Course Handbook of the Bachelor Degree in · 2019. 4. 17. · Holy Quran, the Prophet’s Tradition, and verse and prose literature. This course also aims to analyze the aesthetic

Course Handbook of the Bachelor Degree in

,,Biotechnology and Genetic Engineering”

Last Updated: 1/3/2019

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Prepared, compiled and edited by: Departmental Accreditation Committee

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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 (75 Credit Hours, 147 ECTS)

Page

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

qutaiba ababneh

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TABLES OF CONTENT (continued)

Biotechnology & Genetic Engineering Compulsory Courses (74 Credit Hours, 147 ECTS)

Page

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

Back to tables of content

1

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

examination regulations:

None

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 قوف نصوص قصيره من القران الكريم والحديث الشريف وكذلك االدب شعره ونثره وعلى الو

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

Learning outcomes • التأسيس إلدراك النصوص األدبية وفهمها وادراكها

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 •


2

Summary of indicative content: • سورة هود :تفسير وتحليل

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 •

قات على نص كليلة ودمنة : االستيعاب والمناقشة والتطبيقات اللغويةتطبي •

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 •

مقالة جبران: المناقشة واالستيعاب ، والتطبيقات اللغويةتطبيقات على •

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)


Course Coordinator: Department of Humanities

Lecturer: Variable

Language: Arabic

Assignment in Curriculum Compulsory Course taken any semester


Students workload:


Lecture: 42 42

Assignments: 0 10

Exams: 4 22

Sum: 46 74


Credits 4 ECTS



None

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


1. Written exams:

a. Midterm exam (40% of the final mark): composed of


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)


Course Coordinator: Dr Mutawakil Ubaidat

Lecturer: Dr Mutawakil Ubaidat & others

Language: Arabic and English

Assignment in Curriculum Compulsory Course can be taken any semester


Students workload:


Lecture: 28 56

Assignments: 0 10

Exams & Quizzes: 6 20

Sum 34 86


Credits 4 ECTS



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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1. Computer-based exams:




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


Students workload:


Lecture: 28 28


Sum 32 58

Total Sum: 90 hours

Credits 3 ECTS



English (ENG112)

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.






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)


Course Coordinator: Military science department

Lecturer: Variable

Language: Arabic

Assignment in Curriculum Compulsory Course taken any semester


Students workload:


Lecture: 39 48

Visits 3 6

Exams: 4 20

Sum 46 74


Credits 4 ECTS



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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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


1. Written exams:




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


14

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


Students workload:


Lecture: 0 120

Exams 4 26

Sum 4 146


Credits 5 ECTS



English language 099

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


1. Written exams:

a. First exam (25% of the final mark): composed of essay and


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


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)


Course Coordinator: Dr Amer Darweesh

Lecturer: Dr Amer Darweesh

Language: English

Assignment in Curriculum Compulsory course in the first year


Students workload:


Lecture: 42 42

Exercise 0 70

Exams: 4 22

Sum 46 134


Credits 6 ECTS



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.


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.


18

Course: Mathematical Applications of Biological Sciences (MATH103)


Course Coordinator: Dr. Kamel Bashaireh

Lecturer: Dr. Kamel Bashaireh

Language: English



Students workload:


Lecture: 42 42

Exercise 0 70

Exams: 4 22

Sum 46 134


Credits 6 ECTS



None

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.


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.


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)


20

Course: Elements of Statistics (MATH131)


Course Coordinator: Dr. Mohammad Shakhatreh

Lecturer: Dr. Mohammad Shakhatreh

Language: English



Students workload:


Lecture: 42 42

Exercise 0 70

Exams: 4 22

Sum 46 134


Credits 6 ECTS



None

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


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.


22


1. Written exams:

a. First exam (30% of the final mark)



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


Introduction to Statistics, J. S. Milton and J. J. Meteer, First Edition, D. C. Health and Company, 1986.


23

Course: General Physics (1) (PHY101A)


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


Students workload:


Lecture: 42 42

Exercise 0 70

Exams: 4 22

Sum 46 134


Credits 6 ECTS



None


Course Description:

This course covers mechanics: movement of objects, mechanical properties of solid objects, temperature and thermodynamics, fluids, vibrations and waves


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.


24

Temperature and Heat, Laws of Thermodynamics

Fluid mechanics

Vibrations

Waves


1. Written exams:


choice questions.

b. Second exam (30% of the final mark): composed of multiple-

choice questions.


