Molecular Biology, Medicinal Chemistry and Computer Science for Pharmaceutical Applications

Activity type

Discipline biologiche

SSD

BIO/12

Year

2nd year

Semester

2nd semester

CFU

3

Hours distribution

24 classroom hours

Lecturers

ANDREA FUSO
MICHELE ZAMPIERI

Activity type

Discipline Biologiche e Morfologiche

SSD

BIO/10

Year

2nd year

Semester

2nd semester

CFU

9

Hours distribution

64 classroom hours, 12 training hours

Lecturers

FRANCESCO FIORENTINO

The course in Biochemistry and Clinical Biochemistry covers a wide range of topics related to the chemical processes within living organisms, with a particular focus on the biochemical aspects relevant to clinical medicine and diagnosis. The topics covered include the following:

Introduction to Biochemistry: This section covers the basic principles of biochemistry, including the structure and function of biomolecules such as proteins, carbohydrates, lipids, and nucleic acids. These topics are prerequisites of the Course. Students learn about biochemical pathways and cellular processes that are essential for life.

Enzymes and Enzyme Kinetics: This part focuses on the properties of enzymes, their mechanism of action, factors influencing enzyme activity, and enzyme kinetics. Understanding enzymes is crucial for comprehending metabolic pathways and their regulation.
Bioorganic Chemistry: Understanding the mechanisms by which enzymes catalyze biochemical reactions and designing enzyme inhibitors or mimics for therapeutic purposes. This includes investigating the interactions between small molecules and biological systems to elucidate cellular processes and develop new drugs or chemical tools for biological research.

Metabolism: Metabolic pathways are extensively covered, including glycolysis, the citric acid cycle, oxidative phosphorylation, and metabolic regulation. Students learn about the interconnections between different pathways and how they contribute to energy production and biosynthesis.

Biochemical Techniques: This section introduces students to common laboratory techniques used in biochemistry, such as chromatography, electrophoresis, spectrophotometry, and molecular biology techniques like PCR (Polymerase Chain Reaction) and DNA sequencing.

Protein Structure and Function: This topic covers the structure and function of proteins, including protein folding, post-translational modifications, and protein-protein interactions. Students learn about enzymes, receptors, transport proteins, and other important protein functions.

Clinical Biochemistry: This part of the course focuses on the application of biochemical principles to clinical practice. Topics include the biochemistry of diseases such as diabetes, cancer, cardiovascular diseases, and metabolic disorders. Students learn about biochemical markers used in diagnosis, prognosis, and monitoring of various diseases.

Overall, the course in Biochemistry and Clinical Biochemistry provides students with a comprehensive understanding of the biochemical basis of life processes and its applications in clinical medicine and research.

Essential Objectives of the Integrated Course
Upon completion of the course, the student must:
- know the biochemical-molecular parameters, in biological samples and in vivo, at the different levels of structural and functional organization: from molecules to cells, tissues, organs, and the whole organism.
- to know how to critically interpret laboratory findings also in relation to pathophysiological states.
- to know how to use laboratory findings for the purposes of diagnosis and prognosis.

Knowledge of the general, inorganic and organic chemistry and of the bases of biochemistry

