Download Biochemistry - CEU Cardenal Herrera

COURSE GUIDE
DEGREE
DEGREE: PHARMACY
ACADEMIC YEAR 2016/2017
COURSE: BIOCHEMISTRY
Course Title
BIOLOGY
ECTS
Type
Total
Basic
8
X
Obligatory
Period
Optional
er
1 C
Calendar
2ºC
Weeks
X
17
X
French
Pre-requisites
Course Language
Spanish
Valenciano
English
Departament
BIOMEDICAL SCIENCES
Specific Area of knowledge
BIOCHEMISTRY AND MOLECULAR BIOLOGY
Course Coordinator and other Professors
ENRIC POCH
Name
BEGOÑA BALLESTER
Enric Poch: Room#1455; Seminar Building
Office / Faculty
Begoña Ballester: Room#1455; Seminar Building
[email protected]
Email
[email protected]
Student appointment schedule
Published on internet. Upon request
Introduction to the Course
Biochemistry is the study of the molecular basis of life. This subject aims to provide students with the
fundamental knowledge to understand the molecular basis of biology and its subsequent implementation and
relationship with other subjects such as physiology, pathology and nutrition. In the first part of the course we
will describe the structures of the major biomolecules and their physical and chemical properties, with particular
emphasis on the structure / function.
The second part is focused in the molecular mechanisms of information pathways, an area of biomedical
research with a very important relevance nowadays. The aim of this course is to provide the knowledge about
molecular biology of genes, studying its structure and the different information transmission processes.
Finally, the last part of the course will be focused in the main metabolic pathways of degradation and
biosynthesis of biomolecules. Special emphasis is placed on the idea of the cell as a metabolic unit in which
are integrated and jointly regulate different metabolic pathways.
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Pre-requisites
Students should have a good level of biology and chemistry from High School.
Course Objetives
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To develop the scientific thinking
To use properly biochemistry terms
To practise different experimental protocols in a laboratory
To analyse and criticize the experimental data
Knowledge integration
To understand and solve biological questions
Work in groups
General and Specific Skills Offered by the Course
General Skills.
General Skill 1 Knowledge Acquisition
Building on the foundations laid during their secondary education and with the support of advanced textbooks,
the students will be able to demonstrate a level of knowledge and understanding equivalent to those at the
forefront of their field of study.
General Skill 2 Application of Knowledge
Students will be able to apply their knowledge to their work or vocation in a professional manner and possess
the skills typically demonstrated through devising and sustaining arguments and solving problems within
epidemiology and public health.
General Skill 3 Collect and Interpret and Analyse Relevant Data
Students will gain the ability to gather and interpret relevant data to inform judgments that include reflection on
social scientific and ethical issues.
General Skill 4 Communication
Students will gain the opportunity to improve their communication skills via dissemination of information, ideas,
problems and solutions to both specialist and non-specialist audiences.
General Skill 5 Independent Learning
Students will be required to develop learning skills necessary to undertake in depth, detailed studies with a high
degree of autonomy
Specific Skills related to Pharmacy
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To understand how to applied the scientific method. To acquire abilities in legislation, sources,
bibliography, developing protocols and other aspects considered necessary for the design and critical
assessment of preclinical and clinical trials.
To participate in the health promotion activities, disease prevention having a comprehensive and
multidisciplinary vision of health-disease process.
To Design, to implement and to evaluate reagents, clinical analytical methods and techniques, knowing
the basics of clinical analysis and the characteristics and content of the reports of laboratory diagnosis.
To develop communication skills, both oral and written, to deal with patients and users of the center
where play their professional activity. Promoting work and collaboration capabilities in multidisciplinary
teams and those related to other health professionals.
To recognize the limitations and the need to maintain and update professional skills, with particular
emphasis on self-learning of new knowledge based on scientific evidence.
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General and Specific Skills Offered by the Course
Specific skills related to Biology Module
To understand the structure of biomolecules and their transformations in the cell.
To know the basic structures of biomolecules in relation to their cellular functions.
To know the metabolism of genetic information
To develop skills to identify therapeutic targets of drug production and biotechnology, as well as use of
gene therapy.
To know the main routes of energy metabolism and their regulation and interaction mechanisms in
different tissues of the human body.
To know the main metabolic pathways involved in the degradation of drugs.
Transversal Skills.
The students must show their knowledge of the different areas of knowledge that make up the training
degree program in Pharmacy.
