Face to Face:

Teaching of “Biochemistry of enzymes and human metabolism” consists of lectures, seminars/tutorials and laboratory practicals.  Attendance of Laboratory Practicals and Seminars/Tutorials is obligatory.

The lectures content is described above.

Seminars/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.

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.
• 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
• 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.

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. The performance of the students during 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, with duration of 1,5 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.

Aims of the course

The course examines the chemical composition and processes that characterize living organisms, in general, and humans in particular. The course aims at understanding the physiological and pathological functions of the human body at the molecular and cellular level and introducing the principles and techniques of Laboratory Medicine. It also presents the application of biochemical knowledge in clinical settings such as the diagnosis and treatment of metabolic diseases.

The course also provides the essential background for courses introduced at later semesters such as: “Biochemistry of Gene Expression, Organs and Human Functions”, “Systems Physiology”, “Neurophysiology & Endocrine physiology”, “Clinical Biochemistry”, “Pharmacology”, “Medical Genetics”, “Pathology” and “Pediatrics “.

Finally, another aim of the course is to help students appreciate the importance of correct execution and evaluation of diagnostic laboratory analysis and acquire the corresponding skills which are required  for the specialty of Laboratory Medicine as well as many other clinical medical specialties.

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

• understand the basic human metabolic functions and the molecular-biochemical basis of human metabolic diseases
• have basic knowledge of the structure and properties of proteins and enzymes, the pathways of production, consumption and storage of energy, the intermediate metabolism of the most important biomolecules and basic mechanisms of metabolic regulation.
• distinguish symptoms and propose diagnosis and a suitable therapy of basic metabolic diseases.
• use basic equipment of a biochemical/clinical chemistry lab and perform simple routine biochemical analyses.
• analyze and process basic biochemical analysis results
• – cooperate with their colleagues in the context  of a lab environment for the execution of simple biochemical analyses and processing of 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
• Exercise criticism and self-criticism

• Promoting free, creative and inductive thinking

The content of the course includes the following major items:

Α.The content of the lectures together with the relevant clinical insights the students need to learn/acquire per chapter.

Β.The content of the tutorials/seminars together with the relevant clinical insights the students need to learn/acquire per seminar.

C.The content of the laboratory practical together with the relevant practical & clinical skills the students need to learn/acquire per exercise.

A. Lecture content and relevant clinical insights

1. Introduction to Biochemistry

Biochemistry as a science: Definition, object, history

Biochemistry in everyday life

Biochemistry as a basic component of medicine

Biochemistry as a course: Textbooks, prerequisite knowledge, organization, program, obligations

Clinical insights:

Biochemical tests as means of diagnosis

Diagnosis & treatment of metabolic diseases

Biochemical basis of drug action

2. Enzymes: Basic Properties, Kinetics, Regulation & Catalytic Mechanisms

Review of basic properties and principles of enzyme function, kinetics, regulation of enzyme activity, catalytic mechanisms and inhibition

Clinical insights:

Protease inhibitors as drugs against hypertension & HIV

Carbonic anhydrase inhibitors as anti-cancer drugs

Applications of restriction nucleases in genetic tests

Lactate dehydrogenase isoenzymes in clinical diagnosis

3. Oxygen binding proteins: Myoglobin & Hemoglobin

General structure of heme

The characteristics and the main amino acids of the heme pocket

O₂ binding curve of myoglobin

Structure and subunits of hemoglobin & O₂ binding curve

Molecular basis and significance of the allosteric effect of hemoglobin

2,3-BPG and the BOHR effect

Clinical insights:

Biochemical basis, diagnosis and treatment of sickle cell disease and thalassaemia

4. Connective tissue proteins

The components of connective tissue

Structure, characteristic composition, modifications, biosynthesis and role of Collagen

Structure, characteristic composition, modifications and role of Elastin

Structure, characteristic composition and role of Proteoglycans and Glycosaminoglycans

Clinical insights:

Biochemical basis, diagnosis and treatment of scurvy, laryngitis, Ehlers-Danlos syndromes, incomplete osteogenesis

5. Introduction to metabolism

Basic concepts of metabolism, anabolism and catabolism, recurring reaction motifs

Free reaction energy and the concept of reaction coupling

ATP and its production

Activated carriers: NAD, FAD, NADP, coenzyme A.

The role of muscle creatine phosphate

Regulation of metabolic pathways and energy status of the cell.

