Face to Face:

Teaching of “Biochemistry 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) 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 Biochemistrty as well as to help the students comprehend concepts that are not easily understood theoretically (learning based on practical experience).

Attendance of Seminard/ Tutorials and Laboratory exercises is mandatory. Attendance of Lectures is not mandatory.

Information and Communication Technologies are used for the preparation of the lecture material, the online information andprovision 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.

Α. 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.

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

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. The material of the tutorials is examined together with the lecture material.

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

The course exams are written 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 metabolism and understanding 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 their role in organism homeostasis

– the biochemical properties of different tissues and systems

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

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

 It also aims to train the students in the application 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 properties of various tissues and systems as well as biochemical subjects of special importance such as nutrition and exercise.
• distinguish between the pathological and the physiological laboratory results and suggest a diagnosis or treatment for basic metabolic diseases.
• analyze and process 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 of Gene Expression, Organs and Human Functions” is structured as follows:

A. The lectures & tutorial content and the relevant clinical insights that the students must learn in order to succeed in the course.

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

A1. Lectures content and relevant clinical insights

The flow of genetic information flow

• 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, types and biological role of RNA
• The genetic code

DNA replication, recombination and repair

• The mechanism of replication in prokaryotic and eukaryotic organisms and comparison
• The enzymes involved and their functions:
• DNA polymerase I, II, III in E. coli
• Primase, ligase, major eukaryotic DNA polymerases
• Enzymatic editing 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 damage:

• Autogenous or spontaneous

Base tautomerism,  Polymerase errors, Metabolic Products

• Exogenous

1. A) Chemical mutagens : base analogues & modifications, intercalation agents
2. B) Radiation: ionizing, ultraviolet

Repair mechanisms

• A) Damage reversal
• B) Mismatch repair: Base excision, Nucleotide excision

Ames test

Recombination

Recombinase

Holliday Structures

RNA Synthesis & Gene Expression Regulation in Bacteria

• Properties, content, structure & types of RNA polymerase
• Stages of RNA polymerase action
• Transcription initiation: the role of promoters and the σ subunit
• Elongation: Catalytic mechanism, DNA/RNA hybrid, “bubble” movement, editing
• Termination: Intrinsic & protein-dependent (p factor)
• RNA processing (excision, addition, modification)
• Transcription inhibitors, antibiotics
• Principles of gene expression regulation
• The concept of operon
• Lactose operon: function and regulation
• Repressor, inducer, operator, catabolite repression (CAP protein)
• Riboswitches
• Quorum sensing 

RNA synthesis & gene expression in eukaryotes

• Differences in gene expression/RNA synthesis between prokaryotes and eukaryotes
• Types of RNA polymerase in eukaryotes
• Promoters and cis-acting transcriptional control elements by RNA Pol II
• General transcription factors of RNA Pol II
• Specific transcription factors – trans-acting control elements
• Nuclear hormone receptors
• The role of chromatin in the regulation of transcription

RNA Processing in Eukaryotes

• Differences in mRNA Processing between Prokaryotes and Eukaryotes
• Maturation of Ribosomal RNA (rRNA)
• Maturation of Transfer RNA (tRNA)
• Maturation and Processing of Messenger RNA (mRNA)
• Modification (Capping) of the 5′ End
• Modification (Polyadenylation) of the 3′ End
• Splicing
• Conserved Splice Site Sequences
• snRNPs and the Spliceosome
• Coupling with Transcription
• Splicing Defects and Diseases
• Alternative Splicing
• Self-splicing and Ribozymes
• RNA Modification and Editing

 Protein synthesis

• The components of protein synthesis (translation)
• Structure and role of transfer RNA (tRNA)
• Aminoacylation of tRNA and aminoacyl-tRNA synthetases
• Structure and components of ribosomes
• Principles of translation in bacteria
• Initiation factors
• Peptide bond catalysis
• Elongation factors
• Termination factors
• Fidelity and cost
• Translation in eukaryotes
• Protein targeting/sorting
• Protein entry into the ER, secretory pathway
• Inhibitors of translation
• Antibiotics
• Diphtheria toxin
• Ricin
• Regulation of translation (post-transcriptional regulation of gene expression)
• Translation inhibition & mRNA stabilization
• Cellular homeostasis of iron
• Translation inhibition & mRNA degradation
• Small interfering RNA (siRNA) and miRNA

Principals of cell signaling and biochemistry of cancer

• The system of hormone signal transduction with G protein-coupled membrane receptors and the mechanism of action of cholera toxin.
• The second messengers: characteristics, what they are, how they are produced, how they act, how they are degraded.
• The function of adenylate cyclase: cyclic AMP, activation of PKA.
• The function 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 disorders, oncogenes and toxins that can lead to cancer and other diseases.
• The targeting of signaling pathways in order to treat pathological conditions.

