BIOCHEMISTRY
COURSE 2016-2017
1. Course Description ............................................................................ 1
2. Background....................................................................................... 2
3. Specific Competences. ....................................................................... 2
4. General Competences ........................................................................ 3
5. Outline Content ……………………………………………………………………………………….4
6. Instructional Activities ....................................................................... 7
7. Teaching methodology ....................................................................... 7
8. Ongoing assessment and specific rules ............................................... 7
9. Text Books
…………………………………………………………………………….… 10
10. TimeTable………………………………………………………………………………………………..11
11. Resource………………………………………………………………………………………………….13
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1. Course description
Name of the subject: BIOCHEMIST RY
Code: 9999001108
Title: GRADE IN ODONTOLOGY
Course:
FIRST COURSE
ECTS CREDITS: 6
Nº of hours: 5 hours/week
Modality: in classroom teaching
Name of the Professor: Apolonia Novillo, Maria José Blanco, Maria Antonia Cid, Maria
Angela Tabone, Maria del Rocio González.
Implicated in Active methodologies: David Ballesteros, Marta Lesmes, Alicia Romero,
Francisco Suárez, Ana Sánchez, Emma Muñoz, Iván Rodriguez, Vinatha Sreeramkumar.
Office hours: The calendar of office hours will be published in the blackboard. Students
should send an e-mail to the teacher showing interest for office hours. Office hours will be
available every week.
2. BACKGROUND
The education of future professionals is the principal goal of the University, and the
subject of Biochemistry has become the foundation for understanding all biological
processes in physiological conditions. It provides basic information about the causes
of many diseases in humans and animals.
3. Specific competences.
Upon completion of this course, students with a passing or above grade will have an
understanding of the following content areas:
1 – To understand the role of biochemistry in the structure and function of
living matter at the molecular and cellular level.
• To know the chemical components of cells and the different types of bonds
between molecules, to understand the biochemical basis of cell function.
• To know the physical and chemical characteristics of water and its role in
processes of chemical dissociation of compounds in dilution, given its importance as a
major constituent of cells.
• Integration of pH concept and the mechanisms involved in maintenance of body
fluid and pH homeostasis. Role of buffers in biological processes. Importance of buffers
in the maintenance of the physiological pH.
2 To understand the importance of structural and functional
characteristics of biomolecules, the metabolic processes and how some
molecules store and transmit biological information.
• To know the chemical and structural nature of each set of relevant biomolecules:
water, carbohydrates, lipids, proteins and nucleic acids
• To understand the function of different biomolecules in the cell and in a
multicellular organism
• To understand the importance of storage of genetic information in eukaryotic cells
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• To understand the concepts of transcription, translation and replication processes
as fundamental for understanding gene expression and genotype-phenotype
relationships of organisms
3 – To Develop and understand cellular metabolic processes as a basis for
energy production and for biosynthesis of structural molecules.
• Identification of the source of energy and the source of carbon for the synthesis of
cellular material and for the classification of living organisms.
• To know the metabolic pathways of carbohydrates: catabolism in aerobic and
anaerobic conditions; anabolism from different organic sources.
• To know the bioenergetics according to the physiological status of living organisms
and the source of carbon used.
• To know the catabolism of lipids and their potential energetic value compared to
carbohydrates.
• To know degradation pathways of proteins, the removal processes and reutilization
of proteins by the organisms.
4. General competences (from UEM)
The following competences will have developed and assessed during this course:
Proper oral and written communication
Ability to work in a team
Self-learning (Autonomous learning)
Work-planning and responsibility
Critical reasoning
Ability to integrate information: the basic subjects (biochemistry, genetics,
biology, histology, physiology and anatomy) during the first year are not
isolated disciplines. The student should be able to establish relationships
between them and with the real world.
Sustainability
5. Outline Contents.
BLOCK I: INTRODUC TION AND BIOCHEMISTRY FOUNDATIONS
LESSON 1. Introduction to Biochemistry
1.1.
