Face to Face:

Teaching of “Biochemistry (ΙΙ) of Gene Expression, Organs and Human Functions” consists of lectures, seminars/tutorials and laboratory practicals.

Attendance of Laboratory Practicals and Seminars/Tutorials is

obligatory.

The lectures content is described above.

Tutorials (in two student groups with 1-2 instructors per group) review and extend the lectures content using examples of clinical cases (problem-based learning) that highlight the application of biochemical knowledge in the diagnosis and treatment of serious diseases. In each tutorial, students prepare answers to the questions related to the examined clinical cases and discuss them with the teachers. Optionally, the students may provide answers to a clinical case as a written assignment. The performance of the students during in the tutorials is taken into account in the final evaluation.

Laboratory exercises (in 4 student groups of students, 3 instructors per group of 30 students) composing the students’ practical are complementary to the lectures and they aim to familiarize the student with the application of basic biochemical techniques, the operation of simple laboratory instruments and the experimental procedures that are often used in Clinical Biochemistrt as well as to help the students comprehend concepts that are not easily presented theoretically (learning based on practical experience).

Presence in Seminar/ Tutorials and Laboratory exercises is mandatory. Presence in Lectures is not mandatory.

Information and Communication Technologies are used for the preparation of the lecture material, the online information and provision of supplementary learning material to students.

Specifically:

• Common software (e.g. MS powerpoint) is used to prepare lecture material and display slides and videos.
• The study guide (detailed supplementary material & additional bibliography), the tutorial material (clinical cases), the theory and protocols of the laboratory exercises, the slides of each lecture as well as relevant videos and scientific articles made available electronically and online to students through the e-class system of our university.
• Common software (e.g. MS excel) is used to statistically process student assessment.

Announcements, information etc are available online via e-class.Communication is also done via e-mail.

• Information about the course, instructors and their research interests and in general the Laboratory of Biochemistry of the Faculty of Medicine are available online on the Laboratory website http://www.med.uth.gr/biochemistry/index.html

The language of assessment is English.

Evaluation methods.

A. For the laboratory practical: Laboratory Assignment Reports,Written Examination at the end of the semester with short answer questions and problem solving.

The participation of students in the laboratory exercises as well as the written report of the results of the exercises is mandatory. The report includes the results (presented in tables and diagrams, and the conclusions (e.g. if the results were expected, if not why, sources of possible errors in the experiments) as requested by each exercise. At the end of each exercise, the written report is checked by the instructors and signed when correctly completed. In case of very demanding calculations or diagrams, it is possible to complete the report after the end of the exercise and deliver it at a later predetermined date. Successful participation in the practical is certified by the instructors’ signatures on the written reports. At the end of the semester the students are examined in the content of the Laboratory practical. The examined material consists of the theory, the methodology and the ways results are processed as included in the Guide of the Laboratory Practical or presented by the instructors during the exercises. Only the students that have successfully completed the laboratory exercises can participate in the written laboratory examination. Success in the laboratory examination is a prerequisite for participation in the course exams. 

B. For the Tutorials: Oral Presentation, Oral Examination, Written Assignment. 

In each tutorial, students prepare answers to the questions relatedto the examined clinical cases and discuss them with the teachers.Optionally, the students may provide answers to a clinical case as a written assignment. The performance of the students during in the tutorials is taken into account in the final evaluation. The material of the tutorials is examined together with the lecture.

 C.For the lecture material: Written Exams with multiple-choice and short answer questions.

The course exams are written, last 2 hours and consist of multiple-choice questions (examples are available in the Course Guide) and short answer questions related to a clinical case. The material to be examined is lectures and tutorial material as described above. Only those students who have successfully passed the Laboratory exams have the right to participate in the course exams.

Final Grade:

The final grade of the course is calculated as the sum of 80% of the grade of the written course exams and 20% of the grade of the Laboratory written exams.

All of the above are presented in detail in the Course Guide which is distributed in print to all students and is posted electronically in e-class.