Programme
Structure and function of aminoacids. Physical-chemical properties of aminoacids. Optical activity and
stereoisomerism. Acid-base properties of aminoacids and titration curves. Isoelectric point and principles of
electrophoresis. Peptide bond and its characteristics. Structural organization of proteins. Ramachandran plot.
Alpha helices, beta sheets and beta turns. Biophysical techniques for protein purification and analysis.
Fibrous proteins (collagen, alpha keratin, fibroin): maturation, structure and function. Protein folding in health
and disease. Anfinsen’s dogma and Levinthal’s paradox. Clathrates. Hydrophobic effect. Chaperones and
chaperonines.
Globins: myoglobin and hemoglobin. Myoglobin molecular structure and function. Saturation function.
Hemoglobin molecular structure and function. Saturation function, Hill’s equation and cooperativity. Perutz’s
stereochemical mechanism. Allostery and hemoglobin allosteric modulators (2,3-BPG, carbon dioxide).
Transport of carbon dioxide and oxygen. The Bohr effect. The MWC and KNF models. Hemoglobinopathies:
molecular basis of disease. Sickle cells anemia.
Immunoglobulins: structure and function. Domain structure, immunoglobulin fold and antigen recognition.
Hypervariable and framework regions. Abzymes. Immuno-based assays.
Enzymes: nomenclature and general properties. Thermodynamic aspects of catalysis. Catalytic mechanisms and
strategies: acid-base catalysis, metal-ion catalysis, covalent catalysis, electrostatic catalysis. Features and
catalytic mechanisms of pancreatic ribonuclease, carbonic anhydrase and serine proteases (trypsin and
chymotrypsin).
Enzyme kinetics. Rapid pre-equilibrium hypothesis. The Steady State hypothesis. The Michaelis-Menten
equation and significance of the steady state parameters. Experimental determination of the steady state
parameters: initial rate method. Lineweaver-Burk and Eadie-Hofstee plots. Enzyme inhibition: competitive,
uncompetitive and mixed inhibition. Principles of spectrophotometry and Lamber-Beer law.
Introduction to metabolism: Catabolism, anabolism and regulation. Types of metabolic pathways and organ
specializations. ATP, NAD, FAD and their role in metabolism.
Carbohydrate metabolism: Glycolysis and mechanisms of glycolytic enzymes. Alternative fates of pyruvate:
homolactic fermentation and alcoholic fermentation. Regulation of glycolysis.
Gluconeogenesis and its regulation. Glucose transport (GLUT transporters). Hormonal regulation: insulin and
glucagon.
The pentose phosphate pathway: oxidative phase and non-oxidative phase. ROS and oxidative stress
detoxification mechanisms: glutathione, glutathione reductase and peroxidase. Regulation of the pentose
phosphate pathway.
Metabolism of glycogen. Glycogenolysis and glycogenesis. Glycogenin. Regulatory mechanisms.
Cellular respiration: metabolic fate of pyruvate and the Krebs cycle. Compartmentalization and pyruvate
transporters. Pyruvate dehydrogenase as a multienzymatic complex and conversion of pyruvate into acetyl-
CoA. The citric acid cycle and its regulation. Cataplerotic and anaplerotic reactions. Way of glyoxylate.
Fatty acids metabolism. Fatty acids activation and mitochondrial transport. Carnitine acyltransferase. Beta
oxidation. Ketone bodies as energy fuel. Fatty acids biosynthesis. Citrate shuttle. Fatty acid synthase and
palmitate synthesis. Desaturation. Synthesis regulation.
Introduction to the aminoacids catabolism. Glutamine and glutaminase. Alanine-glucose cycle. PLP and
transdeamination of glutamate. The urea cycle. Aspartate-argininosuccinate shunt. Destiny of carbon
skeletons: glucogenic and ketogenic aminoacids.
Electron transport and oxidative phosphorylation. Mitochondria. The chemiosmotic theory. Mitochondrial
DNA. Coenzyme Q. The mitochondrial respiratory chain, I-V complexes. Molecular structure and mechanism of
ATP synthase. Cellular respiration inhibitors.
Suggested textbooks
1) 2) Nelson D.L., Cox M.M. Lehninger Principles of Biochemistry. 8th Edition. Macmillan Editor (2021). ISBN
9781319381493
Voet D., Voet J.G,, Pratt C.W. Voet's Principles of Biochemistry Global Edition. John Wiley Sons Inc.
(2018). ISBN 9781119451662

General Clinical Biochemistry:
Definition and objectives of clinical biochemistry.
Sources of error & variability of laboratory data and their impact on data quality and interpretation.
Pre-analitical & analytical variability
Biological variability
How errors are controlled and quality is assured.
The diagnostic efficiency of a clinical test. The interpretation of laboratory test results.

Special Clinical Biochemistry:
Metabolic clinical biochemistry.
Clinical tests and the major alterations associated with major macromolecules in biological fluids.
Proteins
Carbohydrates
Lipids
Clinical laboratory tests for studying the pathophysiology of organs/tissues.
Blood
Heart and cardiovascular risk
Renal function
Liver function

Marcello Ciaccio, Clinical and Laboratory Medicine Textbook, Springer
Micahel Bishop, Clinical Chemistry: Principles, Techniques, and Correlations , Wolters Kluwer
Nader Rifai
Tietz, Fundamentals of Clinical Chemistry and Molecular Diagnostics, Elsevier

Module: CLINICAL BIOCHEMISTRY AND MOLECULAR BIOLOGY
N/D
Module: BIOCHEMISTRY
N/D

Lessons in presence

Frontal teaching. In presence

Written examwith multiple choice and open answers. Possibility of an oral question at the end to adjust the grade

Open questions:
- Provide a comprehensive description of the energy recovery phase of glycolysis;
- Write the structure of the following pentapeptide: Gln-Pro-Lys-Met-Asp;
- Describe the catalytic mechanism of pancreatic ribonuclease.

Multiple choice questions:

- Which is the yield of the oxidation of palmitoyl-CoA?
a) 8 acetyl-CoA, 7 FADH2, 7 NADH
b) 8 GTP, 24 NADH, 8 FADH2
c) 2 pyruvate, 2 ATP, 2 NADH, 2H+, 2H2O
d) CoA, 3 NADH, 3H+, FADH2, GTP, 2CO2

- If pH < pI
a) An aminoacid is in the zwitterionic form
b) An aminoacid migrates towards the cathode (in a electrophoretic experiment)
c) An aminoacid has a net charge equal to zero
d) An aminoacid is in the cationic form


- Which is the role of hydroxylated proline and lysine residues in collagen?
a) To provide stability, glycosylation sites and cross linking sites
b) To determine a left handed rotation of the helix
c) To induce catalysis of substrates
d) To determine a right handed rotation of the helix

- Indicate the correct sentence:
a) Hb is completely saturated with low pO2
b) The sigmoid saturation curve perfectly describes the behavior of a storage protein as Mb
c) α1−β1 and α2−β2 interfaces are sites where important quaternary changes take place
d) The F helix is translated towards the heme upon O2 binding

Module: CLINICAL BIOCHEMISTRY AND MOLECULAR BIOLOGY
N/D
Module: BIOCHEMISTRY
N/D