Biochemical endocrinology: peptide-and steroid-hormones

• 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 feedback.
• 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.

Biochemistry ofsensory organs

• The nicotinic and muscarinic acetylcholine receptors: structure, special structural features and mode of action.
• Biochemical basis of vision. Operation of rods, cones and differences.
• 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 osmogenic signal transduction
• Biochemical basis of taste and receptors of taste molecules
• Biochemical basis of hearing.
• Biochemical basis of touch.

Overview of Metabolic pathways and vitamins

• Classification of vitamins and connection with metabolism
• Excitation test
• Biochemical explanation of vitamin deficiencies
• The characteristic participation of each vitamin in the function of the organism
• Conditions and possibilities of vitamin deficiencies in Western culture

Hormonal regulation of Metabolism

• Blood glucose levels remain stable in circulation
• The use of glucose by the body
• Insulin: role, synthesis, maturation and secretion
• Insulin receptor: structure, activation, signal transduction
• Effects on the metabolism of sugars, lipids, proteins
• Glucagon: structure, action, receptor
• Production of ketone bodies in long-term starvation (secretion of glucagon)
• The biochemical basis of DMT1 (Diabetes Type 1) and DMT2. Similarities and differences, therapeutic management.
• Hypoglycemia
• About leptin: where it is produced, where it acts, how it affects the fuel and energy balance of the organism.

Biochemistry of plasma proteins

• Composition of plasma and its difference from serum.
• The electrophoretic separation 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 disorders 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.

Biochemistry of hemostasis

• The role of platelets in blood clotting and the factors 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 therapeutic administration of recombinant factors.
• Connecting the mechanisms of hemostasis with cell signaling

Biochemistry of Liver

• 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 maintenance of blood glucose levels
• Heme metabolism
• Bilirubin
• Assessment of liver function through biochemical tests
• The importance of metabolic mechanisms, their understanding and their applications in clinical diagnosis and practice.

Metabolic adipose tissue functions

• 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

Nutrition and metabolism

• Calorie content of macromolecules.
• The body’s energy balance. The concept of BMP.
• Macromolecular food components
• Carbohydrates
• Content of specific foods in specific carbohydrates
• Reminder of the metabolic pathways of fructose and galactose
• 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.
• Weight-loss diets.
• Anorexia nervosa, bulimia.
• Malnutrition

Metabolic muscle functions

• Muscle contraction and the proteins involved: Actin, myosin, tropomyosin, troponin, sarcoplasmic Ca++ pump, voltage-dependent Ca++ channel.
• The muscle 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 glucose homeostasis.
• Muscle fuel, what factors affect it.

Biochemistry of 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 either duration or intensity or both increase.

• 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.
• Fatigue:

o Peripheral fatigue (in the muscle): causes

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

o Disadvantages and advantages of physical exercise

A2. Tutorials content and relevant clinical insights

1st Tutorial: Summary of Genetic Information Flow Biochemistry Lectures

Overview and Problem-Based Learning: presentation, analysis, discussion of clinical cases of patients with pathological conditions

2nd Tutorial: Summary of Cellular Communication Lectures

Overview and Problem-Based Learning: presentation, analysis, discussion of clinical cases of patients with pathological conditions

3rd Tutorial: Summary of Biochemistry Systems Lectures

Overview and Problem-Based Learning: presentation, analysis, discussion of clinical cases of patients with pathological conditions

1. 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 extracting information

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 (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, Fundamentals of Biomedical Science 2016
2. J. W. Baynes & M. H Dominiczak: Medical biochemistry, 5th edition, Elsevier Limited Tymoczko J.L,

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