Aims of the course

In order to complete the metabolism and to understand the regulation of biochemical functions of the human organism on a molecular, cellular, and systematic level, the course  is going to study:

-the mechanisms of genetic information: preservation, transfer and expression

-the mechanisms of hormone action and it’s role in organism homeostasis

-the biochemical specificity of different tissues and systems

– special biochemical subjects of clinical importance (nutrition, exercise)

The course also provides the essential background for the courses of the later semesters and more specifically in the courses: Clinical Biochemistry, Pathological Physiology, Endocrinology Medical Genetics, Pathology and Pediatrics.

 It also aims to deepen the students in the applications of laboratory medicine techniques and in the evaluation of diagnosis and treatment of patients.

After the successful completion of this course, the students will be able to:

• understand the regulation of the biochemical functions of the human body at the molecular, cellular and systemic level.
• know the mechanisms of conservation, transfer and expression of genetic information, the mechanism of action of hormones and their role in the homeostasis of the organism, the biochemical specificity of various tissues and systems as well as the biochemical issues of special importance such as nutrition and exercise.
• distinguish the laboratory pathological picture from the normal one and propose a diagnosis for the treatment of basic metabolic diseases.
• analyzes and processes the results of basic biochemical analyses
• cooperate with his fellow students in the context of a laboratory environment for performing basic biochemical analyzes and processing their results.

General Abilities

• Research, analysis and synthesis of data and information, using the necessary technologies Adaptation to new situations
• Decision making
• Autonomous work Teamwork
• Working in an international environment Work in an interdisciplinary environment
• Exercise criticism and self-criticism
• Promoting free, creative and inductive thinking

The content of the course “Biochemistry (II) Gene Expression, Human Organs and Functions” is structured as follows:

A.The theoretical clinical skills that students must acquire in order to succeed in the course.

B.The practical and clinical skills that students must acquire in order to considered successful.

C.The knowledge of the material that students must have in order to succeed in the course

A. Lecture content and relevant clinical insights

Lecture 1: Genetic information flow (2 hours)

• the double helix model and types of DNA double helix
• The properties of DNA in solution
• The higher structures of double-stranded DNA
• The structure, species and biological role of RNA
• The genetic code

Lecture 2: Biochemistry and Evolution (1 hour)

• Oparin/Haldane’s ‘primordial soup’ theory, Stanley/Urey’s experiment.
• The ‘RNA world’ theory
• The evolution of the biochemical processes of life until today, based on observations and simulation experiments.
• Examples of organisms of evolutionary interest (D. discoideum, C. elegans)

Exploring evolution

• The comparison of gene sequences and genomes has provided information over the last half century about the evolutionary relationship of man to his environment:
• LUCA
• Ancient
• Position on the tree of life (evolutionary trees)
• The closest evolutionary relative of man is the chimpanzee
• Neanderthals, Denisovans and Homo sapiens
• Why we care about always keeping an evolutionary eye as doctors

Lectures 3, 4 and 5: DNA replication, recombination and repair (5 hours)

• The mechanism of replication in prokaryotic and eukaryotic organisms and comparison
• The enzymes involved and their functions:
• DNA polymerase I, II, III, E. coli
• Primase, ligase, major eukaryotic DNA polymerases
• Enzymatic editing of the reading by polymerases
• PCNA as a prognostic marker of cancer
• The etiology of Huntington’s disease
• Helicases and syndromes
• Type I and II topoisomerases: functions and drugs
• Telomerase: the ribonucleoprotein with reverse transcriptase activity and its importance

DNA repair and recombination

Creating DNA damage:

• Autogenous or spontaneous

-Identity of bases

-Polymerase errors

-Products of metabolism

• Foreigners

1. A) Chemical mutagens
2. a) analogous bases
3. b) modification of bases
4. c) interfering factors
5. B) radiations
6. a) ionizing
7. b) ultraviolet

Repair mechanisms

• A) Damage reversal
• B) Repair of bad connections

– Base excision

– Nucleotide excision

Ames test

Recombination

– Recombinase

– Holliday Structures

Lectures 6 and 7: RNA structure, synthesis and maturation (3 hours)