The students must know how to apply their knowledge to their work or vocation in a professional
manner. To have competences demonstrated through devising and sustaining arguments and solving
problems within the areas.
The students must have the ability to gather and interpret relevant data to make judgments, they
include reflection on issues of social, scientific or ethical knowledge that make up the training degree in
Pharmacy program data.
The students must be able to communicate information, ideas, problems and solutions to specialist and
non-specialist audiences.
The students must be able to develop those skills needed to undertake further studies with a high
degree of autonomy.
Course Contents
THEORETICAL CONTENTS:
I. PRINCIPLES OF STRUCTURAL BIOCHEMISTRY
1. Biomolecules. Carbon chemistry. Functional groups.
2. Water and its effect on the biomolecules in solution. pH and buffer systems.
3. Sugars. Aldoses, cetoses, Monosaccharides, disaccharides and polysaccharides.Starch and glycogen.
4. Lipids. Structure and function. Fatty acids. Membrane and signalling lipids. Transport of fats.
5. Amino acids: concept, classification. Amino acid properties
6. Proteins. Composition, classification and functions. Peptide bond. Physico-chemical properties.
7. Working with proteins: separation and purification. Quantification. Electrophoresis, Western blot.
8. Protein structure: primary, secondary, tertiary and quaternary structures. Native conformation.
II. PROTEIN FUNCTION AND ENZYMOLOGY
9. Oxygen binding proteins: myoglobin and haemoglobin study.
10. Enzymes: concept and general characteristics. Enzymatic cofactors: general characteristics and
properties. Study of redox coenzymes. Main group transference enzymes.
11. General mechanisms of enzymatic reactions. Concept of active site
12. Enzyme kinetics
13. Regulation of enzymes: inhibitors, allosteric regulation and covalent modifications.
III. STORAGE AND METABOLISM OF GENETIC INFORMATION
14. Structure of nucleic acid. Denaturation and renaturation. Genes and genomes
15. DNA replication
16. DNA Repair and recombination
17. Structure of RNA and transcription
18. RNA maturation
19. Protein biosynthesis. Translation
20. Regulation of gene expression
IV. PRINCIPLES OF INTERMEDIATE METABOLISM
21. Introduction. Bioenergetics.
22. The Citric acid cycle.
23. Oxidative phosphorylation. ATP synthesis.
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Course Contents
24. Glycolysis. Concepts, reactions and energy balance. Metabolic fates of pyruvic acid: pyruvate
dehydrogenase. Pentose phosphate
25. Carbohydrate biosynthesis: gluconeogenesis.
26. Regulation of carbohydrate metabolism.
27. Lipids, concept, classification, biological importance. Main characteristics. Plasmatic lipoproteins:
concept, structure, classification, composition and metabolism. Absorption and mobilization of fats.
28. Fatty acid oxidation. Metabolism of Ketone bodies.
29. Fatty acid biosynthesis. Synthesis and metabolic fates of cholesterol.
30. Metabolic fates of amino acids carbons, amino acid degradation. Metabolic fates of alfa-ketoacids.The
urea cycle: steps and regulation
31. Amino acids synthesis.
32. Biosynthesis and degradation of nucleotides.
33. Tissue metabolism. Liver metabolism. Erythrocyte metabolism, Adipose tissue. Renal metabolism.
Muscle and brain metabolism.
PRACTICAL CONTENTS
It is organised in 6 practical (5 sessions, 3.5h each, and 1 session of 4h) during the semester.
THE ATTENDANCE WILL BE MANDATORY FOR ALL THE STUDENTS IN THE FIRST REGISTRATION OR
STUDENTS WHO ENROLL FOR THIS SUBJECT FOR THE SECOND TIME THAT REQUEST CONTINOUS
ASSESMENT.
The practical will be in the laboratory. IT IS MANDATORY TO ATTEND THE PRACTICAL WITH LABCOAT,
OTHERWISE THE ENTRANCE WILL NOT BE ALLOWED. NO CHANGES GROUP ARE ALLOWED, EXCEPT
EXCHANGES BETWEEN TWO PEOPLE FROM DIFFERENT GROUP.
PRACTICAL SESSIONS ARE MANDATORY. NON ASSISTANCE TO PRACTICAL SESSIONS WITHOUT
ANY REASON WILL BE CONSIDERED AS NON PRESENTED AND DISCOUNTED FROM ASSISTANCE.
