Curriculum for Medical Biochemistry

1/1/2017
Curriculum for Medical Biochemistry
For 1st and 2nd year Medical students
Curriculum for Medical Biochemistry

Faculty of Medicine-Department of Biochemistry-University of Benghazi

Course Specifications:

Program is given for: Bachelor Degree of Medicne
Major or Minor element of programs: Single major
Department offering the course: Biochemistry
Academic year – level: First and Second year
Date of specification approval:……………………………….

Basic Information:

Title Biochemistry

Code: …………………….

Course Language: English

Lectures: 5hrs/week

Practical: 3hrs/week

Total: 8hrs/week

Hours of 1st year (theory) 75hrs/year

Hours of 2nd year (theory) 75hrs/year

Credit Hours ……………………

Professional Information

Overall aim of the course:

Understanding of biomolecules is driving the revolution in biology and medical science, pertinent to that is how the basic principles of biochemical structure and molecule behavior govern molecular regulation in normal human health or malfunction in disease. The subject of biochemistry at the University of Benghazi Faculty of Medicine is divided into two distinct and separate courses.

The year 1 course focuses on the basic structure and function of macro and micro biomolecules.The year 2 course focuses on Metabolic Biochemistry, i.e. biochemical pathways involved in intermediary metabolism, in addition to molecular biology and bio signaling. Normal function and how disease states are developed if these functions are abrogated is a main issue handled in these courses.

Finally, the course is designed to help students build up knowledge and skills in an ethical and moral manner.

Knowledge:

At an early stage students must understand that there is a responsibility for lifelong learning to update knowledge and remain in touch with the developing scientific basis of medicine. In order to achieve that they must learn sufficient basic knowledge of the structure and function of biomolecules, cellular and biochemical mechanisms that maintain body homeostasis. They are then able to comprehend molecular basis of disease and incorporate biochemical and molecular mechanism in diagnostics and therapeutic regimens.

The knowledge that students will gain from this course will give them the ability to appreciate how complex biomolecules are created and interconverted in our cells to provide energy, structure and function. Understanding biochemistry will also benefit the students to better understanding other courses such as pharmacology, immunology, physiology, etc., and to explain disease states on molecular basis.

Values Attitudes and Behaviors

Students will be trained to be trustworthy and truthful through handling of their laboratory work and presenting their assignments. At all times they will be encouraged to act with integrity dignity and honesty showing respect for their fellow students and mentors.

COURSE OBJECTIVES:

The objectives and content of the Basic and Metabolic Human Biochemistry course are designed to provide students with a comprehensive understanding of the structure and function of biomolecules, and metabolic pathways involving the major metabolic compounds, i.e., carbohydrates, lipids, amino acids and nucleotides; and the manner by which metabolism is normally integrated and regulated. This course stresses both the normal metabolic function, and how disease states arise if normal metabolic processes are disrupted.

Upon completion of the course student should be able to:

Identify basic principles of structure and function of the compounds involved in metabolic processes.
Keep in mind the subcellular localization of metabolic pathways to coordinate metabolic regulation.
Know and correlate between the anabolic and catabolic pathways and their important enzymatic steps.
Understand energy yield requirements and processes and thermodynamic elements involved in energy production.
Link the regulation of processes of biochemical pathways and show how they lead to normal integrated metabolism.
Reach conclusions on how abrogation of normal integrated metabolism can result in various disease states.

Teaching Strategies

In the first part of this biochemistry course teaching is organized to give students the basic knowledge necessary to appreciate and understand metabolism in the upcoming parts. Hence, structure and function, and enzymology will be covered.

In the second part topics are organized to cover individual pathways separately, discussing the function of each pathway, entry point of substrate and exit points out of the pathway, intermediary substrates and important regulatory reactions or mechanisms, energy and thermodynamic considerations, and stressing how the pathway could be appreciated by the student. During this, students hopefully can begin to think of relevance of biochemistry in medicine, i.e., think about what goes on inside the cells when they deliberate a drug interaction, a hormonal response, or a clinical setting.