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


Physics for Biology and Pre-Medical Students, Burns & MacDonald. Addison-Wesley.


25

Course: General Physics (2) (PHY102A)


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


Students workload:


Lecture: 42 42

Exercise 0 70

Exams: 4 22

Sum 46 134


Credits 6 ECTS



None

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


26

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


1. Written exams:


choice questions.


choice questions.


choice questions.



Physics, Kane & Sternheim. Wiley, New York, USA.


27

Course: General Physics Laboratory (PHY107)


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:


Lab session: 30 30

Reports 0 10

Exams & Quizzes 3 17

Sum 33 57

Total Sum: 90 hours

Credits 3 ECTS



None

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.


28

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.


29


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


Physics for Scientists and Engineers, Serway and Jewett, 9th edition.


30

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


Students workload:


Lecture: 42 42

Exercise 0 70

Exams: 4 22

Sum 46 134


Credits 6 ECTS



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


31

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


1. Written exams:

a. First exam (20% of the final mark):





C++ Programming: From Problem Analysis to Program Design. D. S. Malik, 5th Edition


32

Course: Introduction to Hematology (LM251)


Course Coordinator: Dr. Mohammad A. Audeh

Lecturer: Dr. Mohammad A. Audeh

Language: English

Assignment in Curriculum Compulsory Course in the second year


Practical: 1 credit hour

Students workload:


Lecture: 28 56

Practical 39 13

Exams: 4 40

Sum: 71 109


Credits 6 ECTS



General Biology (2)

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.


33


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


1. Written exams:


choice questions.


multiple-choice questions


choice questions

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

whiteboard


34

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


35

Course: General Chemistry (1) (CHEM101)


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


Students workload:


Lecture: 42 63

Book exercises 0 14


Sum 46 104


Credits 5 ECTS



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.


36

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


37




choice questions.


choice questions.


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


38

Course: General Chemistry (2) (CHEM102)


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


Students workload:


Lecture: 42 63

Book exercises 0 14


Sum 46 104


Credits 5 ECTS



General Chemistry (1)

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..


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.


39

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




choice questions.


choice questions.



40

choice questions.


Exercise:





41

Course: General Chemistry Laboratory (CHEM107)


Course Coordinator: Mr. Ibrahim Jawarneh

Lecturer(s): Mr. Ibrahim Jawarneh and others

Language: English


Course Units/Credit hours Lab session: 1 credit hour

Students workload:


Lab session: 33 33

Lab reports 0 11


Sum 36 54

Total Sum: 90 hours

Credits 3 ECTS




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 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.


42

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






choice questions.

Lab reports:

c. Reports (20% of the final mark): Description, results and

conclusions about lab experiments


Exercise:





43

Course: Organic Chemistry (CHEM217)


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


Students workload:


Lecture: 42 63

Book exercises 0 14


Sum 46 104


Credits 5 ECTS




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


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.


44

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


45

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




choice questions.


choice questions.


choice questions.


Exercise:


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)


46

Course: Analytical Chemistry (CHEM233)


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


Students workload:


Lecture: 40 60

Book exercises 0 14


Sum 46 104


Credits 5 ECTS




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.


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.


47

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


48

Redox Titrations

The shape of redox

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




choice questions.


choice questions.


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


Exercise:



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)


49

Course: Analytical Chemistry Lab (CHEM234)


Course Coordinator: Mr. Ayman Amrat

Lecturer(s): Mr. Ayman Amrat

Language: English



Students workload:


Lecture: 33 84

Book exercises 0 24


Sum 46 134

Total Sum: 90 hours

Credits 3 ECTS



General Chemistry Lab

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


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.


50

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






choice questions.

Lab reports:

a. Reports (20% of the final mark): Description, results and



Exercise:


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)


51

Course: Biochemistry (CHEM262)


Course Coordinator: Dr. Barakat Shabsoug

Lecturer(s): Dr. Barakat Shabsoug, Dr Ayat Bani Irshaid, Dr. Amjad mahasneh

Language: English



Students workload:


Lecture: 42 63

Exams: 4 41

Sum 46 104


Credits 5 ECTS



Organic Chemistry and General Chemistry (2)

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.


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.


52

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-


53

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




choice questions.


choice questions.


choice questions.


Exercise:



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).