Initiation

An RNA polymerase: the binding sites, the p subunit

Elongation

• 8 base DNA/RNA hybrid
• the DNA ‘bubble’ moves
• topoisomerases are necessary

Termination

• With factor p, independent of factor p
• Transcription inhibitors-drugs

Regulation

• General for all carbohydrate operons in the presence of glucose (catalytic repression via CAP protein)
• Specific to each, the example of the lactose operon (the meaning of the operon, its regulation)

RNA synthesis and regulation in eukaryotic organisms

• The eukaryotic RNA polymerases
• Specializations (what does cis trans elements mean)
• A-amanitin: its effect on each RNA polymerase, liver disease
• Initiation of transcription: Promoters, formation of basal initiation complex and its properties, cis-elements, trans-elements
• Key transcription factors
• Role of chromatin structure: histones (details), nucleosome, regulation
• Regulation: specific transcription factors and their properties: structures
• Regulation at the chromatin level
• Histone modifications (acetylation-deacetylation-drugs)
• Nucleosome rearrangements
• Example of chromatin remodeling

RNA maturation and regulation

• Cover
• Polyadenylation
• Splitting
• Breakpoints between introns/exons are selected with absolute precision
• The mechanism
• The splicing particle
• Alternative splicing

Lectures 8, 9, 10, 11 and 12: The mechanism of Protein biosynthesis and Gene expression control (8 hours)

• Ribosome

secretory pathway of proteins

• Transfer RNA (tRNA)

Wobble

• Aa-tRNA synthetases

their importance for translation accuracy (editing)

• Protein Synthesis Mechanism

-Inception

• Opening complex
• Eukaryotic-prokaryotic differences

-Elongation

Elongation factors and their functions

-Termination

• What is the fidelity (accuracy) of protein synthesis
• Antibiotics, diseases, toxins
• Post-transcriptional regulation. Generally
• the example of iron homeostasis
• miRNAs

Lecture 13: 1st Tutorial: Summary of Molecular Biology Courses (2 hours)

Course Overview and Problem-Based Learning: presentation, analysis, discussion of clinical cases of patients with pathological conditions reported in Molecular Biology Courses

Lectures 14 and 15: Principals of cell signaling and biochemistry of cancer: (3 hours)

The system of hormone message transduction with G protein-coupled membrane receptors and the mechanism of action of cholera toxin.

• The second messengers: characteristics, who they are, how they are produced, how they act, how they are degraded.
• The action of adenylate cyclase: cyclic AMP, activation of PKA.
• The action of phospholipase Cβ: IP3 and diacylglycerol, Ca2+ and calmodulin, activation of PKC.
• Examples of hormone receptors / growth factors that have tyrosine kinase activity.
• Receptors acting through JAKs-STATs: growth hormone, α-interferon
• Brief description of the EGF signal transduction and the ras-MAP kinase pathway as well as the correlation between signal transduction pathways and cancer.
• Examples of signaling pathway troubles, oncogenes and toxins that can lead to cancer and other diseases.
• The targeting of signaling pathways in order to treat pathological conditions.

Lectures 16, 17 and 18: Biochemical endocrinology: peptide-and steroid-hormones (5 hours)

• Peptide-hormones and Steroid hormones: characteristics of structure, synthesis, maturation and transport of some hypothalamic hormones.
• Hormones of the hypothalamus, pituitary gland, endocrine glands: regulation of the circuit through retrograde feeding.
• The regulation of steroid hormone secretion: ACTH action on the production of cortisol from the adrenal cortex, FSH and LH action on the production of testosterone, estradiol and progesterone from the gonads, multiple regulation of aldosterone secretion from the adrenal cortex.
• Clinical implications in Cushing’s syndrome, Addison’s disease and Graves’ disease.
• Steroid hormone synthesis disorders due to hereditary lack of enzymes. 21α-hydroxylase deficiency. Clinical implications.
• The steroid hormone receptor family: structure and function (transcriptional coactivators).
• The connection of hormone action with signal transduction mechanisms and their targeting to treat pathological conditions.