In the third part we try to make connections between pathways, this is difficult during the first two parts, before students have been exposed to all of the necessary pathways. As such, discussions of initial disease states of conceptually of more simplistic state often pertain to errors at one specific step within a given pathway. However this is contrary to more complex metabolic diseases, which can affect numerous pathways simultaneously. Therefore, through more complex diseases such as diabetes and dyslipidemia, the pathways are revisited and better integrated together. The ultimate goal is for the students to better understand intermediary metabolism as a whole using these metabolic disease states.

The subject of human or medical biochemistry is conceptually difficult subject to understand. It is built upon the understanding of complex structures, complicated names and mechanisms. Students built the habit of memorizing for the exams. However, it is our responsibility to break this habit, and help studentsunderstand biochemistry rather than memorize it. They need to think about the steps, what are the consequences if a molecule is made over another, how this affects metabolism in general, and what this will mean to cellular health for the patient. This higher level of biochemical appreciation requires more than just memorizing the pathways.

With less time dedicated to labs and small discussion groups, it is strongly recommended that students spend additional time in reviewing other educational resources. We, in addition, encourage students to

Read ahead of time. A systematic and regular study routine is vastly superior to the "cram before the test" approach. In addition to the limited number of labs, to help the students learn the material from lectures, a number of tutorials are designed for a regular study routine.
Students should keep up-to-date, students shouldnot leave the material until they are certain they understand every aspect thoroughly.
Utilize the guides provided by the lecture objective, important lecture concepts, key words and phrases which should be completely understood, and questions that test your basic understanding of the lecture concepts.
Utilize the lecture hand-outs, which include all of the lecture slides and add to that their own additional notes. These are useful in lecture so as to limit the amount of additional writing. Much is already in the hand outs, enabling the student to listen and digest the material given by the lecturers, especially true if the student has already previewed the material before class. After the lecture students should take these notes and fill in the blanks with the text using the study guides. In addition, by sheer repetition, you will have already assimilated much of the material, thereby reducing the need to cram later.
Students should utilize recorded lectures when available. They should be utilized to go over the material as many times as necessary to fully comprehend the lectures. Use this also to help expand your class notes, or to correct any misconceptions or confusions you may have about a topic. Students who do not attend lectures and utilize notes and recordings may put themselves at a disadvantage by not being in contact with the lecturer, get used to absenteeism, and may miss understand certain points if suitable and clear notes are not available.
Students should attend the tutorial sessions. At regular intervals, tutorial sessions are scheduled each weak to reinforce learned knowledge in small groups. During these sessions, the course director will raise certain questions to clarify ideas and discuss relevance of topic to the course and students’ career.
Students should not take information for granted, but rather should study actively and test their knowledge objectively. Much scientific material is provided for students through their teachers and libraries, and online information. However, we encourage them to self-study and self-test them-selves using these materials. They should not feel secure and compile information for exam study.

Intended Learning Outcomes (ILO)

Medical students who have completed the two parts course of Biochemistry program will have the ability to demonstrate:

Understanding of the key principles of biochemistry.
That they are at the required level of awareness of ethical issues of biochemical in relation to laboratory findings and their careers.
To have the ability to recognize how fundamental chemical principles and reactions are utilized in biochemical processes. This requires the ability to integrate prior chemical knowledge with the complex reactions within the living cell.
The ability to recognize how common foodstuffs are turned into metabolic energy, and the ability to predict the energy content and value of different classes of chemical compounds. In addition to the ability to calculate the energy yield from the catabolism of a relevant compound.
Understanding of the three-cornered central paradigm of biochemistry: replication/transcription/translation, and how they are related to metabolism and body homeostasis.
The recognition of the general principles of how chemical signals present in trace amounts are signals that are amplified into whole organism responses.
The ability to reconstruct the anabolism of the essential building blocks of life.
Upon completion of the whole course students should have developed a thorough understanding of the chemical and regulatory interrelationship between major cellular synthetic and catabolic pathways.
Upon completion of the whole course students should have the ability to utilize their biochemistry background knowledge to understand molecular basis of disease, and discuss relevance of laboratory tests to patients’ disease and wellbeing.