Basic concepts in modern biochemistry. Origin of Biochemistry as an
experimental science. Relationship with other sciences. Role of biochemistry within
the context of biomedical sciences.
LESSON 2. Chemical Foundations of Life
2.1. Chemical components of cells.
2.1.1. Inorganic compounds. Atomic structure. Bioelements. The main chemical
elements of human body. Mineral elements related to oral environment: calcium,
phosphorus, magnesium and fluoride.
2.1.2. Organic compounds: Carbon and its functional groups.
2.1.3. Chemical bonds: definition and types.
2.1.3.1. Covalent bonds: Polar, Nonpolar
2.1.3.2. Non-covalent bonds: ionic, metallic, hydrogen bonds, van der Waals forces
and hydrophobic interactions.
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BLOCK II. STRUCTURE OF BIOLOMECULES
LESSON 3. Water.
3.1. Introduction. Structure of the water molecule.
3.2. Physical-chemical characteristics of water.
3.2.1. Water as a solvent. Solubility and precipitation concepts. Polar, nonpolar and
amphipathic molecules. Concentration of a solution: percentage and molarity.
3.2.2. Cohesion, adhesion and capillarity. Surface tension.
3.3. Water ionization. Acid, Bases and Salts. Amphoteric substances
3.4. Acid-Base equilibrium: pH concept.
3.5. Weak acids and bases. Dissociation degree: constant of ionization. Conjugated
Acids and bases. pH maintenance and Buffer systems. Buffers of biological interest.
LESSON 4. Proteins.
4.1. Characteristics
4.2. Amino acids: Structure and classification. Properties
4.3. Peptidic bond
4.4. Structure of proteins. Structure-function of proteins, physic -chemical factors
impacting the structure and function of proteins
4.5. Classification of proteins
4.6. Biological function of proteins
4.7. Proteins that bind ligands: Reversible binding. Proteins that bind oxy gen.
Antigen-antibody binding.
LESSON 5. Carbohydrates.
5.1. General properties
5.2. Structural characteristics and classification.
5.3. Monosaccharides. Chiral molecules, type of isomers, Cyclic forms.
Monosaccharides of biological interest.
5.4. Disaccharides. Disaccharides of biological interest. Glycosidic bond.
Monocarbonilic and dicarbonilic bonds. Reducing sugars.
5.5. Polysaccharides. Classification. Function.
LESSON 6. Lipids.
6.1.General properties
6.2. Structure, properties and functions of lipids. Fatty acids
6.3. Classification I. Lipid saponification: Fat. Functions
6.4. Classification II. Non-saponification Lipids: terpenoids, Steroids, Eicosanoids.
Importance of Prostaglandins.
6.5. Monolayers, bilayers and micelles.
LESSON 7. Nucleic acids.
7.1. Structural elements: nucleosides and nucleotides.
7. 1.1. Types of nucleic acids: DNA, RNA.
7.1.2. Nucleotides of biological interest with energetic function: ATP and GTP.
7.2. Structure of DNA.
7.2.1. Physical-chemical factors that affect DNA structure.
7.2.2. Packaging of DNA in eukaryotes.
7.3. Structure of RNA and different types of RNA molecules.
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7.4. Functions of nucleic acids. Differences and similitudes among different types of
nucleic acids. Cellular location of these molecules.
7.5. Concept of Gen. Differences between eukaryotes and prokaryotes
BLOCK III. FUNCTION OF BIOMOLECULES
LESSON 8. Enzymes.
8.1. Definition and characteristics of enzymes
8.2. Enzymes and catalytic molecules. Enzyme kinetics
8.3. Regulation and control of enzyme activity. Inhibitors. Alosterism. Temperature
and pH.
8.4. International Classification.
8.5. Cyclooxygenase and inflammatory processes
LESSON 9. Hormones. Second Messenger. Vitamins and cofactors.