Lecture 19: Biochemistry of the sensory organs (2 hours)

• The nicotinic and muscarinic acetylcholine receptors: structure, special structural features and mode of action.
• Biochemical basis of vision. Operation of rods, cones and differentials.
• Relationship between structure and function of rhodopsin, conversion of photons into a nerve signal and the adaptation of rods to light
• Genetic basis of color vision and color blindness
• Biochemical basis of olfaction and osmogen signal transduction
• Biochemical basis of taste and receptors of taste molecules
• Biochemical basis of hearing.
• Biochemical basis of touch.

Lecture 20: Overview of Metabolic pathways and vitamins (2 hours)

• Vitamins: their meaning and importance
• Classification of vitamins and connection with metabolism
• Stimulation test
• Biochemical explanation of potential deficiency and disease for each vitamin
• The characteristic participation of each vitamin in the functioning of the body
• Conditions and possibilities of vitamin deficiencies in Western culture

Lectures 21 and 22: Hormonal regulation of Metabolism (3 hours)

• Blood glucose levels remain stable in circulation
• The use of glucose by the body
• Insulin: role, synthesis, maturation and secretion
• receptor: structure, activation, signal transduction
• actions on the metabolism of sugars, lipids, proteins
• Glucagon: structure, action, receptor
• Production of ketone bodies in chronic starvation (secretion of glucagon)
• The biochemical basis of TDM1 (Diabetes Type 1) and TDM2. Similarities and differences, therapeutic management.
• Hypoglycemia
• About leptin: where is it produced, where does it act, how does it affect the body’s fuel and energy balance

Lecture 23: Biochemistry of the plasma proteins (2 hours)

Plasma Protein Biochemistry

• Composition of plasma and its difference from serum.
• The electrophoretic sorting of plasma proteins, acute phase proteins and C-reactive protein
• The nature and biological role of albumin, α1-antitrypsin, ceruloplasmin, transferrin and γ-globins and clinical implications of disturbances in the levels or activity of these proteins.
• Characteristic changes in electrophoretic separation patterns of plasma proteins – indication of pathological conditions.
• The enzymes normally contained in plasma and the diagnostic value of enzymes of tissue origin (transaminases, LDH, CPK) and their isozymes.

Lecture 24: Biochemistry of hemostasis (2 hours)

• The role of platelets in blood clotting and the substances that promote their activation and adhesion.
• The role of phospholipase A2, cyclooxygenase and thromboxane synthase in blood coagulation and the mechanism of action of aspirin.
• The nature of blood clotting factors..
• The structure of fibrinogen and the polymerization stages of cross-linked fibrin clot (thrombin, transglutaminase action).
• Limitation of coagulation: antithrombin III and the role of heparin
• The mechanism of fibrinolysis: tissue plasminogen activator and plasmin.
• Coagulation disorders due to genetic deficiency of factors (hemophilia) and for the therapeutic administration of recombinant factors.
• Connecting the mechanisms of hemostasis with cell signaling

Lectures 25 and 26: Biochemistry of Liver (3 hours)

• The functions of the liver as a central metabolic organ and its communication with other tissues
• The functions of the liver as a metabolic organ of amino acids and proteins
• The functions of the liver as a metabolic organ of nitrogen and urea
• Liver functions in biotransformation, drug metabolism and detoxification
• Synthesis and degradation of glycogen as well as in the maintenance of blood glucose levels
• The heme metabolism
• The metabolism of bilirubin
• Assessment of liver function through biochemical tests
• The importance of metabolic mechanisms, their understanding and their applications in clinical diagnosis and practice.

Lecture 27: 2nd Tutorial: Summary of Intercellular Communication Courses (2 hours)

Course Overview and Problem-Based Learning: presentation, analysis, discussion of clinical cases of patients with pathological conditions reported in Courses of Intercellular Communication.