Communication Skills:

By the end of the course, students should be able to:

1-Work effectively in a group in lab.

2- Respects the role of staff and co-staff members regardless of degree or occupation.

Intellectual Skills

By the end of the course, students should be able to:

1. Interpret the observations of chemical tests to measure unknown concentration of biochemical compounds such as sugar or protein in serum or plasma.

2. Identify abnormalities of biochemical tests (low or high).

3. Interpret the test results and link them to the related clinical conditions.

9.Practical and professinal skills

By the end of the course, students should be able to:

1.Link test abnormality to expected diagnosis and suggest advice about patient state of health.

2. Identify the physical and chemical characters of normal urine under different physiological conditions.

3. Perform chemical tests to detect abnormal constituents of urine.

General and Transferable Skills

1- Use computers efficiently in reaching biomedical information to remain current with advances in knowledge and practice.
2- Communicate with colleagues and work in groups as well as independently.
3- Communicate ideas and arguments effectively and develop speaking skills during tutorial and oral exams.
4- Self learning and manage time and resources effectively and set priorities

Course Outline

Although detailed course contents are produced under separate documents, the following represents the course outline for year 1 and 2.

Syllabus for Part 1 Biochemistry

I)Theory

Introduction of Biochemistry:
Biochemistry of the Cell: a) Introduction to cell (Biochemical point of view) b) Scientific methods to study the cell biochemistry c) Biochemical composition of the cell 2. Biochemistry of the Cell and Body Fluids: a) Ionization of water & weak acids, bases b) Concept of pH, and pH scale c) Dissociation constant & titration curve of weak acids, the concept of pK values d) Buffers, their mechanism of action e) Henderson-Hesselbalch Equation (No derivation) f) Types of particles, solution g) Importance of selectively permeable membranes, osmosis, osmotic pressure, surface tension, viscosity & their importance related to body fluids
Carbohydrates: a) Definition, biochemical function and classification b) Structure and functions of Monosaccharides, and their derivatives c) Disaccharides, their important examples d) Oligosaccharides, their combination with other macromolecules e) Polysaccharides, their important examples and biochemical role f) The biomedical importance of carbohydrates
Proteins: a) Definitions, Biomedical importance and classification of proteins based on - Physiochemical properties - Functional - Nutritional - Structural b) Amino acids, their structure, properties & functions c) Classification and nutritional significance of amino acids d) Dissociation, titration and importance of amino acid in pH maintenance e) Structure of proteins and their significance f) Separation of proteins e.g. salting out, Electrophoresis, Chromatography, Centrifugation g) Immunoglobulins and its biomedical significance h) Plasma Proteins & their clinical significance
