess Haya Biotechnology Center KAUH diagnostic laboratories Royal Medical Services diagnostic laboratories Ministry of Health diagnostic laboratories Cell Therapy Center Private Sector IVF units King Hussein Cancer Center Private Pharmaceutical companies Diabetes and Endocrinology Center

Assessment: The final mark of the course consists of: Pass/Fail grade: Pass grade after the completion of training and upon receiving an evaluation form from the training supervisor . Teaching style: Lab training: demonstrations, supervision and training by supervisors.

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Course: Animal Biotechnology (BT411)

Semester: 2nd Semester Course Coordinator: Dr. Ahmed Elbetieha Lecturer: Dr. Ahmed Elbetieha Language: English Assignment in Curriculum Compulsory Course in 2nd Semester of the fourth year Course Units/Credit hours Lecture: 2 credit hours

Students workload: Contact hours Private study Lecture: 26 52 Presentation: 2 6 Exams: 4 20 Sum 32 88

Total Sum: 120 hours

Credits 4 ECTS Prerequisites according to Basic Biotechnology examination regulations: Recommendations: Passing the Basic Biotechnology course in the first academic year

Course Description The course Animal Biotechnology is devoted to the study of transgenic animals, cloning, stem cells and their applications. In addition, the course covers assisted reproductive technology (ART) and their applications. Furthermore, it also covers embryo splitting and embryo fusion techniques and their application in farm animals

Learning outcomes: Having finished he course lectures, students will be able to: 1. Understanding the concept of transgenic animals and their applications 2. Acquiring the knowledge about cloning and stem cells and their applications 3. Understand the assisted reproductive technology and its application in animals

Having finishing the group project, students will be able to organize group work and Implement team and communication skills.

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Summary indicative content: Animal Biotechnology & Transgenic Animals DNA microinjection method Retrovirus vector (RNA virus) method Engineered embryonic stem cell method Transfer of diploid somatic nuclei Mitochondrial transgenesis

Development and use of transgenic animals (Applications) Transgenic mice Transgenic sheep, goats and pigs Transgenic cattle Transgenic birds and fish

Transgenic animals as bioreactors (recombinant proteins) Production of human proteins Xenotransplantation, animal organs for human patients Altering components of milk such as removing lactose Genetically Engineered hormones and vaccines

Cloning: Embryonic cloning Therapeutic cloning Nuclear transfer cloning (Adult cloning) Applications Ethics of cloning

Embryo Fusion and chimera production

Stem Cells Definition of stem cells Types of stem cells (totipotant, pluripotant, multipotant) Source of stem cells (adult ,fetal, and embryonic) Parthenotes as a source of stem cells (Haploid and diploid parthenotes)

Stem cells therapies Neurogenerative diseases: Parkinson's Disease, Alzheimer Disease, Spinal Cord Injury and other brain syndromes Tissue System Failures; Diabetes (Types 1 and 2), Cardiomyopathy, Kidney failure, cancer and hemophilia

Cancer stem cells

Assisted reproductive technology In vitro fertilization and embryo transfer Hormonal control of reproduction Benefits of IVF Procedure of IVF Intracytoplasmic sperm injection (ICSI) Gamete intra-fallopian injection (GIFT) Zygotic intra-fallopian transfer (ZIFT)

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Assessment: The final mark of the course consists of: 1. Written exams: a. First exam (25% of the final mark): composed of MCQ, Tru/eFalse, Blank filling and short answer essay questions. b. Second exam (25% of the final mark): composed of MCQ , Tru/eFalse, Blank filling and short answer essay questions. c. Final exam (40% of the final mark): composed of MCQ , Tru/eFalse, Blank filling and short answer essay questions 2. Group Project (10%): students should be able to pick a recent topic in animal biotechnology and present it in the class

Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard

Indicative Bibliography/Sources: 1. Biotechnology, an Introduction, Second Edition by Susan R. Barnum, Brooks/Cole Thomson, 2005 2. Transgenic Mammals by John Bishop, Pearson Education Limited 1999

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Course: Plant Biotechnology (BT421) Semester: 2nd Semester Course Coordinator: Dr. Nisreen AL-Quraan Lecturer: Dr. Nisreen AL-Quraan / Laila Ababneh Language: English Assignment in Curriculum Compulsory Course in 2nd Semester of the Fourth year Course Units/Credit hours Lecture: 2 credit hours Practical: 1 credit hour

Students workload: Contact hours Private study Lecture: 28 70 Lab sessions: 39 13 Exams: 6 24 Sum 73 107

Total Sum: 180 hours

Credits 6 ECTS Prerequisites according to Basic Biotechnology examination regulations: Recommendations: Passing the basic biotechnology course in the second academic year Passing the Biochemistry class in the third academic year

Course Description Lectures: This course will include lectures and labs that will introduce you to the field of plant biotechnology, modifications and use of plants for agriculture. You will learn basic techniques of recombinant DNA technology, modern protocols of plant transgenesis including transformation and regeneration, Plant genetics, selection and crossing of Arabidopsis thaliana as well as plant anatomy and development, plant hormones, recent plant molecular technology, plant stress physiology, plant pathology and pest interactions. Since plant biotechnology is a broad subject, you will be provided with Chapters from various books and review articles by the instructor covering the course materials. You are indebted to read those materials and everything in their contents will be open for the exams during the semester. Lab work: The lab exercises/experiments is designed to provide knowledge and understanding of plant biotechnology, the basic principles and application of tissue, cell and protoplast culture, recombinant DNA technology, genetic transformation of plants and their application to

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plant improvement and gain experience with tissue culture methodologies, recombinant DNA technology and genetic transformation techniques. Learning outcomes: Having finished the course lectures and Lab work, students will be able to: 1. Know and describe the Plant Tissue culture media components, Plant structure, growth and development and Plant hormones. 2. Describe and discuss the process of Photosynthesis, Agrobacterium tumefaciens and gene transfer, Plasmid as a vector in plant transformation and Direct DNA transfer, and Plant Transposable elements. 3. Describe and explain the plant RNAi gene function, Plant as Chemical and Pharmacological Factories, Plant and Stress Physiology, Plant Molecular Mechanism of Disease and pest resistance and Plant Model organism (Arabidopsis thaliana). 4. Provide knowledge and understanding of basic principles and application of plant tissue culture methodology, plants cell and protoplast culture, plants recombinant DNA technology and genetic transformation techniques and their application to plant improvement. 5. Summary indicative content: Lecture topics:

Plant Tissue culture media component: plant tissue culture media and its types, constituents, preparation and selection of a suitable medium, Macronutrients, Micronutrients, Carbon source and growth regulators.

Plant structure, growth and development: Organization consist of organs, tissues and cells, different meristems generate new cells for primary and secondary growth, primary growth lengthens roots and shoots, secondary growth increases the diameter of stems and roots in woody plants, growth, morphogenesis, and cell differentiation produce the plant body.

Photosynthesis: Photosynthesis converts light energy to the chemical energy of food, The light reactions convert solar energy to the chemical energy of ATP and NADPH, The Calvin cycle uses the chemical energy of ATP and NADPH to reduce CO2 to sugar, Alternative mechanisms of carbon fixation have evolved in hot, arid climates.

Agrobacterium tumefaciens and gene transfer: Updated information of mechanisms for T-DNA transfer to plant cells by Agrobacterium tumefaciens is provided, focused on the role played by the different components of the virulence system and the general assessments for the establishment of efficient transformation protocols to generate transgenic plants.

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Plasmid as a vector in plant transformation and Direct DNA transfer: Direct and indirect genes transferred to plants, plant genes and their regulation, how elegantly transgenic plants and reporter genes have been applied to study plant development, how efficiently transient expression systems have been used to study gene regulation, how much progress has been achieved in the application of gene technology to the improvement of crop plants,

Transposable elements: Plant Overview: General Features of Transposable Elements, Transposons in Plants, Mutant Kernel Phenotypes, Characteristics of McClintock's Elements, Molecular Analysis of Plant Transposons, Ac and Ds, Mu/MuDR (Mutator), Retro-transposons,Control of Transposons and the Biological Significance of Transposons.

RNAi for revealing and engineering plant gene functions: RNAi Overview, The discovery of RNA interference, miRNAs in plants, RNA-Mediated Gene Silencing, siRNA and Heterochromatin formation, Delivering RNAi to the cell and Advantage of RNAi to determine plant gene function.

Plant as Chemical and Pharmacological Factories: Harvesting chemical diversity, Green plants replace chemical plants, Benefits of using plants to produce chemical, Gene manipulation of crop plants to produce specialty chemicals and permits production of biologically based molecules and compounds , Potential impacts of large-scale chemical production in temperate and tropical crops, Specially chemicals and pharmaceutical can be produced in plants and Factories of the future: Transgenic biotechnology.

Plant and Stress Physiology: Gravity, Mechanical stimuli, Environmental stresses, Salt stress, Drought, Flooding, Heat stress, Cold stress and Plants respond to attacks by pathogens and herbivores.

Plant Molecular Mechanism of Disease and pest resistance: Plant pathogens, Pseudomonas syringae pv. Tomato, Plant Molecular responses to pathogen, Hypersensitive Response, Molecular Interaction between Plant and Pathogens, Resistance Mechanisms of Plant Genotype to Pathogens attack, Resistance of plant to pests: Cyanogenesis.

Model organisms: Arabidopsis thaliana: Arabidopsis thaliana; a model plant for Genome analysis.

Lab work/Lab exercise:

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Week 1: Lab safety and biotech regulations, Lab notebook notation/preparation and Regulation and managements of Plant Biotechnology lab. Week 2: Stock Solution preparation for culture media preparation and sterile techniques.

Week 3: Media preparation: MS hormone free medium, Shooting medium (MS + 0.5mg/L GA3 + 2mg/L BA + 0.3mg/L IBA), Rooting medium (MS + 0.5mg/L GA3 + 2mg/L IAA), Callus medium ( A- MS + 0.5mg/L GA3 + 0.5mg/L 2,4-D, B- MS + 0.5mg/L GA3 + 2mg/L BA+ 0.5mg/L IAA), and Water agar medium.

Week 4: Chickpea seed surface sterilization and inoculation on water agar medium

Week 5: Chickpea micropropagation using nodal fragmentation: A- Multishoot induction (proliferation), B-Root Induction.

Week 6: Chickpea Callogenesis using different explants on callus medium

Week 7: Lab Midterm Exam

Week 8: Chickpea protoplast isolation and culturing.