9.1. Hydrosoluble and lyposoluble hormones. Structure and function.
9.2. Second messengers: Phosphatidylinositol and cAMP.
9.3. Vitamins and cofactors.
9.3.1. Hydrosoluble vitamins. Vitamin C and its effects on oral tissues. Other
hydrosoluble vitamins and cofactors.
9.3.2. Liposoluble vitamins: A, D, E and K.
LESSON 10. Biochemical Composition of Biological Membranes.
10.1. Introduction. Composition and structure
10.2. Membrane dynamics
10.3. Proteins in the membrane: Proteins involved in Transport .
LESSON 11. Biochemical Composition of Extracellular Matrix.
11.1. Components. Proteins: collagen, fibronectin, laminin. Glycoconjugates:
hyaluronic acid, proteoglycans and glycosaminoglycans.
11.2. Basal lamina. Degradation of extracellular matrix and basal membrane;
relationship with periodontal disease.
LESSON 12. Composition and Function of Saliva
12.1. Composition.
12.1.1. Organic compounds. Proteins: mucins, statherins, proline-rich proteins,
histatins and cystatins; saliva enzymes: amylase
12.1.2. Inorganic compounds. Calcium and phosphate levels
12.2. Saliva functions
12.1.1. Buffering function: acid-base equilibrium
12.1.2. Effect of low pH values on demineralization of dental enamel and cariogenic
process.
12.3. Carbohydrates into the oral cavity.
BLOCK IV. METABOLISM
LESSON 13. Cellular Metabolism. Introduction.
13.1. Capture of nutrients and production of energy.
13.2. Nutrition forms: autotroph and heterotroph organisms; phototrophs and
chemotrophs
13.3. Metabolic processes: nutrition, cellular respiration and biosynthesis
13.4. Definition of Metabolism. Types of metabolism: Catabolism and anabolism.
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LESSON 14. Carbohydrate Metabolism.
14.1. Catabolism
14.1.1. Glycolysis; Fermentation and oxidation: Krebs cycle and oxidative
phosphorylation
14.1.2. Catabolism of polysaccharides
14.1.3. Glycogen breakdown
14.2. Anabolism
14.2.1. Gluconeogenesis
14.2.2. Glycogen synthesis.
LESSON 15. Lipid Metabolism.
15.1. Catabolism of lipids. Degradation of triglycerids
15.2. Beta-oxidation
15.3. Anabolism of lipids
15.4. Ketosis
LESSON 16. Protein Metabolism.
16. 1. Catabolism of proteins. Degradation of proteins: deamination of proteins
16.1.1. Urea Cycle
16.2. Anabolism of proteins. Essential amino acids
6. INSTRUCTIONAL ACTIVITIES:
The course will be taught using multiple instructional methods.
A. Lectures: Professor will be responsible to give an oral presentation in class, to
teach students about relevant concepts of subject under study. The lectures are
used to convey background and critical information to help students to
understand and to learn the more relevant concepts of biochemistry.
B. Application of active teaching methodologies in class: Students will go in
depth in theoretical contents of the subjec t using the following methodologies:
- Cooperative learning: Students should work in small groups to solve
problems or questions according to teacher instructions.
-"Flipped classroom": the students will make practical activities in order to
apply their knowledge of the subject in an autonomous way.
- Problem-based learning applied to the integrated content of basic
subjects: the students will be able to integrate information from different
subjects through a clinical case that they need to solve in a team. They
would have to elaborate their answers, and the debate about them will serve
to reinforce the previous acquired knowledge.
C. Performing Laboratory Practice: Students will work individually or in pairs in
the laboratory. The student should get familiar with laboratory equipment and
understand biochemical processes related to the principal topics of the specific
content. Furthermore, students will approach to the scientific method through
the observation and description of a phenomenon, formulation of a hypothesis
and using the hypothesis to predict the existence of other phenomena, or to
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predict quantitatively the results of new observations. Also, students will be able
to perform experimental tests.