   Clinical insights:

Niacin deficiency

6. Regulation of metabolism & metabolic diseases

Regulation of metabolism through signal transduction pathways

Basic signaling components

Structure and function of 7TM receptors, G proteins and adenylate cyclase

Role of cyclic AMP, IP3, DAG and calcium as intracellular messages and importance of reaction cascades

   Clinical insights:

Definition and categories of metabolic diseases

Introduction to the diagnosis and treatment of inherited metabolic diseases.

7. Digestion & absorption of carbohydrates

Biological role and chemical nature of glucose and other essential diet carbohydrates

Carbohydrate digestion reactions and enzymes

GLUT glucose transporters

8. Glycolysis

Glycolysis (reactions and enzymes)

Energy yield of glycolysis

Metabolic fate of pyruvate and maintenance of the redox balance

Importance of glycolysis as an anaerobic energy production pathway

Clinical insights:

Biochemical basis, diagnosis and treatment of pyruvate kinase deficiency and lactic acidosis

9. Hormonal regulation of glycolysis and gluconeogenesis

Regulation of glycolysis, properties and functions of insulin and glucagon

Hormonal regulation of phosphofructokinase and role of fructose 2,6-biphosphate

Importance of isoenzymes for tissue metabolic specificity (hexokinase / glucokinase)

Regulation of glycolysis in muscle

Gluconeogenesis reactions and energy cost

Regulation of irreversible reactions

Inverse regulation of glycolysis-gluconeogenesis

Cori and alanine cycles

Clinical insights:

Biochemical basis and treatment of hypoglycemia

10. Galactose and Fructose metabolism

Galactose metabolism

Lactose intolerance

Fructose metabolism

Fructose intolerance

Clinical insights:

Biochemical basis, diagnosis and treatment of galactosemia, fructose and lactose intolerance

11. The citric acid (Krebs) cycle

Conversion of pyruvate to acetyl-coenzyme A in the mitochondria

Krebs cycle (reactions and enzymes)

Anaplerotic reactions

Intermediate Citric Cycle substrates as biosynthetic precursors

Clinical insights:

Biochemical basis, diagnosis and treatment of pyruvate dehydrogenase phosphatase deficiency, Berry-berry disease & mercury or arsenic poisoning

12. Regulation of the citric acid (Krebs) Cycle

Regulation of the pyruvate dehydrogenase complex

Regulation of key enzymes and energy yield of the reactions

Regulation of by energy status and hormones

Clinical insights:

Biochemical basis, diagnosis and treatment of pyruvate carboxylase deficiency

13. Oxidative phosphorylation: The respiratory chain

Complexes and mobile electron transporters of the respiratory chain

Additional electron transfer groups, structure and evolution of cytochrome c

Production of oxygen radicals (ROS) and their regulation

Mitchell’s Chemiosmotic Theory

Transport of cytoplasmic NADH electrons to the mitochondria

14. Oxidative phosphorylation: ATP Synthesis

General structure and function of F₀F₁-ATPase

Proton-driven force and coupling of the respiratory chain with oxidative phosphorylation

Transport of ATP in and out of the mitochondria.

Energy efficiency of the respiratory chain and complete glucose oxidation

Regulation of oxidative phosphorylation (respiratory control).

15. Thermogenesis & mitochondrial diseases

Inhibition and decoupling of oxidative phosphorylation

Thermogenesis and gray adipose tissue

Mitochondrial diseases

Role of mitochondria in apoptosis, cancer and aging

Clinical insights:

Pathological action & treatment of reactive oxygen species (ROS)

Biochemical basis of cyanide poisoning

Brown adipose tissue and thermoregulation

Biochemical basis of mitochondrial diseases

16. Glycogen metabolism

Structure, physical and chemical properties of glycogen.

Glycogen breakdown and regulation of glycogen phosphorylase (allosteric and hormonal)

Glycogen synthesis and regulation of glycogen synthase.

Importance of glycogen synthesis and breakdown in liver and muscle

Role of protein phosphatase 1 (PP1) in the regulation of glycogen metabolism & phosphorylase A as a sensory system of glucose in the liver

17. Glucose homeostasis and glycogen-storage diseases

Role of glycogen in glucose homeostasis

The effect of glucagon and insulin on glycogen metabolism

Clinical insights:

Biochemical basis, diagnosis and treatment of glycogen storage diseases, Pombe disease, Von Gierke disease, McArdle disease, hypoglycemia

18. The pentose phosphate pathway

Production of NADPH and pentoses and coordination with glycolysis

Tissues with active pathway, when and why

General oxidative and non-oxidative reaction.