Week 9: Transformation of carrot slices with Agrobacterium tumefaciens

Week 10: DNA extraction from plant tissues

Week 11: Ti-plasmid isolation using Alkaline method

Week 12: Agarose gel electrophoresis for Plant DNA and Ti plasmid Week 13: Lab final Report discussion and materials Review

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MCQ and short answer essay questions to the content of the Lab exercises. e. Lab Final exam (10% of the final mark): composed of MCQ and short answer essay questions to the content of the Lab exercises. f. Lab Quizzes (5% of the final mark): 5 quizzes composed of MCQ questions to the content of the Lab exercises.

2. Lab report (5% of the final mark): scientific report written by the student’s lab working group about the lab exercises results.

Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard Lab exercises: running laboratory-based experimentation

Indicative Bibliography/Sources: Lectures: 1. Plant Biotechnology, Ricroch et al. Springer, 2014. 2. Biology; Campbell and Reece, 11th edition, Pearson, 2017. 3. Plants, Genes and Crop Biotechnology; Chrispeels and Sadava, 2nd edition, 2004. 4. Review articles from various Plant Biology international Journals (6 Reviews). Lab exercises: 1. Trigiano, R.N. and Gray, D.J. 2000. Plant Development and Biotechnology. CRC Press 2. Slater, A., N. Scott, M. Fowler (2008) Plant biotechnology. Oxford Univ. Press 3. Stewart, C.N. Jr. (2008). Plant Biotechnology and Genetics: Principles, Techniques and applications. 4. Trigiano, R.N., D.J. Gray (Eds) 2010. Plant tissue culture, development and biotechnology. CRC Press.

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Course: Microbial Biotechnology (BT431)

Semester: 2ndSemester Course Coordinator: Dr. Abdul-KarimJ.Al-Sallal Lecturer: Dr. Abdul-KarimJ.Al-Sallal Language: English Assignment in Curriculum Compulsory Course in 2nd Semester of the third year Course Units/Credit hours Lecture: 2 credit hours Practical: 1 credit hour

Students workload: Contact hours Private study Lecture: 28 56 Practical 39 12 Reports: 0 20 Exams & Quizzes: 5 20 Sum 72 108

Total Sum: 180 hours

Credits 6 ECTS Prerequisites according to General Microbiology (B231) examination regulations: Recommendations: Passing the general microbiology course in the second academic year

Course Description This course traces the development of modern biotechnology from its origins in traditional fermentation processes to strain selection and development of recombinant microbes for industrial applications. Industrial microorganisms, substrate for industrial fermentation, methods of fermentation, product recovery, cell immobilization, and commercial exploitation of industrial microorganisms to produce beer, wine, organic acids, amino acids, enzymes, vitamins, antibiotics and single cell protein will be emphasized.

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Learning outcomes: 1. Know that food provide an ideal environment for microbial survival and growth: so it could be a source of diseases OR a medium to grow industrial microorganisms 2. Know the intrinsic and extrinsic factors affecting the growth of microorganisms for either fermentation processes OR environment 3. To understand how the microorganisms spoil food, pharmaceutical products OR any other material and HOW to preserve them 4. To understand the main principles of initiating a microbiological industry 5. To understand the role of microorganisms in food and pharmaceutical industries 6. Familiarized the student with the industrial application of microorganism such as enzymes, antibiotics production, bioremediation etc.

Summary indicative content: Food as a substrate for microorganisms To know the different types of substrates(raw material) which can be used to feed in certain selected types of microorganisms (industries),the mechanisms of nutrient uptake and the different metabolic pathways which lead to the production of valuable metabolites or products.

Factors affecting the growth of microorganisms in food intrinsic and extrinsic: effect of pH, moisture and nutrient content, temperature, oxygen requirements.

Substrate contamination, spoilage and preservation To know the causes of spoilage, especially the growth and activities of microorganisms beside the other causes of spoilage. To know the different methods of preservation: using high and low temperature, water activity and osmosis, filtration and radiation. Food infection and food intoxication.

Microbiology of fermented food. Dairy, bread, Alcoholic beverages. To know the types of nutrients used for the production of these products and the positive and negative factors influencing the rate of production.

Role of microbiology in: Human therapeutics-production of different drugs, Agriculture-to improve the quality and quantity of products

Wastewater treatment and Hazardous waste management. To know the different treatment processes, the advantages and disadvantages of each process.

Microorganisms and single cell protein production Importance and applications.

Microbial enzymes Their medical and environmental applications

Microbial production of organic acids, e.g. citric acid

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Biodegradation, Biodeterioration, Bioremediation Their roles in industrial and environmental applications.

Assessment: The final mark of the course consists of: 1. Written exams: a. First exam (20% of the final mark): composed of MCQ and short answer essay questions to the content of the lectures. b. Second exam (20% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. c. Final exam (30% of the final mark): composed of MCQ and short answer essay questions to the content of the lectures d. Lab Midterm exam (8% of the final mark): composed of MCQ and short answer essay questions to the content of the Lab exercises. e. Lab Final exam (10% of the final mark): composed of MCQ and short answer essay questions to the content of the Lab exercises. f. Lab Quizzes (5% of the final mark): 5 quizzes composed of MCQ questions to the content of the Lab exercises.

2. Lab report (7% of the final mark): scientific report written by the student’s lab working group about the lab exercises results.

Teaching style: Lecture: Projector, e-learning, power point presentations and white board

Indicative Bibliography/Sources: 1. Prescott, L. M, Harley,J.P.andKlein,D.A. ( 2017).Microbiology. McGraw-Hill Company. 2. Glazer, A.N. and Nikaido, H.(2007).Microbial Biotechnology Freeman Company.

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Course: Human Genetics (BT441) Semester: 1st Semester Course Coordinator: Dr. Asem Alkhateeb Lecturer: Dr. Asem Alkhateeb Language: English Assignment in Curriculum Compulsory Course in 1st Semester of the fourth year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 84 Exams: 4 20 Sum 46 104

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to Molecular Genetics examination regulations: Recommendations: Passing the Genetics course in the third academic year Course Description The course covers topics in human genetics such as human genetic diseases, mapping the human genome; the molecular analysis of single gene disorders; the genetic analysis of complex diseases; gene therapy, gene testing; the human genome project; human population genetics and evolution; DNA fingerprinting; human genetics and society.

Learning outcomes: 1. Describe the organization of the human genome and explain the molecular mechanisms that contribute to genetic variation and gene mutations 2. Explain the chromosomal and molecular basis for simple and complex genetic disease in individuals and populations 3. Use mapping and sequencing analysis to predict the genetic basis for a disease and the risk of inheritance 4. Understand the molecular, biochemical, and cellular basis of genetic disease

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Summary indicative content: • Gene structure & function • Information content of the human genome • The central dogma: DNA>RNA>Protein • Gene organization and structure • Fundamentals of gene expression • Gene expression in action • Epigenetic and epigenomic aspects of gene expression • Gene expression as the integration of genomic and epigenomic signals • Allelic imbalance in gene expression • Variation in gene expression and its relevance in medicine • • Mutation & Polymorphism • The nature of genetic variation • Inherited variation and polymorphism in DNA • The origin and frequency of different types of mutations • Types of mutations and their conequences • Variation in individual genomes • Impact of mutation and polymorphism • • Cytogenetics & Genome analysis • Introduction to cytogenetics and genome analysis • Chromosome abnormalities • • Patterns of Single-Gene Inheritance • Overview and concepts • Pedigrees • Mendelian inheritance • Autosomal patterns of Mendelian inheritance • X-linked inheritance • Pseudoautosomal inheritance • Mosaicism • Parent-of-origin effects on inheritance patterns • Dynamic mutations: Unstable repeat expansions • Maternal inheritance of disorders caused by mutations in the mitochondrial genome • Correlating genotype and phenotype • Importance of the family history in medical practice • • Complex Inheritance of common Multifactorial disorders • Qualitative and quantitative traits • Familial aggregation and correlation • Determining the relative contributions of gene and environment to complex disease • Examples of common multifactorial diseases with a genetic contribution • Examples of Multifactorial traits for which specific genetic and environmental factors are known • The challenge of multifactorial disease with complex inheritance • • Genetic variation in populations • Genotypes and phenotypes in populations • Factors that disturb Hardy-Weinberg equilibrium • Ethnic difference in the frequency of various genetic disease • Genetics and ancestry •

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• Identifying the Genetic Basis of Human Disease • Genetic basis for linkage analysis and association • Mapping human disease genes • From gene mapping to gene identification • Finding genes responsible for disease by genome sequencing • • Molecular Basis of Genetic Disease-Hemoglobinopathies • The effect of mutation on protein function • How mutations disrupt the formation of biologically normal proteins • The relationship between genotype and phenotype in genetic disease • The hemoglobins • The hemoglobinopathies • • Molecular, Biochemical, & Cellular Basis of Genetic Disease • Diseases due to mutation in different classes of proteins • Diseases involving enzymes • Defects in receptor proteins • Transport defects • Disorders of structural proteins • Neurodegenerative disorders • • Developmental Genetics & Birth Defects • Developmental biology in medicine • Introduction to developmental biology • Genes and environment in development • Basic concepts of developmental biology • Cellular and molecular mechanisms in development • Interaction of developmental mechanisms in embryogenesis

Assessment: The final mark of the course consists of: 1. Written exams: a. First exam (30% of the final mark) composed of MCQ or short answer essay questions to the content of the lecture. b. Second exam (30% of the final mark): composed of MCQ or short answer essay questions to the content of the lecture. c. Final exam (40% of the final mark): composed of MCQ questions to the content of the lecture.

Teaching style: Lecture: Projector, e-learning, power point presentations and white board

Indicative Bibliography/Sources: Genetics in Medicine. Nassbaum, McInnes and Willard. 8th ed. 2016

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Course: Molecular Biology I (BIO451) Semester: 1st Semester Course Coordinator: Dr. Nisreen AL-Quraan Lecturer: Dr. Nisreen AL-Quraan Language: English Assignment in Curriculum Compulsory Course in 1st Semester of the fourth year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 73 Exams & Quizzes: 5 30 Sum 47 103

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to General Biology 2, Biochemistry examination regulations: Recommendations: Passing the general biology course in the first academic year Passing the Biochemistry class in the third academic year

Course Description The course aims to provide the student with a comprehensive overview of the basic Molecular Biology in terms of DNA structure, DNA replication, Chromosomal basis of inheritance, mutation and repair of DNA, Recombination and transpostion, mechanism of transcription, and introduction to the basic techniques in molecular biology and Model organisms genomes.