D. Office Hours: Your teacher will be available to answer your questions
immediately before or after class, or at office hours. Attendance at office hours is
strongly encouraged, and should be requested by individual and/or group of
students.
7. TEACHING METHODOLOGY.
Teaching strategies include theory lessons and laboratory practices, which will be
combined with active methodologies and with methodologies directed towards
problem-based learning, case method, flipped classroom, integrated transversal
and vertical activities, online quizzes and assistance to scientific seminars related
with the subject. Activities will be supported by scientific bibliographic resources,
online tools through the Blackboard, and specific web applications in the computer
rooms of the UEM.
8. ONGOING ASSESSMENT AND SPECIFIC RULES.
The overall score of the course is obtained from scores obtained on two types of
assessment which have the following weight:
ASSESSMENT OF RELEVANT CONCEPTS (written examinations):
Written test 70%
ASSESSMENT OF ASSIGNMENTS (Laboratory work and activities):
30% performing individual and group activities.
IMPORTANT: The final score of the course results from the weighted sum of
the grades obtained in the different assessments: written examinations,
laboratory work and activities. It is mandatory to obtain a grade of 5 in
each of the different parts of the subject.
ATTENDANCE
According to the rules of evaluation of the European University of Madrid (Article 1,
Section 4), 50% attendance to class is a mandatory condition to pass the subject in
the first call. Attendance lower than 50% will automatically lead to a failing grade in
the first call.
In order for your attendance to be registered you need to use the appropriate device
located next to the entrance of the class. Make sure you are rigorous in doing this
daily. Your ID card must be activated.
ASSESSMENT OF RELEVANT/SPEC IF IC CONCEPTS
Accounts for 70% of the final score of the course.
TESTS (Written examinations)
Students will have two opportunities (ordinary test and extraordinary test) to pass
the course through the semester. The dates of each test will be published in
advance in the campus virtual (Blackboard).
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Each of the different tests will consist on at least 50 multiple choice questions.
The multiple choice test with 4 options will be corrected penalizing the wrong
answers (-0.33 for wrong answer).
1 -. ORDINARY TEST
During the course (semester) will be two independent MID-TERMs.
Each MIDTERM test will have a maximum score of 10 points. The grade ≥5 points
must be obtained in each midterm to pass the subject.
The FIRST MIDTERM will account for 40% of the final score and the SECOND
MIDTERM will account for 60% of the final score.
The SECOND MIDTERM will contain 10% of questions of the First midterm.
Minimum
grade to
pass
ORDINARY TEST
Written
examination
70%
5
First Midterm
40%
5
Second
Midterm
60%
5
Laboratory
Practices
20%
5
Activities
10%
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The students may add a maximum of 0,5 points to the grade obtained in each
written examination; in this case students must attend at least at 50% of the
classes and perform the class activities proposed by the professor (see Other
activities).
In the case that student has not pass the FIRST midterm test, he will have a new
opportunity at the same time that the second Midterm takes place.
2.- EXTRAORDINARY TEST (in July)
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Students that fail any of the midterms or both will have a written examination in
July. 5 points must be obtained to pass this examination.
ASSESSMENT OF LABORATORY WORK AND ACTIVITIES
This part accounts for 30% of the final score of the course.
It consists of two types of assessments: laboratory work and activities.
1) ASSESSMENT of the laboratory work:
The laboratory work accounts for 20% of the final score of the course.
Attendance at laboratory practice is compulsory; the unexcused absence will
be a zero in that practice. It is compulsory to wear a lab coat and bring a printed
copy of the protocol. It should make good use of the material provided for each
practice.
There will be a total of 5 practices:
-P1: Introduction to the work in the laboratory and application to the Practical work
in the Clinic and in Odontology: risks, management of waste and materials.