Lipids: a) Definition, biomedical function b) Classification of lipids c) Phospholipids, Glycolipids, Sphingolipids and their Biochemical Significance d) Fatty acids, chemistry, classification and biochemical function e) Essential fatty acids f) Eicosanoids, their classification and functions in health and disease g) Steroids, Sterol e.g. Cholesterol, their chemistry, functions and clinical significance h) lipid peroxidation and its significance
Nucleotide & Nucleic Acid: a) Chemistry and structure of nucleosides and their biochemical role b) Nucleotides, structure, their derivatives and their biochemical role c) Synthetic derivatives of purine and pyrimidines, their role in health and disease d) Nucleic acids, their types, structure and functions
Biological Membrane: a) Biochemical composition b) Biochemistry of cell membrane, chemical composition, importance of lipid and proteins in membranes, chemistry of signals and receptors c) Biochemistry of membrane transport mechanism, active transport, passive transport, simple and facilitated diffusion
Enzymes: a) Introduction, definition, mechanism of catalysis b) Coenymes, co-factors c) Isoenzymes, their clinical importance d) Factors affecting enzymes activity, Michaelis-Menten Equation, Lineweaverburk equation and their application in enzyme kinetics (no derivation of equations) e) Enzyme inhibitors and their classification & biomedical importance f) Application of enzyme in clinical diagnosis and therapeutic use
Prophyrins & Hemoglobin: a) Chemistry and biosynthesis of porphyrins and its disorders (Porphyrias) b) Structures, functions and types of haemoglobin c) Oxygen binding capacity of haemoglobin, factors affecting and regulating the oxygen binding capacity of haemoglobin d) Degradation of heme, formation of Bile pigments, its types, transport and excetion e) Hyperbilirubinimea, their biochemical causes and differentiation, jaundice and its types f) Haemoglobinopathies (Hb-S, thalassaemia etc.) and their biochemical causes.
Vitamins: a) Introduction, classification b) Chemistry, Biochemical Functions, Deficiency manifestations, daily allowances and source of water soluble and fat-soluble vitamins c) Hypervitaminosis
Biochemistry of Digestive Tract: a) Introduction of digestion and absorption b) Introduction, composition, functions, daily secretion, stimulants and depressants of - Saliva - Gastric Juice & HCL - Pancreatic Juice - Bile Juice - Succus Entericus c) Digestion and absorption of carbohydrates, proteins, nucleic acid and lipids d) Biochemical disorders of GIT, e.g. achlorhydria, peptic ulcers, lactose intolerance, cholelithiasis and related disorders
Mineral & Trace Elements: a) Classification and Biochemical role of: - Macro minerals (Na, K, Ca, Cl, PO4) - Micro minerals (Fe, Zn, Mg, Se, I, Cu, Cr, Cd, Mn)
Nutrition: a) Caloric requirements of the body b) Balanced Diet c) Protein Energy Malnutrition - Marasmus - Kwashiorkor - Marsmic-Kwashiorkor d) Nutritional requirements in: - Pregnancy - Lactation - New born - In nutritional disorders
Biochemistry of water & Electrolyte imbalance and Acid Base Balance.