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Learning outcomes: Having finished the course lectures presentations and quizzes, students will be able to: 1. Know and describe the complete structures and the chemistry of DNA/RNA components, DNA topology, the histone and nonhistone components of chromatin, copying mechanism in detail and the enzymes that synthesize DNA and the complex molecular machines that allow both strands of the DNA to be replicated simultaneously. 2. Describe and discuss the mechanisms by which DNA can be damaged, the molecular mechanisms by which protein complexes repair or bypass different forms of DNA damage and provide examples of how homologous recombination is used to ensure genome stability and promote genetic diversity.. 3. Define and explain how endogenous biological processes like site-specific recombination, transposition, and V(D)J recombination system are being used to modify eukaryotic genomes. 4. Trace the process of transcription by which nucleotide sequence information is transferred from DNA to RNA, flow of information from the copying of the gene into an mRNA in prokaryotes and eukaryotes. 5. Describe and understand many of the fundamental techniques of molecular biology that are widely used in studying nucleic acids and proteins and understand the important feature of various model organisms that can be manipulated and studied genetically with the use of the many traditional and new powerful tools of molecular biology. 6. Demonstrate the effective reading and critical thinking in this course in term of short answer questions after the finish of each chapter.

Summary indicative content: Lecture

The Structure of DNA and RNA • DNA structure • DNA topology • RNA structure • Chromosomes, chromatin, and nucleosome Chromosome sequence and diversity Chromosome Duplication and segregation The Nucleosome High order chromatin structure Regulation of Chromatin Structure Nucleosome Assembly

The Replication of DNA • The Chemistry of DNA synthesis • The mechanism of DNA polymerase

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• The Replication fork • The specialization of DNA polymerases • DNA synthesis at the replication fork • Initiation of DNA replication • Binding and Unwinding in DNA replication • Finishing Replication

The Mutability and Repair of DNA Replication Errors and Their Repair • DNA damage • Repair of DNA damage

Homologous Recombination at the Molecular Level • Models for homologous recombination • Homologous recombination protein machines • Homologous recombination in Eukaryotes • Mating type switching

Site-Specific Recombination and Transposition of DNA Conservative Site-Specific Recombination • Biological Roles of Site-Specific Recombination • Transposition • Examples of Transposable Elements and Their Regulation • V(D)J Recombination

Mechanism of Transcription RNA polymerase and transcription cycle • The Transcription Cycle in bacteria • Transcription in Eukaryotes

Techniques of Molecular Biology • Nucleic Acids Techniques • DNA labeling and sequencing • Proteins Techniques

Model Organisms • Caenorhabditis elegans (C.elegans); Drosophila melanogaster • Xenopus Laevis; Mus Musculu; Arabidopsis thaliana • Bacillus subtilis, Mycoplasma, Escherichia coli (E.coli) • M. jannaschii; Saccharomyce cerevisiae; Fugu rubripes Assessment: The final mark of the course consists of: 1. Written exams: a. First exam (25% of the final mark): composed of MCQ and short answer essay questions to the content of the lectures. b. Second exam (25% of the final mark): composed of MCQ and short answer essay questions to the content of the lectures. c. Final exam (40% of the final mark): composed of MCQ and short answer essay questions to the content of the lectures. 2. Quizzes (10% of the final mark): 9 quizzes composed of MCQ questions (quiz after finishing each chapter).

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Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard

Indicative Bibliography/Sources: Molecular Biology of The Gene, James Watson et al., Seventh edition, 2014. Publisher: Cold Spring Harbor Laboratory Press, USA

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Course: Molecular Biology Laboratory (BIO453) Semester: 1st Semester Course Coordinator: Dr. Nisreen AL-Quraan Lecturer: Ms. Rehan BaniHani Language: English Assignment in Curriculum Compulsory Course in 1st Semester of the fourth year Course Units/Credit hours Lecture: 1 credit hours Students workload: Contact hours Private study Lab Lecture: 36 24 Lab Reports: 0 6 Exams & Quizzes: 4 20 Sum 40 50

Total Sum: 90 hours

Credits 4 ECTS Prerequisites according to General Biology 2, Molecular Biology I examination regulations: Recommendations: Passing the general biology course in the first academic year Passing the Molecular biology I course in the fourth academic year

Course Description Students will learn principles and practice of basic bacterial culture techniques, Agarose gel electrophoresis, nucleic acid purification (plasmid and genomic DNA, RNA), nucleic acid quantification, DNA restriction digestion and analysis, polymerase chain reaction (PCR), and basics computer-based DNA sequence analysis and data acquisition over the internet. In addition, students will learn about the nature and selection of DNA cloning vectors, restriction enzymes and other reagents used in molecular biology techniques.

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Learning outcomes: Having finished the course Lab lectures/exercises, students will be able to: 1. Know, List and explain safety issues and proper practices associated with standard molecular techniques, including bacterial culture, electrophoresis, and nucleic acid purification. 2. Explain, demonstrate and practice principles of sterile technique and DNA and RNA purification and quantification 3. Understand and explain many types of PCR techniques and its application and the troubleshooting in PCR protocol. 4. Use and explain the application of various standard bioinformatics techniques to experimental planning and analysis, including sequence accessing and manipulation, restriction endonucleases, multiple sequence alignment and PCR primers design. 5. Independently plan, execute and document a basic DNA cloning experiment involving PCR amplification, cloning into an appropriate DNA vector, plasmid DNA isolation, DNA sequencing and restriction enzyme analysis with agarose gel electrophoresis to evaluate success of the procedure in total.

Summary indicative content: Lab1: Introduction: lab rules and biosafety Lab2: DNA Isolation I Lab3: DNA Isolation II &Plasmid Isolation Lab4: RNA Isolation Lab5: Gel Electrophoresis & DNA Quantitation Lab6: Polymerase Chain Reaction I Lab7: Polymerase Chain Reaction II Lab8: Restriction Endonucleases Lab9: Primer Design + SNP Genotyping By RFLP Lab10: DNA Sequencing I Lab11: DNA Sequencing II Lab12: Transformations & Cloning

Assessment: The final mark of the course consists of: 1. Written exams: a. Lab Midterm exam (30% of the final mark): composed of MCQ and short answer essay and problem-solving questions to the content of the Lab exercises. b. Lab Final exam (40% of the final mark): composed of MCQ and short answer essay and problem-solving questions to the content of the Lab exercises. c. Lab Quizzes (10% of the final mark): composed of MCQ to the content of the Lab exercises 2. Lab practical (15% of the final mark): composed of problem- solving tasks and group discussion related to the lab exercise.

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3. Lab participation (5% of the final mark): evaluation of student attendance, running the experiment and cleaning the experiment working area after finishing the lab exercise.

Teaching style: Lecture: Projector, e-learning, power point presentations and white board Lab exercises: running laboratory-based experimentation

Indicative Bibliography/Sources: Stefan Surzycki. 2008. Human Molecular Biology Laboratory Manual. 2nd ed. Blackwell Publication

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Course: Molecular Biology II (BIO454)

Semester: 2nd Semester Course Coordinator: Dr. Nisreen AL-Quraan Lecturer: Dr. Nisreen AL-Quraan Language: English

Assignment in Curriculum Compulsory Course in 2 nd Semester of the fourth year Course Units/Credit hours Lecture: 2 credit hours Students workload: Contact hours Private study Lecture: 26 52 Quizzes: 1 16 Exams: 4 20 Sum 32 88

Total Sum: 120 hours

Credits 4 ECTS Prerequisites according to Molecular Biology I and Molecular Biology Laboratory examination regulations: Recommendations: Passing the Molecular Biology, I course in the fourth academic year Passing the Molecular Biology Laboratory course in the fourth academic year Course Description The course aims to provide the student with a comprehensive overview of the basic Molecular Biology in terms of RNA splicing, Translation, Genetic Code, Regulation of gene expression in prokaryotes, Regulation of gene expression in eukaryotes and RNA regulation role in biological processes.

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Learning outcomes: Having finished the course lectures and quizzes, students will be able to: 1. Know and describe the chemistry of RNA spicing and mRNA transport, the Ribosome, Initiation of Translation, Translation Elongation, and Termination of Translation. 2. Describe and discuss the degeneracy of Genetic code, roles Govern the Genetic Code, Gene expression regulation in prokaryotes and the layers of regulation in Bacteriophage . 3. Describe and explain the gene regulation in Eukaryotes, Signal integration and combinatorial control, Transcriptional repressor & signal transduction, Epigenetic and Gene silencing regulation. 4. Trace the process of Regulation by RNA in bacteria, RNA interference as a regulatory mechanism in Eukaryotes, and explain RNA world, Self-replicating Ribozymes and protocells and Early Evolution of Life. 5. Demonstrate the effective reading and critical thinking in this course in term of short answer questions after the finish of each chapter. 6. Summary indicative content: Lecture

• RNA Splicing The Chemistry of Splicing, The Spliceosome Machinery, Splicing Pathways, Alternative Splicing, Exon Shuffling, RNA Editing, and mRNA Transport.

• Translation Attachment of Amino Acids to tRNA, The Ribosome, Initiation of Translation, Translation Elongation, and Termination of Translation.

• The Genetic Code The code is Degenerate, Three roles Govern the Genetic Code, Suppressor mutations can reside in the same or different gene, and The Code is nearly Universal.

• Gene regulation in Prokaryotes Principles of transcriptional regulation, Regulation of transcription initiation: examples from prokaryotes, and The case of Bacteriophage : Layers of regulation.

• Gene regulation in Eukaryotes Conserved mechanisms of transcriptional regulation, Recruitment of protein complexes to genes, Signal integration and combinatorial control, Transcriptional repressor & signal transduction, and Gene silencing and epigenetic gene regulation.

• Regulatory RNA Regulation by RNA in bacteria and RNA interference as a regulatory mechanism in Eukaryotes.

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• The Origin and Early Evolution of Life Life history, RNA world, Self-replicating Ribozymes and protocells.

Assessment: The final mark of the course consists of: 1. Written exams: a. First exam (25% of the final mark): composed of MCQ and short answer essay questions to the content of the lectures. b. Second exam (25% of the final mark): composed of MCQ and short answer essay questions to the content of the lectures. c. Final exam (40% of the final mark): composed of MCQ and short answer essay questions to the content of the lectures. 2. Quizzes (10% of the final mark): 7 quizzes composed of MCQ questions (quiz after finishing each chapter).