54

Course: Biochemistry Laboratory (CHEM266)


Course Coordinator: Mr. Adeeb Al-Faqeeh

Lecturer(s): Mr. Adeeb Al-Faqeeh and others

Language: English



Students workload:


Lab session: 33 84

Book exercises 0 24


Sum 46 134

Total Sum: 90 hours

Credits 3 ECTS



Biochemistry

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.


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.


55

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.






choice questions.

Lab reports:

a. Reports (20% of the final mark): Description, results and



Exercise:


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).


56

Course: General Biology 1 (BIO101)


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


Students workload:


Lecture: 42 84


Sum 46 104


Credits 5 ECTS



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..


57

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


58

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


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.


59

Course: General Biology 2 (BIO102)


Course Coordinator: Dr. Asem Alkhateeb

Lecturer: Dr. Asem Alkhateeb

Language: English



Students workload:


Lecture: 42 84


Sum 46 104


Credits 5 ECTS



General Biology 101

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.


60

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


61

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


1. Written exams:


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.


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


62

Course: General Biology Laboratory (BIO107)

Semester: 2ed Semester

Course Coordinator: Bayen Mahawreh

Lecturer: TA’s

Language: English

Assignment in Curriculum Compulsory Course


Students workload:


Lab session: 26 13

Reports 0 8


Sum 29 31

Total Sum: 60 hours

Credits 2 ECTS



General Biology (2)

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.


63

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.


64

• 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.


65




multiple-choice questions on the content of the lectures and

practical works.


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.


66

Course: General Microbiology (BIO231)


Course Coordinator: Dr. Abdullkarim Al Sallal

Lecturer: Dr. Abdullkarim Al Sallal and Dr Ziad Jaradat

Language: English



Students workload:


Lecture: 42 84

Exams 4 20

Sum 46 104


Credits 5 ECTS



General Biology 1 & 2

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


67

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


68

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.



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


69

Course: General Microbiology Laboratory (BIO232)


Course Coordinator: Mr. Bayen Mahawreh

Lecturer: Mr. Bayen Mahawreh and others

Language: English



Students workload:


Lab session: 39 12

Reports 0 12


Sum 43 47

Total Sum: 90 hours

Credits 3 ECTS



General Biology 1 & 2


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


70

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




multiple-choice questions on the content of the lectures and

practical works.


choice questions on the content of the lectures and

practical work.


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 by the lecturer.

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


71

Course: Cell Biology (BIO251)


Course Coordinator: Dr. Khaldon Bodoor

Lecturer: Dr. Khaldon Bodoor

Language: English



Students workload:


Lecture: 40 80

Exams: 4 36

Sum 44 106


Credits 5 ECTS



General Biology (2)


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.


72


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.


73

• • 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


74


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.


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

https://www.bookdepository.com/author/Jeff-Hardin

https://www.bookdepository.com/author/Gregory-Paul-Bertoni

https://www.bookdepository.com/author/Lewis-J-Kleinsmith


75

Course: Immunology & Serology (BIO333)


Course Coordinator: Dr. Nizar Abuharfeil

Lecturer: Dr. Nizar Abuharfeil

Language: English

Assignment in Curriculum Compulsory Course in 1st semester of the second year


Students workload:


Lecture: 42 63

Oral presentation: 2 9


Sum 48 102


Credits 5 ECTS



Microbiology & Biochemistry


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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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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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.



2. Presentation (10% of the final mark): students present

about recent advances in immunology from the available

primary literature.



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



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:


Lab session: 33 33

Reports 0 9


Sum 38 52

Total Sum: 90 hours

Credits 3 ECTS



Immunology and serology

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


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


Radioimmunoassay



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1. Written exams:

a. Midterm exam (40% of the final mark): composed of MCQ

and short answer essay questions.


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)


Course Coordinator: Dr. Osamah Batiha

Lecturer: Dr. Osamah Batiha

Language: English

Assignment in Curriculum Compulsory Course in 1st Semester of the third year


Students workload:


Lecture: 40 80

Assignment: 0 6


Sum 44 106


Credits 5 ECTS



General Biology 2

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


• 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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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)



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


Students workload:


Lab sessions: 36 24

Assignment 0 6

Exams 3 21

Sum 39 51

Total Sum: 90 hours

Credits 3 ECTS



General Biology (2)

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


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

coordinator


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Course: Basic Biotechnology (BT232)


Course Coordinator: Dr. Qutaiba Ababneh

Lecturer: Dr. Qutaiba Ababneh

Language: English


Semester of the second year


Students workload:


Lecture: 26 52


Exercise 0 10


Sum 32 88


Credits 4 ECTS



General Biology 2


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


• 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.