FAILURE TO ATTEND THREE OR MORE ABSENCES WILL PREVENT FROM THE PRACTICAL REPORT
PRESENTATION AND WILL BE SCORED AS A ZERO.
- Practical 1: Problems: Dissolution preparation, buffer solutions.
- Practical 2: Ionic Exchange chromatography.
- Practical 3: Protein analysis by electrophoresis (SDS-PAGE)
- Practical 4: Enzymology. Enzyme activity. Calculation of kinetic parameters
- Practical 5: Purification and analysis of plasmid DNA
- Practical 6: Analysis of digestive enzymes: amylase and pancreatic lipase
WEEK 22-26 OF MAY 2017: SUBMISSION OF PRACTICAL REPORTS. NO DELIVERY OF PRACTICAL
REPORT WILL BE SCORED AS A ZERO ON THE CORRESPONDING ITEM OF THE CONTINOUS
EVALUATION.
Course Structure and Design
Lectures: Training activity oriented mainly to knowledge acquisition (General Skill 1) and representative of the
more theoretical subjects. The priority being the transmission of knowledge from the teacher, the student
requires prior preparation or further study.
It is evaluated by
- Attitude and participation in class
- Midterm exams
- Theory-practical final exam (all the chapters included)
Workshops: Training activity oriented mainly to application of knowledge skill. It prepares the student for
written and oral communication, and transmission of knowledge, after the development of specific subject and
their capacity to be defended in public.
In general, all the projects are related to pathologies. The professor proposes the topics or the students can
suggest one. At the beginning of the course, the topic is assigned and the deadlines are scheduled.
The presentation consists in a 20 minutes of oral defense (power point) and 10 minutes of questions related to
the topic. The same day the students must submit a summary (max 2 pages).
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Course Structure and Design
ASSISTANCE TO SEMINARS AND SUBMISSION OF WORK / EXPOSURE ARE NECESSARY TO PASS
THE FINAL EVALUATION. TO STUDENTS THAT DO NOT ATTEND OR DO THE WORK, AN ADITIONAL
QUESTION ON THE FINAL EXAM WILL BE ADDED.
The attendance to the seminars and the presentation is mandatory in order to pass the course. In case of
absence in this activity and extra question will be added at the final exam.
Assessment:
- Attitude and participation
- Report submission
Seminars: Training activity that promotes student participation in reasoned interpretation of knowledge and
sources in the study area. Is oriented mainly to application of knowledge (General Skill 2) as well as the ability
to gather, interpret and judge information and data (General Skill 3). It is representative of mixed profile
materials or activities, theoretical-practical.
During the course, different techniques and scientific news related to Molecula biology and its application in
Biomedicine will be studied.
Assessment:
- Attitude and participation in class
Practicals: Training activity oriented mainly to application of knowledge (General Skill 2) and representative of
the subjects or practical activities (laboratories, field work, supervised practice, regulated practices, care
practices, practicum, etc).
Assessment:
- Attitude and active participation
- Practical report
Finally, as extracurricular activities, we recommend the attendance to the “Jornadas de Divulgación Científica”,
(CEU-DESCUBRE) that this University offers.
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Estimation od Student Workload
NAME OF SUBJECT
Crédits ECTS:
Breakdown of Student Work Hours
Contact Hours
(A)
Formative Activity
Total Work Hours (C)
Independent
Study (B)
C=A+B
TAUGHT CLASSES
Presentation
1
1
Theory Classes
34
40
74
21.5
15
31.5
7.5
30
37.5
8
5
13
80
80
Debates
Feedback and Review of Assignments
Others
PRACTICAL CLASSES
Problem Solving
Debates
Feedback and Review of Assignaments
Simulaciones
Laboratory
Practicals in the Computer Lab
Visits
Presentation and discussion
coursework assignments
about
Other
SEMINAR CLASSES
Problem Solving
Debates
Feedback and Review of Assignaments
WORKSHOPS
Feedback and Review of Assignaments
Oral Presentations
COURSEWORK
Preparation time required
EXAMS AND ASSESSMENTS
Exam preparation time
3
Exams and Tests
Others
TOTAL
240
RELATIONSHIP BETWEEN WORK HOURS AND ECTS CREDITS
(The result of dividing the number of work hours by the number of ECTS credits
assigned for the course should equal 30 hours as this is the value of 1 ECTS credit at
the Universidad CEU Cardenal Herrera)
30
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Assessment Criteria
Student evaluation will be carried out by a system of continuous assessment based on student’s active
participation and attitude. The purpose of continuous assessment is to encourage and motivate the progress of
pupils throughout the course. It is calculated as a combination of the degree of student involvement, the
acquisition of knowledge and the completion of the assignments set during the practical sessions.