-P2: pH and buffer solutions
-P3: Integrated Activity: Structure and Function of Blood components.
-P4: Integrated Activity: Salivary composition and enzymatic activity.
-P5: Integrated Activity: Anatomy, Physiology, Histology and Metabolism of the
skeletan muscle.
If a student does not justify the absence to two practices; or has an average score
< 5 he will fail this part of the subject and the course. The laboratory work c an be
retaked in the July session.
The assessment of the laboratory work will be performed as follows:
1) - performing a score sheet, setting out clearly and accurately the work related to
the development of the practice, which must be agreed by partners.
2) - performing an individual test to check the level of integration of the knowledge
acquired during the development of the practice (to be determined).
Furthermore, to pass laboratory practices will require compliance with the following
competences:
• Responsibility: punctuality, wearing the robe, and bringing the protocol and
material specified for each practice
• Adequacy of experimental work: cleanliness, order, compliance with safety rules in
the laboratory and proper use of the material,
The performance of the laboratory practices is a mandatory activity. The
student must get ≥5 points to pass the laboratory work and the course.
2) ASSESSMENT OF COMPULSORY ACTIVITIES
This part accounts for 10% of the final score of the course. The student must get 5
points to pass the ACTIVITIES and the course.
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The activities will allow to the teacher perform an ongoing assessment of the
progress of the student through the acquisition of specific and general competences.
The activities will be performed in class and are compulsory. The average rating of
the activities must reach the value of ≥ 5 for passing the subject.
The performance of these activities is mandatory. The student must get ≥5
points to pass the course.
3) ASSESSMENT OF OTHER ACTIVITIES:
Furthermore, students could perform other activities proposed by the teacher. The
assessment of these activities will be performed according to a rubric that will be
provided to the student to have a priori knowledge of the grading criteria.
Students that perform the activities will get 0,5 points more in the final score of
each written examination only if the attendance of the students to the classes is
above 50% and they perform the different activities.
SPECIFIC RULES
If a student does not attend to test exams, activities, and laboratory work he must
justify the absence. If the absence is justified he will have a rating of "not
presented: NP”; and he will have a second opportunity retaking the corresponding
missed activity and/or test. The reasons to consider a valid JUSTIFICATION are:
official sporting participation, legal warning, family illness and death. If a student
does not justify the absence to laboratory work, activities or Midterms will have a
rating of CERO.
To attend to laboratory work, the student must bring a lab coat and appropriated
shoes.
Disciplinary action will be taken in the following cases:
1. Use of mobile phones or any other electronic device during the tests.
Students who are in a situation "suspicious" during the assessment tests and
are carriers of any electronic device (on or off) will be punished according to
the internal regulations of the University.
2. Plagiarism of intellectual property of the teacher. Any recording media
(voice, image, presentations ...), may be considered cause for suspension.
3. Lack of respect (physical or verbal) to any member of the university
(teaching staff, non-teaching staff or students).
9. TEXT BOOKS
- ONLINE FREE BOOKS: http://www.ncbi.nlm.nih.gov/books/?term=Biochemistry
-LEHNINGER, David L. Nelson, Michael M. Cox. Principles of Biochemistry 6th Edition.
Macmillan Higher Education. 2013. Hard Cover. Colección General QH345 .L445 2013
- LEHNINGER. Principles of Biochemistry PDF. Publisher : W.H. Freeman. Publication
date : November 21, 2012. Language. English. ISBN-10: 1429234148. File
format : PDF. File size : 79 MB
-MATHEWS C.K. and VAN HOLDE K.E.. Biochemistry. 2nd. McGraw -Hill, 2008
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-HORTON H. R. et al. Principles of Biochemistry. 4th. Prentice Hall 2007
-McKEE, T. and McKEE, J.R. Biochemistry. Molecular bases of life. 3rd. McGraw HillInteramericana.
- MARTIN LEVINE. Topics in dental Biochemistry. 2011. Edi. Springer.