Teaching style: Lecture: Projector, e-learning, power point presentations and white board Indicative Bibliography/Sources: Molecular Biology of The Gene, James Watson et al., Seventh edition, 2014. Publisher: Cold Spring Harbor Laboratory Press, USA

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Course: Cytogenetics (BT456) Semester: 2nd Semester Course Coordinator: Dr. Asem Alkhateeb Lecturer: Dr. Asem Alkhateeb and Ms. Enas Al-Satari Language: English Assignment in Curriculum Compulsory Course in 2nd Semester of the fourth year Course Units/Credit hours Lecture: 2 credit hours & Laboratory 1 credit hour Students workload: Contact hours Private study Lecture: 28 28 Laboratory work: 45 45 Exams & Quizzes: 8 26 Sum 81 99

Total Sum: 180 hours

Credits 6 ECTS Prerequisites according to Human Genetics examination regulations: Recommendations: Passing the Human Genetics course in the fourth academic year Course Description The major goal of this course will be to introduce all students to the basic principles of cytogenetics as they apply to basic and clinical genetics. The focus of the course will include chromosome structure and function, the underlying features of cytogenetic disorders, as well as the common numerical and structural abnormalities involved in the diagnosis and evaluation of patients with a likely cytogenetic disorder.

Learning outcomes: 1. Describe the structure of the chromosome, karyotyping, banding patterns, other cytogenetic tools, and consequences of chromosome pathology 2. Understand principles and consequences of chromosome translocations, insertions, and inversions 3. Explain mechanisms and effects of aneuploidy, polyploidy, deletions, and duplications of the chromosomal material on human health 4. Obtain hands-on experience with chromosome analysis techniques in Laboratory

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Summary indicative content: Elements of medical cytogenetics Chromosomal morphology Chromosomal structure Chromosome abnormality Autosomal imbalance Sex chromosomal abnormality Functional imbalance The frequency and impact of cytogenetic pathology

Chromosome analysis Classic cytogenetic analysis Microarray analysis Next generation sequencing

Origins and consequences of chromosome pathology Meiosis in chromosomally normal persons Malsegregation and nondisjunction in meiosis Meiosis in chromosomally abnormal persons Nondisjunction in mitosis and the generation of mosaicism Detecting mosaicism Structural rearrangement Microdeletions and microduplications of incomplete penetrance and variable expressivity Epigenetics and genomic imprinting Consequences of genetic abnromality

Autosomal reciprocal translocations Modes of segregation Prediction segregant outcomes

Sex chromosome translocations The X-autosome translocation Details of meiotic behavior: female meiosis, male meiosis Y-autosome translocations X-Y translocations

Robertsonian translocations Formation of the translocation The heterologous robertsonian translocation The homologous robertsonian translocation

Insertions The interchromosomal insertion The intrachromosomal insertion

Inversions The pericentric inversion The paracentric inversion

Down syndrome, aneuploidy, polyploidy Autosomal trisomy Polyploidy The influence of parental age in predisposing to aneuploidy

Autosomal deletions & duplications Mechanisms of formation of structural rearrangement

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Deletion Duplication

Uniparental disomy and disorders of imprinting Epigenetics and imprinting Uniparental disomy for a complete chromosome Uniparental disomy phenotypes

Reproductive failure Gametic cytogenetics Cytogenetics of the preimplantation, embryonic, and early fetal period Cytogenetics of very early pregnancy loss Cytogenetics of spontaneous abortion and later pregnancy loss

Prenatal testing procedures Prenatal laboratory diagnostic procedures Prenatal diagnostic clinical procedures Screening for fetal trisomy Secular trends in prenatal screening and diagnosis of aneuploidy Fetal ultrasonographic anomalies

Preimplantation genetic diagnosis Patients and circumstances in which chromosomal preimplantation genetic diagnosis may be appropriate Embryology procedures

Assessment: The final mark of the course consists of: 1. Written exams: a. First exam (20% of the final mark) composed of MCQ or short answer essay questions to the content of the lecture. b. Second exam (20% of the final mark): composed of MCQ or short answer essay questions to the content of the lecture. c. Mid-term exam (10% of the final mark) composed of MCQs or short answer essay questions to the content of the laboratory d. Final laboratory exam (10% of the final mark) composed of MCQs or short answer essay questions to the content of the laboratory e. Final exam (30% of the final mark): composed of MCQ questions to the content of the lecture. 2. Lab reports and Quizzes (10% of the final mark): 10 quizzes composed of MCQ questions.

Teaching style: Lecture: Projector, e-learning, power point presentations and white board Laboratory: demonstration, hands-on experiments, open lab assignments

Indicative Bibliography/Sources: Chromosome Abnormalities and Genetic Counseling. Gardner and Amor. 5th ed. 2018.

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Course: Seminar (BT491) Semester: 1st / 2nd Semester Course Coordinator: Dr. Qutaiba Ababneh Lecturer: Dr. Qutaiba Ababneh and others Language: English Assignment in Curriculum Compulsory Course in 2nd Semester of the fourth year Course Units/Credit hours Lecture: 1 credit hour Students workload: Contact hours Private study Lecture: 14 16 Sum 81 99

Total Sum: 30 hours

Credits 1 ECTS Prerequisites according to None examination regulations: Recommendations: Passing all compulsory courses Course Description A one-credit seminar course designed for senior biotechnology & genetic engineering students to develop skills in conducting scientific research, scientific writing, public scientific presentation as well as in preparation for job seeking.

Learning outcomes: 1. Search the scientific literature in order to choose a topic of interest. 2. Write an effective cv/resume. 3. Organize and orally communicate scientific information in a logical and effective manner. 4. Critically read and summarize science research articles. 5. Search the scientific literature in order to choose a topic of interest

Summary indicative content: Course introduction, organization and syllabus

How to find and read a Primary Research Paper Taxonomy of scientific primary research articles Structure of research articles How to read a primary article (3-pass approach) Searching the literature for primary research article

How to give an Oral Presentation Principles of effective Presentations Tips to develop confidence in presentationsHow to write a

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Structure of a 20 minutes presentation Preparing the presentation (Lists and visuals Presentation styling Common mistakes in oral presentations

Curriculum vitae (CV) Purpose Structure of the CV CV examples Europass CV Cover letter

Presentation practice

Student Presentations

Assessment: The final mark of the course consists of: 1. Assignments: a. CV (10% of the final mark): Students will write and submit their CV’s b. Article summary (10% of the final mark): Students will write a one-page summary of the paper they are presenting. 2. Attendance (10% of the final mark) 3. Presentation Practice with peers (20% of the final mark) 4. Article presentation (50% of the final mark): Students will present a primary research article related to the field of biotechnology & genetic engineering.

Teaching style: Lecture: Projector, e-learning, power point presentations and white board

Indicative Bibliography/Sources: 1. Jones A, Reed R, Weyers J.. 2016. Practical Skills in Biology. 6th edition. Pearson. 2. Alley, M. 2013. The Craft of Scientific Presentations: Critical steps to succeed and critical errors to avoid. 2nd edition. Springer, NY.

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Course: Research Project (BT493) Semester: 1st / 2nd Semester Course Coordinator: Dr. Amjad Mahasneh & Dr. Qutaiba Ababneh Lecturer: Department faculty members Language: English Assignment in Curriculum Compulsory Course in 1st or 2nd Semester of the fourth year Course Units/Credit hours Lecture: 1 credit hour Students workload: Contact hours Private study Lecture: 8 16 Lab work 140 24 Oral presentation 2 20 Sum 150 60

Total Sum: 210 hours

Credits 7 ECTS Prerequisites according to Successful completion of 90 credit hours examination regulations: Recommendations: Passing all compulsory courses Course Description The Department of Biotechnology & Genetic Engineering is committed to providing research experience within the fields of biotechnology and genetics to all students through the BT493 research project course. The course is designed to provide students with direct research experience including aspects of literature search, planning and designing experiments, data collection, analysis, and interpretation. Students will also gain experience in scientific communication by submitting a written final report and defend the results of their research in front of a faculty committee.

Learning outcomes: 1. Demonstrate the use of modern biological research methods to solve a given scientific task. 2. Utilize skills relating to the process of conducting science and apply the scientific method. 3. Apply the basics of experimental design, data collection, data analysis and hypothesis testing 4. Communicate ideas, scientific knowledge and experimental results through written report and oral presentation. 5. Make connections between theoretical and practical knowledge

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Summary indicative content: Examination The research project examination consists of a written research report, a written abstract and an oral presentation. The examination committee sets the course grade after consultation with the project supervisor based on the work performance, the project report and the oral presentation.

Experimental Work The research project is performed by student groups (research group) under the guidance of a supervisor. Experimental work or data collection begins shortly after the beginning of the semester and is completed by two weeks before the start of the final exam to allow adequate time for data analysis and report writing. Each student is expected to spend a minimum of 9 hours per week in the lab for the duration of the project. The quality of the experimental work/data collection is assessed by the project supervisor and is worth 40% of the final grade of the project. Presentation practice

Oral presentation of project Research groups will present and defend the results of their project in an oral presentation during the BioBiotech Research Week, scheduled before the last day of classes. Oral presentations will be 12 minutes followed by a 3-minute question period from the examination committee, who will then assign a mark. The oral presentation and defense of research projects is worth 30% of the final grade of the project.

Roles and Responsibilities

Role of the Student Student are responsible for the following: 1. Develop and enhance information literacy skills 2. Complete the laboratory health and safety training. 3. Set a weekly schedule for lab work. 4. Set appropriate weekly meeting with project supervisor 5. Develop and enhance research skills 6. Develop and enhance professional writing skills. 7. Promote a respectful work environment. 8. Attend and participate in all course workshops 9. Complete all components of the research project: Lab work, Abstract, project report and presentation 10. Submit all paperwork and documentation by designated deadlines 11. Present the project results to the project evaluation committee 12. Understand what scientific plagiarism is and how to avoid it. 13. Be familiar with the course procedures, regulations and timelines

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Role of the Supervisor Supervisor responsibility may include: 1. Be familiar with the course procedures, regulations and timelines 2. Select the project topic 3. Arrange for infrastructure and guidance for the proposed topic. 4. Ensure that projects comply with expectations established for the course 5. Ensure students receive a health and safety training prior to the start of the project 6. Meet with students on a regular basis to discuss the project related issues. 7. Evaluate the performance and work efforts of students for whom they are supervisor 8. Facilitate a smooth integration of students into the existing lab environment.

Examination committee The course coordinator will select the members of each examination committee. A panel of 3 examiners will participate in the evaluation of each presentation during the BioBiotech Research Week. Examiners are expected to: 1. Attend all their assigned presentations. 2. Evaluate the written report 3. Ask questions during presentations. 4. Assign a mark to the presentation, based upon the quality of: a. The quality of presentation. b. The interpretation and collection of data c. The answers to questions.