1. Written exams:


and short answer essay questions to the content of the lecture.




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.



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


Students workload:


Lecture: 26 26

Assignments: 0 12

Exams: 4 22

Sum 30 60

Total Sum: 90 hours

Credits 3 ECTS



C++ Programming Language

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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1. Written exams:

a. Midterm exam (30% of the final mark): composed of short

answer essay questions and 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



Language: English



Lab session: 1 credit hour

Students workload:


Lecture: 15 30

lab 36 12


Sum 44 52


Credits 4 ECTS



Immunology and serology

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


95

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


96


1. Written exams:


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



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


97

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


Students workload:


Training: 180 30

Sum 180 30


Credits 7 ECTS



Passing 90 credit hours

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


98

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


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)


Course Coordinator: Dr. Ahmed Elbetieha

Lecturer: Dr. Ahmed Elbetieha

Language: English

Assignment in Curriculum Compulsory Course in 2nd Semester of the fourth year


Students workload:


Lecture: 26 52

Presentation: 2 6

Exams: 4 20

Sum 32 88


Credits 4 ECTS



Basic Biotechnology

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.


100

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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1. Written exams:

a. First exam (25% of the final mark): composed of MCQ,

Tru/eFalse, Blank filling and short answer essay questions.


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)


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



Students workload:


Lecture: 28 70

Lab sessions: 39 13

Exams: 6 24

Sum 73 107


Credits 6 ECTS



Basic Biotechnology

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


103

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


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 (10% of the final mark): composed of


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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.


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



Students workload:


Lecture: 28 56

Practical 39 12

Reports: 0 20


Sum 72 108


Credits 6 ECTS



General Microbiology (B231)

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:





lecture.


short answer essay questions to the content of the lectures

d. Lab Midterm exam (8% of the final mark): composed of


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.


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)



Lecturer: Dr. Asem Alkhateeb

Language: English

Assignment in Curriculum Compulsory Course in 1st Semester of the fourth year


Students workload:


Lecture: 42 84

Exams: 4 20

Sum 46 104


Credits 5 ECTS



Molecular Genetics

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


1. Written exams:


b. Second exam (30% of the final mark): composed of MCQ or


c. Final exam (40% of the final mark): composed of MCQ

questions to the content of the lecture.


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


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Course: Molecular Biology I (BIO451)



Lecturer: Dr. Nisreen AL-Quraan

Language: English


Semester of the fourth year


Students workload:


Lecture: 42 73


Sum 47 103


Credits 5 ECTS



General Biology 2, Biochemistry


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.


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


1. Written exams:





lectures.




MCQ questions (quiz after finishing each chapter).


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


117

Course: Molecular Biology Laboratory (BIO453)



Lecturer: Ms. Rehan BaniHani

Language: English


Semester of the fourth year


Students workload:


Lab Lecture: 36 24

Lab Reports: 0 6


Sum 40 50

Total Sum: 90 hours

Credits 4 ECTS



General Biology 2, Molecular Biology I


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.


118

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


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.


board

Lab exercises: running laboratory-based experimentation

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


120

Course: Molecular Biology II (BIO454)

Semester: 2 nd Semester


Lecturer: Dr. Nisreen AL-Quraan

Language: English

Assignment in Curriculum Compulsory Course in 2 nd Semester of the fourth year


Students workload:


Lecture: 26 52

Quizzes: 1 16

Exams: 4 20

Sum 32 88


Credits 4 ECTS



Molecular Biology I and Molecular Biology Laboratory

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.


121

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.


• 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.


1. Written exams:





lectures.




questions (quiz after finishing each chapter).


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)



Lecturer: Dr. Asem Alkhateeb and Ms. Enas Al-Satari

Language: English


Course Units/Credit hours Lecture: 2 credit hours & Laboratory 1 credit hour

Students workload:


Lecture: 28 28

Laboratory work: 45 45


Sum 81 99


Credits 6 ECTS



Human Genetics

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


124

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


125

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


1. Written exams:



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.


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)



Lecturer: Dr. Qutaiba Ababneh and others

Language: English



Students workload:


Lecture: 14 16

Sum 81 99

Total Sum: 30 hours

Credits 1 ECTS



None

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


127

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


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.