To pass the subject, the student must get 50% of the final degree, obtained from:
- Final exam 60%
- Continuous assessment 20%
- Practicals and practical report: 10%
- Seminars’ project: 10%
- Attitude and participation: 5%
1. Final exam (60% of the final degree) will consist in True/False questions (0.1 points each, one wrong answer
will remove 0.1 points). Short questions (0.5 points) and open questions (1 point each). The students will have
2 h to do the exam.
2. There are 3 midterm exams that will not eliminate content for the final exam. They will consist in True/False
questions (0.2 points each, one wrong answer will remove 0.2 points) and 1-2 short questions. The exam will
be during one class.
3. Practical assessment: attendance and submission of a report. The report will consist in a summary of the
different practical sessions, based on the questions thereby posted. Non appropriate behaviour during practical
sessions will be considered as a reducing mark obtained in this part.
PRACTICAL SESSIONS ARE MANDATORY. NON ASSISTANCE TO PRACTICAL SESSIONS WITHOUT
ANY REASON WILL BE CONSIDERED AS NON PRESENTED AND DISCOUNTED FROM ASSISTANCE.
FAILURE TO ATTEND THREE OR MORE ABSENCES WILL PREVENT FROM THE PRACTICAL REPORT
PRESENTATION AND WILL BE SCORED AS A ZERO.
4. The assessment of the project will be based on the oral presentation. Attendance to the seminars and the
presentation are mandatory to pass the course.
ASSISTANCE TO SEMINARS AND SUBMISSION OF WORK / EXPOSURE ARE NECESSARY TO PASS
THE FINAL EVALUATION. TO THOSE STUDENTS THAT DO NOT ATTEND NOR DO THE WORK, AN
ADITIONAL QUESTION ON THE FINAL EXAM WILL BE ADDED.
5. Finally, the student attitude during the semester will count 5% of the final degree.
Continuous assessment will be only computed if the student get 5 points out of 10 in the final exam.
Resit call (July)
The students that do not pass the final exam can retake the exam in July. Those students can choose another
assessment system. In this case, the students must previously request it, and the final mark will be based
purely on the final exam.
For students who enrol this subject for the second time and choose continuous evaluation must fill the request
(available in intranet), during the first week of the course. Otherwise, the final mark will be based purely on
the final exam.
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Course Program
I. PRINCIPLES OF STRUCTURAL BIOCHEMISTRY
1. Biomolecules. Carbon chemistry. Functional groups.
2. Water and its effect on the biomolecules in solution. pH and buffers
3. Amino acids: concept, classification. Amino acid properties
4. Proteins. Composition, classification and functions. Peptide bond. Physico-chemical properties.
5. Working with proteins: separation and purification. Quantification. Electrophoresis, Western blot
(immunotransference)
6. Protein structure: primary, secondary, tertiary and quaternary structures. Native conformation.
II. PROTEIN FUNCTION AND ENZYMOLOGY
7. Oxygen binding proteins: myoglobin and haemoglobin study.
8. Enzymes: concept and general characteristics. Enzymatic cofactors: general characteristics and
properties. Study of redox coenzymes. Main group transference enzymes.
9. General mechanisms of enzymatic reactions. Concept of active site
10. Enzyme kinetics
11. Regulation of enzymes: inhibitors, allosteric regulation and covalent modifications.
III. STORAGE AND METABOLISM OF GENETIC INFORMATION
12. Structure of nucleic acid. Denaturation and renaturation. Genes and genomes
13. DNA replication
14. DNA Repair and recombination
15. Structure of RNA and transcription
16. RNA maturation
17. Protein biosynthesis. Translation
18. Regulation of gene expression
IV. PRINCIPLES OF INTERMEDIATE METABOLISM
19. Introduction. Bioenergetics.
20. The Citric acid cycle.
21. Oxidative phosphorylation. ATP synthesis.
22. Glycolysis. Concepts, reactions and energy balance. Metabolic fates of pyruvic acid: pyruvate
dehydrogenase. Pentose phosphate
23. Carbohydrate biosynthesis: gluconeogenesis.
24. Regulation of carbohydrate metabolism.
25. Lipids, concept, classification, biological importance. Main characteristics. Plasmatic lipoproteins:
concept, structure, classification, composition and metabolism. Absorption and mobilization of fats.