Course Coordinator(s) The research project course is coordinated by at least one faculty member. The course coordinator(s) is/are responsible for: 1. Assign students to supervisors randomly 2. Collect all submitted course materials and grades 3. Organize workshops about plagiarism, report and presentation preparation, ect. 4. Organizing the BioBiotech Research Week 5. Select the members of each examination committees 6. Coordinate student access to appropriate university resources.

Assessment: 1. Experimental Work (40%) (Evaluator: Supervisor) Evaluation criteria: • Professional integrity • Scientific ability • Time management

2. Abstract & Workshop Attendance (10%) (Evaluator: Supervisor)

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Evaluation criteria: • Clarity of content • Appropriate presentation • Workshop attendance

3. Written report (20%) (Evaluator: Supervisor & Examination Committee) Evaluation criteria: • Clarity of content • Adequacy of literature review • Development of research questions • Completeness of methods • Appropriate presentation and analysis of data • Clarity of data interpretation; • Quality of the written thesis

4. Presentation and Questions (30%) (Evaluator: Examination Committee) Evaluation criteria: • Clarity of content • Research question • Methodology • Interpretation of data • Conclusions • Quality of visual aids • Quality of oral presentation • Ability to answer questions

Teaching style: Lecture: Projector, e-learning, power point presentations and white board

Laboratory: demonstration, hands-on experiments, open lab assignments

Indicative Bibliography/Sources: 1. Practical Skills in Biology, Allan Jones, Rob Reed & Jonathan Weyers. Sixth Edition. Pearson

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Course: Clinical Biochemistry (LM321)

Semester: 1st Semester Course Coordinator: Dr Refat Nimer Lecturer: Dr Refat Nimer Language: English Assignment in Curriculum Elective course where students can take in third year and later Course Units/Credit hours Lecture: 4 credit hours Students workload: Contact hours Private study Lecture: 56 98 Exams: 5 21 Sum 61 119

Total Sum: 180 hours

Credits 6 ECTS Prerequisites according to Biochemistry examination regulations: Recommendations: Passing the Biochemistry courses in the second year Course Description This course is an introduction to general fundamentals and principles of clinical bioanalytical chemistry. It is a combined lecture and laboratory course covering methods of analysis as well as the biochemical components of body fluids. Topics include analysis of blood electrolytes, blood gases, amino acids, plasma enzymes, proteins, carbohydrates, and lipids. Quality control and assurance are also covered in this course.

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Learning outcomes: The students who take this course are expected to: 1. Learn about various biochemical components (electrolytes, trace elements, amino acids, proteins, enzymes, lipids, carbohydrates, and nonprotein nitrogen compounds) in human body fluids, and understand their biochemistry, physiology, and clinical significance. 2. To be able to correctly use of basic equipment and supplies and to achieve an understanding of fundamental concepts critical to any bioanalytical procedure.

3. To learn clinical chemistry procedures that yield accurate and precise information that aid in the patient’s diagnosis. 4. To provide basic information about quality control, quality assurance, and method evaluation. 5. Assess various biochemical analytes of clinical significance

Summary of indicative content: • Introduction to clinical chemistry-basic principles and practice of clinical chemistry • Units of Measure • Laboratory Mathematics and Calculations • Specimen Considerations

• Method Evaluation • Method selection and evaluation, Quality assurance • Reference Interval Studies • Quality control, diagnostic efficiency

• Amino acids • Aminoacidopathies • Amino Acids analysis

• Proteins • Plasma proteins • Total Protein Abnormalities • Methods of Analysis

• Nonprotein Nitrogen Compounds • Creatinine, GFR • Urea • Uric Acid • Ammonia

• Enzymes

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• Plasma enzymes (ALP, ALT, amylase, Lipase, AST, CK, GGT, LDH, Alkaline phosphatase, Acid phosphatase)

• Carbohydrates • Pancreatic function: regulation of blood sugar (hyperglycemia, hypoglycemia) • Diabetes (FBS, RBS,2 hr PP, OGTT, HbA1c, Ketones,Microalbuminuria)

• Lipid profile I (lipoproteins, cholesterol, triglycerides)

• Lipid profile II (lipoproteins, cholesterol, triglycerides)

• Electrolytes • Water: osmolality • Electrolytes (Sodium, Potassium, Chloride, Bicarbonate, Magnesium,Calcium, Phosphate, Lactate) • Electrolyte disorders • Anion Gap • Electrolytes and Renal Function

• Electrolyte disorders (hyperkalemia, hypokalemia) • Calcium (hypocalcemia, hypercalcemia) • Calcium disorders (Osteoporosis, Paget’s disease of bone, osteomalacia)

• Blood Gases, pH, and Buffer Systems • Blood gases, transport of CO2 in the human body and 17 formation of blood buffer. • Acid-base balance • Measurement & Interpretation of Results

• Trace elements; Instrumentation and methods

• Trace element's toxicity

Assessment: 1. Written exams: a. First exam (30% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. b. Second exam (30% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. c. Final exam (40% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture

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Teaching style: Lectures with discussion, Brainstorming, Case studies and Problems solving

Indicative Bibliography/Sources: Clinical Chemistry-Techniques, Principles, Correlations By M. Bishop et al. Publisher Lippincott's Williams and Wilkins. Eighth Edition E, 2018

edition Book website http://thepoint.lww.com

Other references;

Tietz Fundamentals of Clinical Chemistry and Molecular Diagnostics. Carl A, Burtis, David E.Burns. Saunders. 7thOther references Edition 2014

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Course: Diagnostic Bacteriology (BIO334) Semester: 1st / 2nd Semester Course Coordinator: Dr. Homa Darmani Lecturer: Dr. Homa Darmani Language: English Assignment in Curriculum Elective Course in the Fourth year Course Units/Credit hours Lecture: 3 credit hours Practical: 1 credit hour

Students workload: Contact hours Private study Lecture: 42 42 Lab sessions 30 30 Lab reports: 0 10 Exams: 6 20 Sum 78 102

Total Sum: 180 hours

Credits 6 ECTS Prerequisites according to General Biology examination regulations: Recommendations: Passing the Microbiology courses in the second academic year

Course Description Bacteria not only populate the human body by the billions as normal flora but they also participate in our bodily functions whilst others cause disease. In this course, we primarily consider the role of bacteria in the initiation and spread of human diseases and focus on the diagnosis of these illnesses. Identification of the organism causing an infectious process is usually essential for effective antimicrobial and supportive therapy. In this course the student will gain an insight into some common microbial pathogens, the diseases they cause, their modes of pathogenicity, the ways to control them and the steps that are required for definitive microbiologic diagnosis.

Laboratory work: The practical part of this course is designed to give the student a full understanding of the essential laboratory techniques commonly used in the diagnosis of bacterial diseases. The student will gain experience in methods for specimen collection, isolation and identification of different bacterial species including both Gram positive and Gram-negative cocci, acid fast coccobacilli as well as Gram positive and Gram-negative bacilli.

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Learning outcomes: Having finished the course lectures and Lab sessions, students will be able to: 1. Understand the nutritional requirements of pathogenic bacteria and know the methods used to visualize them microscopically. 2. Know the important steps in the collection of different clinical specimens, and be able to handle and process them on reaching a diagnostic microbiology laboratory. 3. Recover pathogens from different clinical specimens (blood, urine, sputum, etc) by cultivation on various differential and selective media. 4. Identify the different pathogens isolated from clinical material to the species level using biochemical tests as well as immunological methods. 5. Understand the major modes of action of some antibacterial drugs and be able to determine the susceptibility of bacteria to antimicrobial agents. 6. Describe the different virulence mechanisms that are involved in bacterial infections. 7. Understand the clinical significance, pathogenicity, laboratory diagnosis, treatment, prevention and control of commonly encountered pathogens in a clinical microbiology setting.

Summary indicative content: Lectures: Microscopy and in vitro culture Types of culture media; selective and differential media; specialized media; cell culture; optical methods in specimen examination; microscopic methods; direct examination and stains used in diagnostic microbiology. Laboratory diagnosis of Bacterial Diseases Clinical specimen selection, collection and transport for microbiological procedures; specimen processing, selection of primary media for cultivation and methods in obtaining pure culture; bacterial detection and identification. Serologic Diagnosis Antibodies; methods of detection; immune assays for cell associated antigens; immunoassays for antibody and soluble antigens; serology. Mechanisms of bacterial pathogenesis Entry into the human body, colonization, adhesion, invasion, pathogenic actions of bacteria, immunopathogenesis, mechanisms for escaping host defenses Antibacterial agents Inhibitors of: cell wall synthesis; protein synthesis; nucleic acid synthesis; other antibiotics; vaccines. Clinical significance; laboratory diagnosis; treatment, prevention and control of diseases caused by the following medically important bacteria: Staphylococci, Streptoccocci, Gram positive rods, Neisseriae, Gastrointestinal Gram-negative Rods, Other Gram-

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Lab sessions: I. Methods in staining and obtaining pure cultures: a. Gram stain, spore stain, and capsule stain. b. Streaking method. c. Dilution method. II. Methods for specimen collection, isolation and identification of both aerobic & anaerobic bacterial species: 1. Gram positive cocci a. Staphylococcus spp. (coagulase positive and coagulase negative spp. ) b. Streptococcus spp. (Group A, B, viridans and S. pneumoniae) 2. Gram negative cocci (Neisseria spp.) 3. Acid fast coccobacilli (Mycobacterium spp.) 4. Gram positive bacilli (Bacillus spp.) 5. Gram negative bacilli (Enterobacteriaceae: E. coli, Salmonella, Shigella, Klebsiella, Proteus spp.) 6. Gram-negative nonfementers bacilli (Pseudomonas)

Ill. Recovery of pathogenic microorganisms from clinical material by culturing on selective media and the identification of these pathogens to the species level. Clinical material will include specimens from: a. Blood: from patients having bacteremia b. Respiratory tract: such as sputum. c. Gastrointestinal tract: stool specimens from patients with diarrhea and gastroenteritis. d. Urine: from patients with urinary tract infections. e. Genital tract: vaginal swabs from women with vaginitis or other infections. f. Cerebrospinal fluid (CSF): from cases of meningitis. g. Wounds: aerobic and anaerobic procedures. h. Material removed at operation. IV. Serological methods for identification of pathogens

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Assessment: The final mark of the course consists of: 1. Written exams (90%): a. First exam (20% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. b. Second exam (20% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. c. Final exam (40% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture d. Lab Midterm exam (10% of the final mark): The student will be given cultures of either unknown bacteria or clinical specimen to recover etiologic agents and identify them during the laboratory period. e. Lab Final exam (15% of the final mark): The student will be given cultures of either unknown bacteria or clinical specimens to recover etiologic agents and identify them during the laboratory period. 2. Lab reports (15%)

Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard

Indicative Bibliography/Sources: 1. Medical Microbiology, Patrick Murray, Ken Rosenthal, Michael Pfaller. 8th Edition, 2015. 2. Todar's Online Textbook of Bacteriology. 2019. www.textbookofbacteriology.net. 3. Lippincott Illustrated Reviews-Microbiology. Cynthia Nau Cornelissen, Marcia Metzgar . 2020.