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)


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


Students workload:


Lecture: 8 16

Lab work 140 24

Oral presentation 2 20

Sum 150 60


Credits 7 ECTS



Successful completion of 90 credit hours

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


129

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


130

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)


131


• Clarity of content

• Appropriate presentation

• Workshop attendance

3. Written report (20%) (Evaluator: Supervisor & Examination Committee)



• 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)



• Research question

• Methodology

• Interpretation of data

• Conclusions

• Quality of visual aids

• Quality of oral presentation

• Ability to answer questions


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)


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


Students workload:


Lecture: 56 98

Exams: 5 21

Sum 61 119


Credits 6 ECTS



Biochemistry

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:






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)


Course Coordinator: Dr. Homa Darmani

Lecturer: Dr. Homa Darmani

Language: English

Assignment in Curriculum Elective Course in the Fourth year



Students workload:


Lecture: 42 42

Lab sessions 30 30

Lab reports: 0 10

Exams: 6 20

Sum 78 102


Credits 6 ECTS



General Biology

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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negative Rods, Clostridia and Other Anaerobic Rods, Mycoplasma, Chlamydiae, Mycobacteria and Actinomycetes, Rickettsiae

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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1. Written exams (90%):







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%)


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)


Course Coordinator: Dr. Ahmed Elbetieha

Lecturer: Dr. Ahmed Elbetieha

Language: English




Students workload:


Lecture: 42 84

Exams: 4 20

Sum 46 104


Credits 5 ECTS



General Biology (2)

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


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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2. Assignments (10%)

a. Students write a summary of project related to the

course material and present it in the class.


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

Second edition.


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Course: Scientific Writing and Presentation (BT391)


Course Coordinator: Dr. Homa Darmani

Lecturer: Dr. Homa Darmani

Language: English

Assignment in Curriculum Elective course in the third year


Students workload:


Lecture: 14 20


Assignment 1 2

Exams 3 10

Sum 20 40

Total Sum: 60 hours

Credits 2 ECTS



Basic Biotechnology

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.


• 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.


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)




Language: English




Students workload:


Lecture: 26 53

Practical 36 10

Exams: 5 20

Sum 67 83


Credits 5 ECTS



Biochemistry & Molecular Biology

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.


149


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


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


150

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


151

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


152

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)







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



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


153

Course: Pharmaceutical Biotechnology (BT437)


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


Students workload:


Lecture: 42 84

Assignments: 0 5

Exams: 4 15

Sum 46 104


Credits 5 ECTS



Molecular Genetics and Basic Biotechnology

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


154

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-


155

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



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


156

Course: Protein Biotechnology (BT452)




Language: English




Students workload:


Lecture: 26 53

Practical 36 10

Exams: 5 20

Sum 67 83


Credits 5 ECTS



Biochemistry & Molecular Biology

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.


157


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


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







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


whiteboard


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


160

Course: Special Topics A (BT492A)


Course Coordinator: Dr. Khaldon Bodoor

Lecturer: Dr. Khaldon Bodoor

Language: English

Assignment in Curriculum Elective Course for fourth-year students


Students workload:


Lecture: 28 56


Assignments 0 23

Poster: 2 23

Sum 44 106


Credits 5 ECTS



Passing 90 credit hours

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.


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


163

Course: Laboratory Management (BT495)


Course Coordinator: Dr. Rami Alkhatib

Lecturer: Dr. Rami Alkhatib

Language: English

Assignment in Curriculum Compulsory Course in Second Semester of the Fourth year


Students workload:


Lecture: 14 28


Sum 16 44

Total Sum: 60 hours

Credits 2 ECTS



The student should pass 90 credits and above successfully.

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.


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


1. Written exams:



lecture.




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.


165

Course: Ethical Aseptic of Biotechnology (BT496)


Course Coordinator: Dr. Abdulkareem Al-Sallal

Lecturer: Dr. Abdulkareem Al-Sallal

Language: English/Arabic

Assignment in Curriculum Compulsory Course in Fourth year


Students workload:


Lecture: 14 28



Sum 16 44

Total Sum: 60 hours

Credits 2 ECTS



Basic Biotechnology

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.


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


1. Written exams:



lecture.



2. Activities (10%): Students will present about topics related to

course material


whiteboard

Indicative Bibliography/Sources: Cross-cultural Issues in Bioethics: The Example of Human Cloning

Roetz, H., 1st Edition.

Documents

Course Handbook of the Bachelor Degree in · 2019. 4. 17. · Holy Quran, the Prophet’s Tradition, and verse and prose literature. This course also aims to analyze the aesthetic