Lectures 28 and 29: Functions of adipose tissue (3 hours)

• Adipose tissue in general: distribution in the body, morphology, separation between white and gray.
• Growth and differentiation of adipose tissue cells. Molecular differentiation, PPARγ and coactivators.
• The biochemical function of WAT as a storage tissue.
• The sensitivity and response of adipose tissue to nerve stimuli.
• The function of adipose tissue as an endocrine organ: Leptin, actions, adiponectin.
• Adipose tissue in relation to inflammation
• Adipose tissue in relation to obesity
• Gray adipose tissue.
• The action of PGC-1 and UCP-1.
• The biochemical function of BAT as thermoregulatory tissue

Lecture 30 and 31: Nutrition and metabolism (3 hours)

• Calorie content of macromolecules.
• The body’s energy balance. The concept of BMP.
• In general about macromolecular food components.
• Especially for carbohydrates
• Content of specific foods in specific carbohydrates
• Reminder of the metabolic pathways of fructose and galactose
• Especially for fats
• Essential fatty acids, foods that contain them, the biochemical basis of their deficiency, their functions, symptoms and frequency of deficiency.
• Trace elements
• Normal diet and nutrition. Food preservatives
• Digestion of carbohydrates, fats and proteins.

• The evolution of human nutrition. Relationship with the ‘diseases of culture’.
• The metabolic state of the organism in feeding, early starvation, prolonged starvation, refeeding.
• Obesity:

o As a result of overnutrition.

o As a genetic disease.

o As an inflammatory disease.

o Leptin resistance.

o Insulin resistance.

o The relationship between obesity and diabetes.

• Lipodystrophy.
• Slimming diets.
• Anorexia nervosa, bulimia.
• Malnutrition

Lecture 32: Functions of the muscle (2 hours)

• Muscle contraction and the proteins involved: Actin, myosin, tropomyosin, troponin, sarcoplasmic Ca++ pump, taso-dependent Ca++ channel.
• The muscle’s stores of ATP.
• The role of creatine phosphate.
• The types of muscle fibers, their function and their importance.
• Myocyte differentiation, myogenic regulatory factors.
• Satellite cells, their activation factors.
• Muscle tissue also contains intracellular fat droplets. (IMTG- intramuscular triglycerides).
• Muscle tissue is important for movement, thermogenesis and the body’s glucose homeostasis.
• Muscle fuel, what factors affect it.

Lectures 33 and 34: Biochemistry of exercise (3 hours)

Generally for exercise.

• At the start of the exercise. The role of adenylate kinase (myokinase), fuels and their flow. Exercise parameters.
• High intensity exercise.
• Duration exercise:

o Metabolism of free amino acids.

o Metabolic changes in duration exercise, when increasing either duration or intensity or both.

• Muscle hypertrophy: when it happens, molecular mechanism.
• Mitochondrial biogenesis: when it occurs, molecular mechanism.
• Muscle fibers are mutually converted depending on the exercise state of the muscle.
• The importance of the transcriptional coactivator PGC-1α for metabolism.
• Kama:

o Regional kama (in the muscle): causes

o Central stroke (in the brain): definition, possible causes.

o Disadvantages and advantages of physical exercise

Lecture 35: 3rd Tutorial: Summary of Biochemistry Systems Courses (2 hours)

Course Overview and Problem-Based Learning: presentation, analysis, discussion of clinical cases of patients with pathological conditions reported in Biochemistry Systems Courses.

B.Laboratory Practical content

Hands-on learning: Acquisition of general and specific practical & clinical skills:

General Skills

Observing biochemical phenomena, obtaining and analyzing experimental data

Interpretation of experimental data

Resolving practical problems

Producing graphical displays of data and extract informations

Operating basic Biochemistry & Clinical Chemistry equipment

Working as a team

Following instructions

Following safety regulations

Understanding laboratory errors and identifying their sources

Assessment of laboratory results 

Specific Skills 

Practical 1. Preparation of recombinant plasmid DNA and restriction endonuclease digestion

Clinical Applications of Recombinant Plasmid Preparation and Restriction Endonucleases Digestion

 Preparation of plasmid DNA from bacteria by the alkaline lysis method.

 DNA quantification by spectroscopy

Practical 2. Recombinant plasmid mapping

Construction of agarose gel and electrophoretic DNA separation based on its molecular weight.