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Course: Developmental Biology (BIO411) Semester: 1st / 2nd Semester Course Coordinator: Dr. Ahmed Elbetieha Lecturer: Dr. Ahmed Elbetieha Language: English Assignment in Curriculum Elective Course in the Fourth year Course Units/Credit hours Lecture: 2 credit hours Practical: 1 credit hour

Students workload: Contact hours Private study Lecture: 42 84 Exams: 4 20 Sum 46 104

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to General Biology (2) examination regulations: Recommendations: Passing the Cell biology course in the second academic year Passing the Biology courses in the first academic year

Course Description This course investigates cellular and molecular mechanisms that regulate organismal development. Topics include; fertilization cleavage, gastrulation, neurulation and axis specification, organogenesis and morphogenesis. At least four animal models will be used which are amphibians, Sea urchin, birds and mammals

Learning outcomes: Having finished the course lectures, students will be able to: 1. Recognize the main features distinguishing each stage of development 2. Know the differences between cell fate, potency and determination 3. Comprehend the principle of genomic equivalence and the role of cytoplasmic determinants in development 4. Appreciate the molecular basis of development 5. Understand how each of the three germ-layers will differentiate to give different structures

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Summary indicative content: Analysis of Development: The principle of epigenesis Classical strategies in developmental biology Genetic analysis of development Reductionist and synthetic analysis of development

Gametogenesis: The discovery of mammalian egg The germ line concept and the dual origin of gonads Meiosis Spermatogenesis Oogenesis

Fertilization: Interaction before sperm-egg adhesion Fertilization in sea urchins Fertilization in mammals Egg activation Blocks to polyspermy The principle of overlapping mechanisms Parthenogenesis

Cleavage: Yolk distribution and cleavage pattern Cleavage patterns of representative animals\ Special control of cleavage The timing of cleavage division

Cell fate, Potency, and Determination Fate mapping The strategy of clonal analysis Potency of embryonic cells Determination of embryonic cells Properties of determined state Regulation of development

Genomic Equivalence and the Cytoplasmic Environment Theories of cell differentiation Observations on cells Observations on chromosome Molecular data on genomic equivalence

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Totipotency of differentiated plant cells Totipotency of nuclei from embryonic animal cells Pluripotancy of nuclei from differentiated animal cells Control of nuclear activities by cytoplasmic environment

Localized Cytoplasmic Determinants: The principle of cytoplasmic localization Polar lobe formation as a means of cytoplasmic localization Germ cell determinants in insect eggs Bicoid mRNA in Drosophila eggs Cytoplasmic localization at advanced embryonic stages Bioassay for cytoplasmic determinants Properties of cytoplasmic determinants

Gastrulation: Gastrulation in sea urchin Gastrulation in amphibians Gastrulation in birds Gastrulation in humans

Neurulation and Axis Induction; Neurulation as an example of organogenesis Mechanisms of neurulation in amphibians The role of induction in axis formation

Ectodermal organs: Neural tube Neural crest Ectodermal placodes Epidermis

Ectodermal and Mesodermal Organs: Endodermal derivatives Axial and paraxial mesoderm Connective tissue and skeletal muscle Intermediate mesoderm, lateral mesoderm and exrtraembryonic membranes

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Assessment: The final mark of the course consists of: 1. Written exams (90%): a. First exam (25% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. b. Second exam (25% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. c. Final exam (40% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture 2. Assignments (10%) a. Students write a summary of project related to the course material and present it in the class.

Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard

Indicative Bibliography/Sources: Analysis of Biological Development. Kalthoff, K., McGraw Hill. 2001 Second edition.

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Course: Scientific Writing and Presentation (BT391) Semester: 2nd Semester Course Coordinator: Dr. Homa Darmani Lecturer: Dr. Homa Darmani Language: English Assignment in Curriculum Elective course in the third year Course Units/Credit hours Lecture: 1 credit hour Students workload: Contact hours Private study Lecture: 14 20 Oral presentation: 2 8 Assignment 1 2 Exams 3 10 Sum 20 40

Total Sum: 60 hours

Credits 2 ECTS Prerequisites according to Basic Biotechnology examination regulations: Recommendations: Passing Biology courses in the first year Passing Basic Biotechnology course in the second year

Course Description Good writing is an essential skill. This course outlines the basic requirements in scientific writing. The course prepares the student on how to write a scientific report, an essay, a literature survey and review, or a scientific paper. It will also prepare students on how to design and display a scientific poster, how to prepare a CV and how to give a professional oral presentation.

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Learning outcomes: Upon completion of the course, students should: 1. Be familiar with the different types of scientific literature; know how to read and dissect scientific papers and interpret the results; know how to avoid plagiarism and be familiar with the general aspects of scientific writing. 2. Understand how to locate sources of information using the library services and computerized databases; know how to make in text citations; understand word processors, databases and other packages. 3. Know how to prepare a CV and letters of application when applying for jobs/graduate studies. 4. Know the golden rules for essay writing as well as short exam answers; understand instructions used in essay questions and the basic features of writing class practical and project work, paying attention to writing the citations in the required format. 5. Understand the processes involved in writing literature reviews and surveys and preparing papers for formal publication; know how to prepare research posters and understand the integral parts of oral presentations namely clarity, organization, and ability to communicate points that are presented to the audience in a logical sequence.

Having completed the oral presentation, students will gain experience in public speaking and practice their oral communication skills.

Summary indicative content: Lecture • Introduction & General Rules Aim of scientific writing, the scientific method, types of scientific writing that students and scientists are exposed to, some keys to successful scientific writing. • General Advice on Reading, Lectures and Note Taking Primary, secondary and tertiary literature, how to read the scientific literature, compartmentalization of information in a research article, types of questions to ask when reading scientific literature, plagiarism, note taking from lectures, books and primary literature. • Information Technology and Library Resources: Locating Useful Resources Sources of information for essays literature surveys, project work and specialized information, library classification of books, obtaining and organizing research papers, indexing references, making in text citations, listing citations in a bibliography, searching computerized databases. • Word Processors, Databases And Other Packages Range of computer skills such as word processing, spreadsheets, presentations, databases, graphic packages, statistical analysis packages.

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• General Aspects Of Scientific Writing Organizing your time, information and ideas, use of spider diagrams, adopting a scientific style, how to achieve a clear, readable style, creating text outlines, words and phrases, punctuation, sentences and paragraphs, linking words, using appropriate writing styles for different purposes namely, comparative writing and analytical writing. • Writing Letters of Application and Curriculum Vitae Skills and personal qualities, developing your CV, basic CV structures and their presentation, the structure and components of a typical CV and covering letter, drafting and modifying each cover letter and CV carefully and proofreading meticulously, obtaining effective letters of recommendation. • Preparing Research posters Preliminaries- following guidelines closely, organizing logically, effective design and layout, title, text, subtitles and headings, color, content, how to create a poster using powerpoint, keep text to a minimum, make contents visible at a distance, minimize distracting elements. • Preparing Oral presentations Developing oral presentations for maximum impact, Tips on preparing and using powerpoint slides in a spoken presentation, logical sequences, manner of speech, initial planning, rehearsing, opening comments, transitions, concluding remarks, avoiding jargon, timing, visual aids, bad lecturing, hints on spoken presentations, active listening, answering questions. • Writing Essays/short answers in exams Function of an essay, organizing your time (course assessment/exam conditions), making a plan, address the question that is being asked, introductory section, middle of essay, conclusion, reviewing your answer, ten golden rules of essay writing, instructions used in essay questions and their meanings. • Reporting Practical and Project Work Steps in the production of a practical report or thesis. Components of report-title, abstract, introduction, materials and methods, results, discussion, acknowledgements, references. • Writing Literature Surveys and Reviews Making up a timetable, selecting a topic, scanning the literature and organizing the references, deciding on structure and content. • Preparing Papers for Formal Publication Assessing potential content, deciding on authorship, writing, references, submitting for publication, responding to reviewers’ comments, checking proofs and waiting for publication. Assignments:

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• Preparing a CV and letter of application. • Preparation and delivery of a powerpoint presentation.

Assessment: The final mark consists of: 1. Written exams: a. Midterm exam (40% of the final mark). The questions are in the form of short answer essay questions and MCQs covering the topics discussed in the lectures. b. Final exam (30% of the final mark): The questions are in the form of short answer essay questions and MCQs covering the topics discussed in the lectures. 2. Assignments: a. Preparation of a CV (15% of the final mark) and a letter of application (5% of the final mark). b. Preparation and delivery of a PowerPoint presentation (10% of the final mark).

Teaching style: Lecture: Projector, e-learning, power point presentations. Assignments: e-learning

Indicative Bibliography/Sources: 1- PRACTICAL SKILLS IN BIOLOGY, A. Jones, R. Reed and J. Weyers, Sixth Edition. Publisher: Pearson, USA. 2- SHORT GUIDE TO WRITING ABOUT BIOLOGY, J.A. Pechenik, Ninth Edition. Publisher: Pearson, USA.

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Course: Microbial genetics (BT432) Semester: 1st / 2nd Semester Course Coordinator: Dr. Qutaiba Ababneh Lecturer: Dr. Qutaiba Ababneh Language: English Assignment in Curriculum Elective Course in the Fourth year Course Units/Credit hours Lecture: 2 credit hours Practical: 1 credit hour

Students workload: Contact hours Private study Lecture: 26 53 Practical 36 10 Exams: 5 20 Sum 67 83

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to Biochemistry & Molecular Biology examination regulations: Recommendations: Passing the General Microbiology and Molecular Biology in the third academic year

Course Description This course covers the fundamental genetic approaches used to study the physiology of bacteria and phages. The course focuses on problem-solving, utilizing experimental data to uncover microbial processes as well as the usage of the genetic approaches to solve novel problems. Topics covered in this course include genetics of bacteria, phages, mutation, gene transfer and vectors, gene regulation, adaptive and stress responses, and genomics of individual bacteria and whole bacterial communities.