II)Laboratory Practicals-Part 1

Laboratory Safety and Introduction to use of laboratory facilities
Equipment Basic techniques and fundamental information Preparation of solutions-Normal solution and Normal saline
Experiments on Carbohydrates qualitative analysis
Experiments on proteins-qualitative analysis
Experiments on Fats-qualitative analysis
Chemical analysis of Urine-Normal and abnormal specimens
Fundamentals of The techniques and instrumentation of clinical biochemistry
Spectrophotometry
Flame photometry c) UV Spectrophotometry
PH metery
Collection and preservation of clinical specimens
Electrolytes

Syllabus for Part 2 Biochemistry

I)Theory

Bioenergetics and Biological Oxidation: a) Endergonic and exergonic reactions, their coupling through ATP b) Biologic oxidation and reduction, methods of electron transferring, redox potential, enzymes and coenzymes of biologic oxidation and reduction c) Respiratory chain and oxidative phosphorylation, components of respiratory chain, electron carriers d) ATP synthesis coupled with electron flow, phosphorylation of ADP coupled to electron transfer e) The ATP-synthase, their relation to proton pump, PMF, and active transport f) Uncouplers and inhibitors of oxidative phosphorylation
Introduction to Metabolism:
Metabolism of Carbohydrates a) Glycolysis - Phases and reactions of Glycolysis - Energetics of Aerobic and Anaerobic gylcolysis and their importance - Regulation of Glycolysis - Cori’s cycle - The fate of Pyruvate b) The Citric Acid Cycle c) Reactions, energetics and regulation and importance of Citric acid cycle - Amphibolic nature of citric acid cycle. The anpoleratic reactions and regulations of TCA cycle d) Gluconeogenesis - Important three by-pass reaction of gluconeogenesis - Entrance of amino acids and intermediates of TCA cycle and other nutrients as gluconeogenic substrates - Significance of gluconeogenesis e) Glycogen Metabolism - Reactions of Glycogenesis and gylocogenolysis - Importance of UDP-Glucose - Regulation of Glycogen Synthase and Glycogen Phosphorylase - Glycogen phosphorylase ‘a’ and the blood glucose sensor - Disorders of Glycogen metabolism (Glycogen Storage Diseases)-
Secondary pathways of carbohydrate (Hexose) metabolism - Hexose Mono Phosphate Shunt, its reactions and importance - Glucuronic acid pathway, its reactions and importance g) Metabolism of Fructose, Galactose and Lactose- Regulation of Blood Glucose Level - Hyperglycemia, hypoglycemia and their regulating factors - Biochemistry of Diabetes Mellitus, its Laboratory findings and Diagnosis
Metabolism of Lipids: a) Mobilization and transport of fatty acids, tricylglycerol, and sterols b) Oxidation of fatty acids - Activation and transport of fatty acid in the mitochondria - B-oxidation, fate of Acetyl CoA, regulation of B-oxidation - Other types of oxidation, i.e. alpha-oxidation, w-oxidation, peroxisome oxidation, oxidaton of odd number carbon containing fatty acids and Unsaturated fatty acids etc. c) Ketogenesis - Mechanism and utilization of Ketone bodies and significance - Ketosis and its mechanism d) Biosynthesis of fatty acids e) Eicosanoids, synthesis from Arahidonic acid, their mechanism and biochemical functions f) Triacylgycerol synthesis and regulation g) Synthesis and degradation of phospholipids and their metabolic disorders h) Cholesterol synthesis, regulation, functions, fate of intermediates of Cholesterol synthesis, Hypercholesterolemia, Atherosclerosis i) Plasma Lipoproteins, VLDL, LDL, HDL, and Chylomicrons, their transport, functions and importance in health and disease j) Glycolipid metabolism and abnormalities
Metabolism of Proteins and Amino Acids: a) Amino acid oxidation, metabolic fates of amino acid, transamination, deamination decarboxylation, deamidation and transamination b) Transport of amino group, role of Pyridoxal phosphate, Glutamate, Glutamine, Alanine c) Ammonia intoxication, Nitrogen excretion and Urea formation, Urea cycle and its regulation, genetic defects of Urea cycle d) Functions, pathways of amino acid degradation and genetic disorders of individual amino acids
Integration and regulation of Metabolic Pathways in Different Tissues:
Metabolism of Nucleotide: a) De Novo Purine synthesis b) Synthesis of Pyrimidine c) Recycling of purine and pyrimidine bases (The salavage pathway) d) Degradation of purine, formation of Uric acid e) Disorders of purine nucleotide metabolism
Molecular Biology: a) The structural basis of the cellular information b) DNA, Chromosomes, Discovery and organization of DNA in Genomes c) Super coiling of DNA d) The replication of DNA (DNA dependant DNA synthesis) - DNA polymerase, its components and functions - Initiation, elongation and termination of Replication - DNA Repair, Mutation and Cancers e) The Transcription (DNA dependant RNA synthesis) - RNA polymerase, its components and functions - Initiation, elongation and termination of transcription - RNA processing - RNA dependant synthesis of RNA and DNA - Reverse transcription — DNA synthesis from Viral RNA - Retroviruses in relation to Cancer and AIDS f) The Translation (Protein Synthesis) - The genetic codes and their characteristics - Initiation, elongation and termination of protein synthesis - Post-translational modification - Regulation of Gene Expression g) Molecular biology technology - DNA isolation - DNA-recombinant technology - Hybridization, blotting techniques h) Genetic disorders
Signal Transduction and Hormone Biochemistry: a) Chemistry, Secretion, Mechanism of action, regulation and effect on Carbohydrates, Lipids, Proteins, Mineral and water metabolism and disorders of various endocrine glands

II)Laboratory Practical’s -Part 2