 Recombinant plasmid mapping after restriction endonucleases digestion and agarose gel electrophoresis

Practical 3. Determination of transaminases and urea in blood serum

Clinical application of laboratory analysis of GOT and GPT transaminases

 Diagnostic significance of aspartate aminotransferase transaminase (GOT or AST) and alanine aminotransferase (GPT or ALT).

 Pathological causes of a decrease or increase in GOT and GPT in the blood

 Determination of GOT and GPT concentrations in the blood of patients

 Assessment of laboratory results

Clinical application of laboratory analysis of urea

 Diagnostic significance of serum urea determination

 Pathological causes of decreased or increased urea

 Determination of urea concentration in the blood of patients

 Assessment of laboratory results and correlation with the results of GOT and GPT concentration in the blood of patients

Practical 4. Determination of bilirubin in blood serum

Clinical application of laboratory analysis of bilirubin

 Diagnostic significance of serum bilirubin

 Pathological causes of a decrease or increase in bilirubin

 Determination of bilirubin concentration in the blood of patients

 Assessment of laboratory results

 Α. Lecture Material

Main suggested textbooks:

1. Nessar Ahmed: Clinical Biochemistry, Fondamentals of Biomedical Science 2016
2. Medical biochemistry , J. W. Baynes & M. H Dominiczak, 5th edition, Elsevier Limited Tymoczko J.L,
3. Berg J.M. & L. Stryer: BIOCHEMISTRY, A SHORT COURSE 3rd edition, W.H. Freeman and Company

Further reading:

Berg, Tymoczko & Stryer: BIOCHEMISTRY (7th Edition)

Ferrier R. D.: Lippincott’s Illustrated Reviews: BIOCHEMISTRYm6th edition, Lippincott Williams & Wilkins, USA

Marshall W.J. & S.K. Bangert: Clinical Chemistry

Branden C. & J. Tooze: Introduction to Protein Structure

Devlin Τ. Μ.: Biochemistry with Clinical correlations Part I and II

1. A. Lieberman & A. Marks: Marks Basic Medical Biochemistry: A clinical approach (4th Edition)

Koolman J. & K.-H. Roehm: Colour Atlas of Biochemistry

Murray et al.: HARPER’S Illustrated Biochemistry

Nelson D. L. & M. M. Cox : Lehninger, Principles of Biochemistry Part I, II, and III

Β. Laboratory Practical supplementary Material

Tietz N. W. (editor): Textbook of Clinical Chemistry, W. B. Saunders Co

Alexander R. R. & J. M. Griffiths: Basic Biochemical Methods, Wiley-Liss

Holme D. J. & H. Peck: Analytical Biochemistry, Longman Scientific & Technical

Anderson S. C. & S. Cockayne: Clinical Chemistry – Concepts and Applications, W. Saunders Co

Dryer R. L. & F. G. Lata: Experimental Biochemistry, Oxford University Press

Plummer D. Τ.: Practical Biochemistry – An Introduction, McGraw-Hill

Wilson U. & K. H. Goulding: Principles and Techniques of Practical Biochemistry, Edward Arnold 

Relevant Scientific Journals:

Annual Review of Biochemistry

Archives of Biochemistry and Biophysics

Biochemical and Biophysical Research Communications

Biochemical Journal

Biochemistry

Biochemistry and Cell Biology

Biochimica et Biophysica Acta

Biochimie

Biological Chemistry

Cell

Cell Metabolism

Cellular Physiology and Biochemistry

Cellular Signalling

Cellular and Molecular Life Sciences

Clinical Biochemistry

Critical Reviews in Biochemistry and Molecular Biology

EMBO Journal

FEBS Letters

Free Radical Biology and Medicine

Free Radical Research

The International Journal of Biochemistry & Cell Biology

Journal of Biochemistry

Journal of Biological Chemistry

Journal of Cell Science

Journal of Cellular Biochemistry

Journal of Lipid Research

Journal of Medical Biochemistry

Journal of Molecular Biology

Journal of Molecular Medicine

Methods in Enzymology

Molecular and Cellular Biology

Molecular Cell

Nucleic Acids Research

Protein Science

RNA

The FEBS Journal

Trends in Biochemical Sciences