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Learning outcomes: Having finished the course lectures, students will be able to: 1. Solve theoretical problems in genetic analysis, especially gene mapping and strain construction 2. Understand the relationship between genotype and phenotype 3. Explain how genetic selections, screens, and enrichments can be used to isolate mutants 4. Demonstrate familiarity with the different types of mutations 5. Calculate mutation rate and frequency from experimental data 6. Understand the mechanisms of mutagenesis and mutagenesis frequencies 7. Describe the process of genetic mapping using conjugation, transformation and transduction 8. Determine complementation groups from experimental data, and understand the meaning of the complementation data 9. Demonstrate familiarity with the different types of mutant suppressors and their uses 10. Demonstrate familiarity with the with the different types of transposons, the mechanism of transposition, and how transposons are used for genetic selection and analysis 11. Demonstrate familiarity with the mechanisms of transcriptional regulation 12. Demonstrate familiarity with the mechanism of common regulatory systems 13. Demonstrate familiarity with the developmental cycles of phage, and how genetic and molecular approaches can be used to identify these processes

Having finished the group Lab sessions students will be familiar with the different techniques used for genetic manipulation such as PCR, site-directed mutagenesis, DNA cloning, etc. Also, students will be able to understand the common experimental methods in microbial genetics. At the end of the lab sessions, students will develop the ability to interpret data, analyze results and discuss these with respect to the aims of the experiment

Summary indicative content: Lecture

The Bacterial Chromosome DNA Structure The Mechanism of DNA Replication Replication Errors Impediments to DNA Replication Replication of the Bacterial Chromosome and Cell Division The Bacterial Nucleoid

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The Bacterial Genome Antibiotics That Affect Replication and DNA Structure Molecular Biology Manipulations with DNA

Bacterial Gene Expression The Structure and Function of RNA Transcription RNA Degradation The Structure and Function of Proteins Translation Protein Folding and Degradation 105 Membrane Proteins and Protein Export 108 Regulation of Gene Expression 108 Genomes and Genomics 109 Antibiotics That Block Transcription and Translation

Bacterial Genetic Analysis Definitions Inheritance in Bacteria Types of Mutations Reversion versus Suppression Genetic Analysis in Bacteria Isolation of Tandem Duplications of the his Operon in Salmonella

Plasmids What Is a Plasmid? Functions Encoded by Plasmids Plasmid Structure Properties of Plasmids Plasmid Replication Control Mechanisms Mechanisms To Prevent Curing of Plasmids Plasmid Cloning Vectors

Conjugation & Transformation Classification of Self-Transmissible Plasmids The Fertility Plasmid Mechanism of DNA Transfer during Conjugation in Gram-Negative Bacteria Chromosome Transfer by Plasmids Transfer Systems of Gram-Positive Bacteria Integrating Conjugative Elements

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Natural Transformation Importance of Natural Transformation for Forward and Reverse Genetics Artificially Induced Competence

Bacteriophage Genetics Regulation of Gene Expression during Lytic Development Phage DNA Genome Replication and Packaging Phage Display Genetic Analysis of Phages Recombination and Complementation Tests with Phages Phage Defense Mechanisms 309 Restriction-Modification Systems CRISPR Loci Generalized Transduction

Transposition and Recombination Transposition Mechanisms of Transposition 368 General Properties Transposons Transposon Mutagenesis 382 Site-Specific Recombination

Regulation of Gene Expression Transcriptional Regulation in Bacteria Negative Regulation of Transcription Initiation Negative Inducible Systems Positive Regulation of Transcription Initiation Regulation by Transcription Attenuation Regulation of mRNA Degradation Regulation of Translation Posttranslational Regulation

Global Regulation: Regulons and Stimulons Carbon Catabolite Regulation Regulation of Nitrogen Regulation of Ribosome and tRNA Synthesis Stress Responses in Bacteria Iron Regulation in E. coli Regulation of Virulence Genes in Pathogenic Bacteria

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Bacterial Cell Biology and Development Membrane Proteins and Protein Export Genetic Analysis of Transmembrane Domains of Inner Membrane Proteins in Gram-Negative Bacteria Protein Secretion Bacterial Cell Biology and the Cell Cycle Genetic Analysis of Sporulation in B. subtilis

Practical: 1. Molecular Identification of Bacteria (Listeria Identification using the 16s rRNA gene sequencing) 2. Isolation of Spontaneous Antibiotic-Resistant Mutants 3. Mobilization of Genetic Markers by Phages 4. From Genotypes to Phenotypes (Genetic analysis of Bacillus subtilis motility)

Assessment: The final mark of the course consists of: 1. Written exams (70%): a. Midterm exam (30% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. b. Final exam (40% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. 2. Practical (30%) a. Final exam (10% of the final mark): composed of problems and questions about lab experiments and results. b. Reports (10% of the final mark): students will write reports about the lab experiments, results and conclusions. c. Practical participation (10% of the final mark): students’ involvement in the lab sessions and experiments will be evaluated

Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard

Laboratory: demonstration, hands-on experiments, open lab assignments

Indicative Bibliography/Sources: Molecular genetics of bacteria. Larry Snyder ... [et al.]. 4th ed. 2013. ASM press, USA.

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Course: Pharmaceutical Biotechnology (BT437)

Semester: 1st Semester Course Coordinator: Dr. Saied A. Jaradat Lecturer: Dr. Saied A. Jaradat Language: English Assignment in Curriculum Elective Course that can be taken any time after the third year Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 42 84 Assignments: 0 5 Exams: 4 15 Sum 46 104

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to Molecular Genetics and Basic Biotechnology examination regulations: Recommendations: Passing the pre-request courses Course Description Pharmacogenetics is the study of genetic variability influencing drugs responses in individuals. The course will discuss definite genetic mutations and polymorphisms in several genes encoding drug- metabolizing enzymes contributing to drug efficacy and toxicity. This course will focus on platform technologies utilized in genotyping and/or discovering new genetic variants such as microarray and next-generation sequencing. Understanding of the basics of pharmacogenomics, technologies utilized in drug development and drug treatment and practicing accessing to public databases such as the human genome, HapMap, 1000 genomes projects and PharmGKB will enable students to build up research interest in pharmacogenetics and prepare them for graduate study

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Learning outcomes: 1. Describe the basic of pharmacology and the human genome variations such as single nucleotide polymorphism (SNP) and the role of these functional SNPs in defining the inter-individual variation in responding to drugs treatments. 2. Describe the conventional and advance platform technologies used to determine alleles genotype for known SNPs and how advance methods used in discovering new polymorphic markers in correlation to phenotype variability in drug response 3. Use the e-resources of pharmacogenomics knowledge base 4. Familiar with diagnostics tools available for pharmacogenetic applications 5. Define mutations and haplotypes in the genome that correlates with drug adverse reaction 6. Describe the application of genotypic data in reclassification of genetic diseases 7. Understand the implications of pharmacogenomics in personalized medicine

Summary of indicative content: Course introduction and Overview of pharmacogenetics and pharmacogenomics Gene structure and Sanger Method of DNA Sequencing: Several example on Sequencing chromatograms and interpretations Mutation and Polymorphism (SNPs) Polymerase Chain Reaction (PCR)/ principle, Primers design, nested, semi-nested PCR. Amplification refractory mutation system (ARMS), allele genotyping Restriction fragment length polymorphism/ allele genotyping, allele genotyping Real-Time Polymerase Chain Reaction/ allele genotyping using TaqMan probes and Multiplexing High-throughput microarrays expression and genotyping technology principle. Microarray expression data application: Burkitt?s lymphoma and diffuse large-B-cell, application for cyclophosphamide chemotherapy; Onco type DX and MammaPrint ? test. Microarray expression data application. Drug Repositioning, Crohn?s disease (CD) example. SNP Microarray/ Pharmacogenetic application DMET-Chip Pharmacogenomics of Cancer: Thiopurine methyltransferase (TPMT). Mercaptopurine and acute lymphoblastic leukaemia Pharmacogenomics of Cancer: UDP-glucuronosy-ltransferase 1A1 (UGT1A1) alleles: Irinotecan and colon cancer. Pharmacogenomics of Cancer: Dihydropyrimidine dehydrogenase (DPD) alleles: 5-Fluorouracil and solid tumors. Pharmacogenomics of Cancer: Thymidylate synthase (TS) alleles. 5-

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Fluorouracil and solid tumors. CYP450 genes family/ allele nomenclature CYP2D6 allelic variants and pseudogenes, CYP2D6: Tamoxifen drug and breast cancer, CYP2D6: Codeine drug CYP3A: drug-drug interaction CYP2C19: Clopidogrel Therapy (Plavix) CYP 2C9 & VKORC1: Warfarin G6PD: Hemolytic anemia and antimalarial drug, RYR1 gene: Malignant Hyperthermia Pharmacogenomics in Psychiatry Next generation sequencing technology Next generation sequencing: implications in personalized medicine and pharmacogenomics Pharm GKB: The Pharmacogenomics Knowledgebase

Assessment: The final mark of the course consists of: 1. Written exams (90%): a. First exam (25% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. b. Second exam (25% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. c. Final exam (40% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture 2. Assignments (10%) b. Students write a summary of project related to the course material and present it in the class.

Teaching style: Students mainly will be lectured using power point; assignments will also be given and discussed in the class.

Indicative Bibliography/Sources: There is no designated text book, the instructor gives handouts for the students, and some references students might refer to.

Reference Pharmaceutical Biotechnology Concepts and Applications, 2007 by Gary Walsh

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Course: Protein Biotechnology (BT452) Semester: 1st / 2nd Semester Course Coordinator: Dr. Qutaiba Ababneh Lecturer: Dr. Qutaiba Ababneh Language: English Assignment in Curriculum Elective Course in the Fourth year Course Units/Credit hours Lecture: 2 credit hours Practical: 1 credit hour

Students workload: Contact hours Private study Lecture: 26 53 Practical 36 10 Exams: 5 20 Sum 67 83

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to Biochemistry & Molecular Biology examination regulations: Recommendations: Passing the Biochemistry in the second academic year Passing the Molecular Biology in the third academic year

Course Description This course is designed to introduce students to protein structure and function as well as the laboratory skills needed to work with proteins. Topics of protein structure-functions relationship, folding, modifications and sources will be covered. An overview of the molecular, genetic principles and techniques used to engineer and produce proteins on different scales will be discussed. Students will learn the theory of protein purification and electrophoresis techniques. In addition, principles of proteomics, diagnostic, therapeutic, and industrial applications of protein products will be presented

In the practical part of this course, the first part will focus on protein purification and analysis. Students will learn and practice the techniques of cell disruption, chromatography, concertation as well as SDS-PAGE and immunoblotting. Also, assays of protein detection and quantification will be included. The second part focus is protein engineering by random and site-directed mutagenesis. Students will learn how to use PCR and gene cloning to produce modified proteins. Students will also be introduced to protein bioinformatics tools.