26. Fatty acid oxidation. Metabolism of Ketone bodies.
27. Fatty acid biosynthesis. Synthesis and metabolic fates of cholesterol.
28. Metabolic fates of amino acids carbons, amino acid degradation. Metabolic fates of alfa-ketoacids.The
urea cycle: steps and regulation
29. Amino acids synthesis.
30. Biosynthesis and degradation of nucleotides.
31. Tissue metabolism. Liver metabolism. Erythrocyte metabolism, Adipose tissue. Renal metabolism.
Muscle and brain metabolism.
Detailed Course Contents
Day 1: Course presentation
WEEK 1
1. Biomolecules. Carbon chemistry. Functional groups.
2. Water and its effect on the biomolecules in solution. pH and buffers
WEEK 2
3. Amino acids: concept, classification. Amino acid properties
4. Proteins. Composition, classification and functions. Peptide bond. Physico-chemical properties.
5. Working with proteins: separation and purification. Quantification. Electrophoresis, Western blot
(immunotransference)
6. Protein structure: primary, secondary, tertiary and quaternary structures. Native conformation.
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Detailed Course Contents
WEEK 3
7. Oxygen binding proteins: myoglobin and haemoglobin study.
8. Enzymes: concept and general characteristics. Enzymatic cofactors: general characteristics and
properties. Study of redox coenzymes. Main group transference enzymes.
WEEK 4
9. General mechanisms of enzymatic reactions. Concept of active site
10. Enzyme kinetics
11. Regulation of enzymes: inhibitors, allosteric regulation and covalent modifications.
WEEK 5
12. Structure of nucleic acid. Denaturation and renaturation. Genes and genomes
13. DNA replication
Mid-term test. Chapters 1-11
WEEK 6
14. DNA Repair and recombination
WEEK 7
15. Structure of RNA and transcription
16. RNA maturation
WEEK8
17. Protein biosynthesis. Translation
18. Regulation of gene expression
Mid-term test. Chapters 12-18
WEEK 9
19. Introduction. Bioenergetics.
20. The Citric acid cycle.
WEEK 10
21. Oxidative phosphorylation. ATP synthesis.
22. Glycolysis. Concepts, reactions and energy balance. Metabolic fates of pyruvic acid: pyruvate
dehydrogenase. Pentose phosphate
WEEK 11
23. Carbohydrate biosynthesis: gluconeogenesis.
24. Regulation of carbohydrate metabolism.
WEEK 12
Mid-term exam, chapters 19-24
25. Lipids, concept, classification, biological importance. Main characteristics. Plasmatic lipoproteins:
concept, structure, classification, composition and metabolism. Absorption and mobilization of fats.
WEEK 13
26. Fatty acid oxidation. Metabolism of Ketone bodies.
27. Fatty acid biosynthesis. Synthesis and metabolic fates of cholesterol.
28. Metabolic fates of amino acids carbons, amino acid degradation. Metabolic fates of alfa-ketoacids.The
urea cycle: steps and regulation
WEEK 14
29. Amino acids synthesis.
30. Biosynthesis and degradation of nucleotides.
31. Tissue metabolism. Liver metabolism. Erythrocyte metabolism, Adipose tissue. Renal metabolism.
Muscle and brain metabolism.
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Basic Bibliography
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NELSON, DAVID L.; COX, MICHAEL M. Lehninger Principles of Biochemistry. 6th ed. W. H. Freeman
and Company, New York. 2012
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BERG, JOHN L.; TYMOCZKO, JEREMY M. Biochemistry: A Short Course. 3rd ed. Palgrave
Macmillan, London. 2015
Additional Reading
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BAYNES, J.; DOMINICZAK, M.H. Medical Biochemistry. 4th ed. Saunders Elsevier, Saint Louis. 2014
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FERRIER, D.R. Biochemistry, 6th Ed. Lippincott’s Illustrated Reviews Series. Lippincott, Williams &
Wilkins, Baltimore. 2013
Other Support Materials
Recommendations to Students Taking This Course
All students are expected to adhere to the university rules governing attitude and behavior in class. The rules
are available upon request on the Academic Coordinator/ Dean Office.
Links to Ongoing Research
Links to the Profession
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