Clinical insights:

Biochemical basis, diagnosis and treatment of G6PD deficiency (drug-induced hemolytic anemia, favism), Thiamine deficiency, Wernicke-Korsakoff syndrome

Principles of neonatal screening

19. Digestion & absorption of lipids

Structural characteristics and nomenclature of lipids

Comparison of energy storage efficiency between triacylglycerols and glycogen

Digestion of food lipids: organs, enzymes, chylomicrons

Lipid mobilization from adipose tissue: hormone-sensitive lipases

Utilization of lipid glycerol

20. Degradation of fatty acids and production of ketone bodies

Activation of fatty acids and their transport to the mitochondria (role of carnitine)

β-oxidation of fatty acids and energy yield

Degradation of very long fatty acids

Degradation of fatty acids in the absence of glucose

Ketone bodies: production, the role in metabolism, importance in fasting and diabetes and diabetic ketoacidosis

Clinical insights:

Biochemical basis, diagnosis and treatment of carnitine deficiency, Vit. B12 insufficiency (megaloblastic anemia), Zellweger syndrome, diabetic ketoacidosis

21. Membrane lipids and membrane structure

Structure, biological role and synthesis of phospholipids, sphingolipids and gangliosides,

Structural characteristics, chemical composition and properties of biological membranes

Factors that affect the fluidity of membranes

Clinical insights:

Biochemical basis, diagnosis and treatment of sphingolipidosis, respiratory distress syndrome, Tay-Sachs disease

22. Fatty acid synthesis, regulation of fatty acid metabolism and weight-loss diets

Basic reactions and energy cost of fatty acid biosynthesis

Importance and origin of acetyl-CoA and NADPH

Regulation of fatty acid degradation and synthesis in response to nutrition

Classic and ketogenic weight loss diets

Essential fatty acids

Clinical insights:

Nutritional causes & treatment of obesity

Structure, metabolism and action of non-steroid anti-inflammatory drugs

23. Synthesis of lipids, cholesterol and cholesterol derivatives

Synthesis of triacylglycerols

Biological roles of cholesterol & basic principles of its synthesis

Reduction of HMG-CoA and its regulation

Structure and function of bile salts, gallstones

Synthesis of steroid hormones – Cytochrome P450

Structure and role of vitamin D

Clinical insights:

Biochemical basis, diagnosis and treatment of cholelithiasis (gallstones) and pediatric rickets

24. Lipoproteins

Classification, composition, function and diagnostic significance of lipoproteins

Structure and function of the LDL receptor and its role in hypercholesterolemia and atherosclerosis

Clinical insights:

Biochemical basis, diagnosis and treatment of hyperlipidemia, familial hypercholesterolemia,

Atherosclerosis, hypertriglyceridemia, lipoprotein lipase deficiency

25. Digestion and degradation of proteins and amino acids

Digestion of food proteins

Intracellular degradation of proteins

General principles of amino acid catabolism

Nitrogen transport and release reactions: transamination, oxidative and hydrolytic deamination, glutamine hydrolysis.

Importance and role of vitamin B6 and pyridoxal phosphate

Clinical insights:

Clinical significance of transaminases

26. Nitrogen metabolism and the Urea cycle

Role of alanine and glutamine in the transport of amino groups

General principles of nitrogen excretion

Urea cycle reactions

Clinical insights:

Biochemical basis, diagnosis and treatment of hyperammonemia

27. Amino acid metabolism

General principles of catabolism of the carbon skeleton of amino acids

Glycogenetic and ketogenetic amino acids

Genetic diseases of amino acid catabolism

Incorporation of nitrogen into biomolecules

Essential and non-essential amino acids

Synthesis of non-essential amino acids

Clinical insights:

Biochemical basis, diagnosis and treatment of albinism, phenylketonuria, hyperhomocysteinemia

28. The activated methyl cycle and amino acid derivatives

Transfer reactions of monocarbon groups

Role of tetrahydrofolic acid and S-adenosylmethionine

Biologically important mino acid derivatives: biogenic amines, catecholamines, glutathione, nitric oxide

Clinical insights:

Physiological and pathological role of homocysteine, hyperhomocysteinemia

29. Heme and iron metabolism

General principles of biosynthesis and catabolism of heme

Biological importance and excretion of bilirubin

Biological functions of iron

The daily cycle of iron

Disorders in iron metabolism

Maintaining iron homeostasis

Clinical insights:

Biochemical basis, diagnosis and treatment of hyperbilirubinemia (Jaundice), porphyrias, hemochromatosis, iron deficiency anemia.