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Learning outcomes: Having finished the course lectures, students will be able to: 1. Understand the basics of protein structure and function. 2. Describe from start to finish the entire process of protein production on different scales. 3. Describe the recent methodological developments in biotechnology pertaining to proteins 4. Describe the wide range of applications of protein products.

Having finished the group Lab sessions students will be able to apply basic biochemical and genetic principles related to protein purification and manipulation. Also, students will be able to organize group work, and implement team and communication skills

Summary indicative content: Lecture

Protein structure & engineering Primary structure, Higher-level structure, Protein classification on the basis of structure, Protein structural stability, Higher-order structure prediction, Protein folding, Intrinsically disordered proteins, Protein engineering, Protein post-translational modification

Proteomics Genes, genomics and proteomics, Bioinformatics, Proteomics: goals and applications

Proteins sources Recombinant versus non-recombinant production, Approaches to recombinant protein production, Heterologous protein production in E. coli, Heterologous production in bacteria other than E. coli, Heterologous protein production in yeast, Heterologous protein production in fungi, Proteins from plants, Animal tissue as a protein source, Heterologous protein production in transgenic animals, Heterologous protein production using animal cell culture, Insect cell culture systems

Protein purification and characterization Protein detection and quantification, Initial recovery of protein, Removal of whole cells and cell debris, Concentration, Chromatographic purification, Protein inactivation and stabilization, Protein characterization

Large-scale protein production Upstream processing, Downstream processing

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Therapeutic proteins: blood products, vaccines and enzymes Blood products, Anticoagulants, Thrombolytic agents, Vaccine technology, Therapeutic enzymes

Therapeutic antibodies Antibody therapeutics: polyclonal antibody preparations, Antibody therapeutics: monoclonal antibodies, Therapeutic applications of monoclonal antibodies

Hormones and growth factors used therapeutically Insulin, Glucagon, Gonadotrophins, Growth hormone, Erythropoietin, Growth factors Further reading

Proteins used for analytical purposes The IVD sector, The basis of analyte detection and quantification, Enzymes as diagnostic/analytical reagents, Biosensors, Antibodies as analytical reagents

Industrial enzymes: an introduction Sales value and manufacturers, Sources and engineering, benefits, Enzyme detection and quantification 11.5 Immobilized enzymes, Extremophiles

Practical: 1. Molecular visualization of proteins using Pymol 2. Preparation of the protein source 3. Protein purification I: Cell disruption, enzyme assay, protein quantitation 4. Protein purification II: Ammonium sulfate precipitation & salt removal 5. Protein purification III: Gel filtration chromatography 6. Protein purification IV: Ion-exchange chromatography 7. Protein analysis I: SDS-PAGE and staining 8. Protein analysis II: Western blotting 9. Protein engineering I: Random and site-directed mutagenesis by PCR 10. Protein engineering II: Digestion of PCR products and plasmids

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11. Protein engineering III: Gene cloning and transformation 12. Protein engineering IV: Screening of transformants & analysis

Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard

Laboratory: demonstration, hands-on experiments, open lab assignments

Indicative Bibliography/Sources: Protein Biochemistry & Biotechnology, Welsh, G., Second Edition. Publisher: Wiley Blackwell

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Course: Special Topics A (BT492A)

Semester: 2nd Semester Course Coordinator: Dr. Khaldon Bodoor Lecturer: Dr. Khaldon Bodoor Language: English Assignment in Curriculum Elective Course for fourth-year students Course Units/Credit hours Lecture: 3 credit hours Students workload: Contact hours Private study Lecture: 28 56 Oral presentation: 14 14 Assignments 0 23 Poster: 2 23 Sum 44 106

Total Sum: 150 hours

Credits 5 ECTS Prerequisites according to Passing 90 credit hours examination regulations: Recommendations: Recommended for fourth-year students

Course Description This a single semester course in special topics in genetics that focuses on contemporary genetic concepts. Genetics and genomics have important health and societal implications that students will need to comprehend. Genetic topics of popular interest discussed in the course, include stem cell research, the Human Genome, genetic testing, genealogical tracing, bioethics, bioinformatics, nature and nurture, and DNA barcoding, to name a few.

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Learning outcomes: Having finished the course lectures and presentations, students will be able to: 1. Understand the issues pertaining to the use of genetic medicine. 2. Understand the concept of epigenetics. 3. Understand the concept of nature versus nurture in shaping human traits 4. Get a brief introduction to the tools and methodologies related to human genetics in correlation to inheritance. 5. Students should be able to discuss and analyze contemporary issue the field of genetics and inheritance.

Summary indicative content: Lecture • A Preview of the human genome:

Introduction the human genome and its relevance to disease and the society

• Epigenetics:

A preview of the field of epigenetics and its effect on inheritance

• The Nature Vs. Nurture debate:

Discussions related to the effect of genes and the evolvement on the inheritance of human traits

• The effect of genes and the environment on human traits:

Analysis of the contribution of genes and the environment on shaping human behavior and traits

• Genetics and the society:

Issues on the effect of the new discoveries of genetics on the society.

• Tools and methodologies in in human research:

Analysis of the tools and approaches for research on humans.

• Ethical issues in genetics:

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Discussion of the legal and ethical issues of genetics and its effects on the society.

• Genetics and personalized medicine:

Concepts in the new field of personalized medicine and its correlation to genetics.

• Twin studies and genetics:

The use of family studies and twin studies to understand Inheritance

• Psychology and genetics:

Concepts in the interplay between genetics and psychology and their effect on human behavior.

Assessment: The final mark of the course consists of: 1. Oral presentations: 30% of the final mark Students present articles related to the concept of nature vs. nurture and their role in the inheritance of human traits. 2. Assignments: 20% of the final mark Students will be given assignments related to the topics discussed in the class room and are required to refer back to recent articles in the field of genetics. 3. Posters: 50% of the final mark Students will work individually to pick a topic related to the material of the discussed in the class room and prepare a poster at the end of the course to be judged by a committee from the department during a poster-day session at the end of the course.

Teaching style: Oral presentations, class discussions, and poster presentation

Indicative Bibliography/Sources: Recent review articles and research articles will be provided by the instructor through the e-learning website

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Course: Laboratory Management (BT495) Semester: 2nd Semester Course Coordinator: Dr. Rami Alkhatib Lecturer: Dr. Rami Alkhatib Language: English Assignment in Curriculum Compulsory Course in Second Semester of the Fourth year Course Units/Credit hours Lecture: 1 credit hour Students workload: Contact hours Private study Lecture: 14 28 Exams & Quizzes: 2 16 Sum 16 44

Total Sum: 60 hours

Credits 2 ECTS Prerequisites according to The student should pass 90 credits and above successfully. examination regulations: Recommendations: Passing all the biology courses in the first, second, and third years. Course Description This course is designed to introduce students to the basic concept of the nature of management in the clinical lab, lab planning, organization, control and decision making, managerial organizational communications, leadership styles and group effectiveness, managerial leadership: conductive effective meetings, and educational responsibilities of managers and supervisors.

Learning outcomes: Having finished the course lectures, students will be able to: 1. Describe the nature of management in the clinical lab 2. Become familiar with Lab Planning, organization, control and decision making 3. Become familiar with Leadership styles and group effectiveness [ 4. Become familiar with the Basics of lab safety

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Summary indicative content: Administration: art or science Educating lab administrators Definition of administration Managerial duties and responsibilities Doing vs managing The supervisor circle influence The administrative process Elements of planning Establishing policies Design of clinical lab floor plan Lab organization structure Controlling operations in the clinical lab Nature of motivation Assumptions about individual human behavior Assumption about small group behavior Managerial Organizational communications Interpersonal communication within the lab Interpersonal communication The climate reflecting leader behavior The leadership role of managers and supervision Basic of power and influence Meeting purposes Planning Conducting the meeting Avoiding nonproductive meeting Lifelong learning, educational issues Approaches to educational activities

Assessment: The final mark of the course consists of: 1. Written exams: a. Midterm exam (40% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture. b. Final exam (60% of the final mark): composed of MCQ and short answer essay questions to the content of the lecture.

Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard

Indicative Bibliography/Sources: • Lynne Garcia. Clinical Lab management, Blackwell + lecture notes and handouts. • John Synder. Administration and supervision in clinical lab, 2nd edition, ASM press.

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Course: Ethical Aseptic of Biotechnology (BT496) Semester: 2nd Semester Course Coordinator: Dr. Abdulkareem Al-Sallal Lecturer: Dr. Abdulkareem Al-Sallal Language: English/Arabic Assignment in Curriculum Compulsory Course in Fourth year Course Units/Credit hours Lecture: 1 credit hour Students workload: Contact hours Private study Lecture: 14 28 Oral presentation: 1 6 Exams & Quizzes: 3 10 Sum 16 44

Total Sum: 60 hours

Credits 2 ECTS Prerequisites according to Basic Biotechnology examination regulations: Recommendations: Passing all biotechnology courses. Course Description This course will discuss the regulatory challenges of the rapid advances in genetic engineering. Moral, religious, legislation and public perspectives regard the human cloning, human genome, In vitro fertilization, pre-natal diagnosis, genetically engineered plants and foods.

Learning outcomes: Having finished the course lectures, students will be able to: 1. Know the ethics of conducting experiments related to human or animals 2. Understand the ethical issues concerning human genome, cloning, IVF, prenatal diagnosis, genetically engineered foods and plants 3. Understand the ethics in using biology in industries and in environmental applications

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Summary indicative content: The interaction between human culture and civilization and the basis of human ethics of the society

Ethical issues of the human genome project

Ethics of genetic screening and prenatal diagnosis

The ethics of genetic research on sexual orientation

In vitro fertilization: an Islamic view

Human cloning and ethics

Human cloning-Embryo style and ethics

Biotechnology and ethics

Genetically engineered food-A serious health risk

Genetically engineered plants: A future prospects

A view on environmental and genetically engineered compounds

Potential ethical issues in pharmacogenetics

Ethics and bioweapons

Teaching style: Lecture: Projector, e-learning, power point presentations and whiteboard

Indicative Bibliography/Sources: Cross-cultural Issues in Bioethics: The Example of Human Cloning Roetz, H., 1st Edition.

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