Hardcover. ISBN 978-3-540-88115-5
e-book: ISBN 978-3-540-88116-2
- VOET D, VOET J.G. Biochemistry. 4ª John Wiley and Sons,
Inc 2011. Colección
General QD415.3 .V64 2011.
- STRYER L, Biochemistry, 8ª Ed. Macmillan Learning, 2015. Hard cover: ISBN-10:
1-4641-2610-0; Format: Cloth Text, 1120 pages
10.
TIME TABLE
WEEK 1-2
Aim: To study basic concepts in Modern Biochemistry. To know the importance of
Biochemistry as an experimental science and to understand the importance of Biochemistry
within the framework of experimental sciences and their contribution in the context of
Biomedical Sciences. To know the organic and inorganic chemical components of cells. To
know the types of chemical bonds present in the molecules, to further understand the
biochemical basis that underlies the cellular function. To know the risks and residues
generated in a laboratory and in the dental clinic.
Homework: Watching videos produced by the Biomedical department about working rules in
the laboratory: risks, waste management and material handling. Identification of different
functional groups and types of bonds in different biomolecules. To study the new concepts
explained in class.
Homework: Visionado de videos producidos por el departamento de CC. Biomédicas sobre el
trabajo en el laboratorio: riesgos, gestión de residuos y manejo de materiales. Identificación
de diferentes grupos funcionales y tipos de enlaces en distintas biomoléculas. Estudio de
nuevos conceptos explicados en el aula.
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WEEK 3-7
Aim: To know the physico-chemical characteristics of the water and its participation in
processes of dissociation and solubility, given its relevance as a major compound of the cells.
Integrate the concept of pH within the regulation of the internal environment of the cell a nd
organism. To understand the biological function of buffer solutions. To know the chemical and
structural nature of organic biomolecules: proteins, carbohydrates, lipids and nucleic acids.
Identify the different types of carbohydrates, lipids, proteins and nucleic acids , and to
recognize the biomolecules of biological interest. To be familiar with the classification and
biological importance of the different organic biomolecules studied according to their function,
and their cellular location. To get familiar with the concept of Isomers. To know the concept of
gene. Integrate all acquired concepts.
Homework: Resolution of practical problems related to the concepts explained in the
classroom. To read the recommended bibliography. To study of new concepts explained in the
classroom. To review the previously acquired knowledge for the preparation of t he first
midterm exam.
WEEK 8-12
Aim: To know about the characteristics of the enzymes. To understand enzymatic kinetics
through problem solving. To know the International classification of enzymes and the
mechanisms of regulatory activity of enzymes. To know the characteristics of hormones,
vitamins and second messengers; and identify the structure of these molecules with the
biological function. To integrate the concepts previously learned, and to apply these concepts
through the specific study of saliva, biological membranes and extracellular matrix.
Homework: To perform the practical activities proposed by the teacher related to the
subject. To study of new concepts explained in the classroom.
WEEK 13-14
Aim: To know the different types of metabolism. To know how organisms obtain chemical
energy. To know the main catabolic and anabolic routes of carbohydrates . To learn the
regulation of studied metabolic pathways.
Homework: To sketch a scheme that compiles the main characteristics of the metabolic
routes studied. To read the recommended bibliography. To watch different multimedia
resources. To study of new concepts learned in class.
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WEEK 15-18
Aim: To know the main catabolic and anabolic routes of lipids and proteins. To learn the
regulation of studied metabolic pathways.
Homework: To sketch a scheme that compiles the main characteristics of the metabolic
routes studied. To read the recommended bibliography. To watch different multimedia
resources. To study of new concepts learned in class. To review and intensive study session of
the previously acquired knowledge for the preparation of the second midterm exam.
11. Resources
Laboratory of practical work in biochemistry (C203-205)
Interactive board
Blackboard
Multimedia resources
UPDATED
September 2016
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