30. Nucleotide metabolism

Structure, nomenclature and biological role of nucleotides

Precursors and basic principles for de novo ribonucleotide synthesis & salvage pathways

Synthesis of deoxyribonucleotides

Regulation of nucleotide synthesis

Nucleotide catabolism

Clinical insights:

Biochemical basis and symptoms of Lesch-Nyhan disease, biochemical basus of cytotoxic anti-cancer drugs, biochemical basis, diagnosis and treatment of gout

31. Overview & Integration of metabolism

Recurring patterns in metabolic regulation

Main metabolic pathways,their regulatory sites and key intermediates

Main metabolic pathways in brain, muscle (skeletal and cardiac), adipose tissue and liver

Major hormones of metabolism

Metabolic changes during the starved-fed cycle

Metabolic adaptation to prolonged starvation

Metabolic disorders in diabetes

Metabolic changes during exercise and alcohol consumption

Clinical insights:

Biochemical basis, diagnosis and treatment of diabetes and ethanol-mediated disorders

32. Metabolism and Cancer

The special characteristics of cancer cells

The Warburg effect (aerobic glycolysis)

Importance of the Warburg effect in the diagnosis and treatment of cancer

Metabolic oncogenes and tumor suppressors, oncometabolites

Hypoxia and cancer

Hypoxia-induced HIF factors and their role in cancer

Modern research and targeting of cancer metabolism

Clinical insights:

Principles of PET application in the diagnosis of cancer

B. Seminar/Τutorial content and relevant clinical insights

Problem-based learning: Presentation, analysis and discussion of clinical cases

Tutorial 1: Enzymes, enzyme inhibitors and diseases

1. Penicillin resistance
2. Osteogenesis imperfecta
3. Sickle-cell anemia
4. Antitrypsin deficiency & emphysema

Tutorial 2: Carbohydrate metabolism and enzymopathies

1. Alcoholic coma
2. Glucose-6-phosphate dehydrogenase deficiency & drug-induced hemolytic anemia
3. Pyruvate dehydrogenase deficiency
4. Fructose intolerance
5. Glycogen storage disease type I

Tutorial 3: Lipid and protein metabolism, nutrition and diseases

1. Anorexia nervosa
2. Obesity & non-alcoholic fatty liver disease
3. Hyperhomocysteinemia & myocardial infarction
4. Hyperammonemia
5. Acetyl-coenzyme A carboxylase deficiency

 C. 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

Operating basic Biochemistry & Clinical Chemistry equipment

Working as a team

Following instructions

Following safety regulations

Trouble-shooting in laboratory results

Clinical significance of lab results

Specific Skills

Practical 1. Enzymatic catalysis Ι

Spectrophotometric detection of the catalytic activity of alkaline phosphatase

Practical 2. Enzymatic catalysis ΙΙ

Analysis of the effects of substrate concentration and/or an inhibitor on the catalytic activity of alkaline phosphatase, determination of catalytic constants

Practical 3. Enzymatic catalysis ΙΙΙ

Determination of alkaline phosphatase concentration in an unknown sample.

Practical 4. Hemoglobin analysis

Measurement of hemoglobin concentration in patient blood and detection of abnormal hemoglobins using electrophoresis

Practical 5. Lipid analysis

Determination of triglyceride, total, HDL and LDL cholesterol concentration in patient serum samples

 Α. Lecture Material

Main suggested textbooks:

1. Tymoczko J.L, Berg J.M. & L. Stryer: BIOCHEMISTRY, A SHORT COURSE

                3^rd edition, W.H. Freeman and Company

2. Ferrier R. D.: Lippincott’s Illustrated Reviews: BIOCHEMISTRY

                6^th edition, Lippincott Williams & Wilkins, USA

Further reading:

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

Baynes J. W. & M. H.  Dominiczak: Medical Biochemistry (2nd Edition)

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

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

Murray et al.: HARPER’S Illustrated Biochemistry

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

Β. Laboratory Practical supplementary Material

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

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

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

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

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

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

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