Learning objectives
To understand, to acquire skills and to be able to communicate relevant concepts concerning:
structure and functions of the main bio-molecules (proteins, nucleic acids, enzymes and co-enzymes);
the mechanisms of metabolic energy production, energetic and structural homeostasis of living cells, the molecular mechanisms of genetic information,
Prerequisites
Before taking the exam of "Biochimica e Biologia Molecolare" students have to pass:
Chimica e propedeutica Biochimica
Course unit content
The course introduce relevant information and knowledge on the main molecules constituting living organisms. The course is organized in 3 modules:
Biochemistry A:
Myoglobin, hemoglobin and oxygen transport. Enzymes and enzyme kinetics. Cofactors and coenzymes used in metabolic reactions. Bioenergetics and biological oxidation. ATP, structure and functions. Reducing power, oxidative phosphorylation, the role of oxygen metabolism.
Biochemistry C:
Protein structure, protein folding and folding models. Protein homeostasis: post-translational modifications, targeting and quality control of folding. Protein misfolding and aggregation.
Water-soluble vitamins: structure, function, mechanism of action and deficiency syndromes.
MOLECULAR BIOLOGY:
The course provides basic knowledge on the molecular aspects of the transmission of genetic information. The course initially introduces the basics of the concept of inheritance, and then introduces nucleic acids as molecules able to ensure the transmission of the genetic information through DNA replication, RNA transcription and proteins translation. Then will be introduced the concepts of DNA damage/mutation and the impact of DNA mutation on human health. Finally the course will provide the basis for the knowledge of the main techniques used for DNA/RNA manipulation, and their application in various fields of research, diagnosis, forensic medicine and treatment of human diseases.
Full programme
BIOCHEMISTRY C:
Protein structure - Peptide bond: planarity, configuration, rigidity and rotations. Peptides and proteins, detailed description of protein structure levels.
Motifs and structural domains - Definitions of structural motif and domain. Examples of motifs and domains of alpha, beta and alpha / beta type. Multiple domain proteins.
Fibrous proteins – Keratin and collagen: structural and functional aspects. Collagen diseases. Structural elements of Immunoglobulin G. Structural features of membrane proteins.
Protein homeostasis - Post-translational modifications, protein targeting to nucleus, mitochondria, endoplasmic reticulum; secretory pathway, localization in lysosome and cell membrane.
Protein folding - Thermodynamics and folding, Anfinsen experiment, Levinthal paradox, folding models, energy landscape model.
Protein homeostasis - Folding quality control: disulfide isomerase protein, peptidylprolyl cis /trans isomerase, molecular chaperones, chaperonin, unfolded protein response.
Protein degradation mediated by lysosome and ubiquitin-proteasome system.
Protein misfolding and aggregation - Conformational diseases, amyloid fiber: cross-beta structure, aggregation, growth and propagation mechanisms. Prions and conformal contagion.
Water-soluble vitamins, B-complex and vitamin C:
- structural formula
- natural sources
- biological action, mechanism of action of the coenzymatic form
BIOCHEMISTRY A:
Structure of the heme. Myoglobin and hemoglobin: structure and function. The human globin chains. Heme ligands. Protein-ligand interaction. Association and dissociation constants. Graphic representation of protein-ligand interaction. Hemoglobin: transition from state T to state R. The cooperative binding and Hill equation. Saturation curve of Hb and Mb. Bohr effect. CO2 transport. 2,3 BPG binding. Effect of temperature and pH on the saturation curve. Hb and NO. Hb and CO. Abnormal hemoglobins.
Classification and nomenclature of enzymes. Gibbs free energy. Transition state. Mechanisms of catalysis. Enzymatic kinetics: Michaelis Menten equation, Lineweaver Burk graph. Catalytic efficiency. Enzymatic inhibition. Allosteric enzymes. Enzymatic regulation. Regulation of metabolic pathways. Bioenergetics and biological oxidation. ATP, structure and functions. Cellular energy charge. Redox potentials. Structure and function of NAD, NADH, FAD, FADH2. Respiratory chain of mitochondria. Reducing power, oxidative phosphorylation, the role of oxygen in metabolism. Cycle of Q.
Shuttle of glycerol 3-phosphate. Shuttle malate-aspartate. Regulation of energy metabolism. Respiration uncoupling and uncoupling agents.
MOLECULAR BIOLOGY: From Darwin to Mendel to the discovery of the transforming principle: bases of the transmission of genetic information.
Nucleic acids: composition and structure.
3D structure of DNA, DNA topology: coiling and supercoiling.
Topoisomerases.
Histones, chromatin, chromosomes.
Basics of epigenetic modifications of DNA and histones.
DNA replication: characteristics of DNA polymerases, replication mechanism.
Drugs that interfere with the replication process.
Replication forks, replisome assembly, replication coupling mechanisms.
Origin of replication, mechanism of origins control in eukaryotes.
Termination of replication.
The ends of linear chromosomes: telomerase.
DNA damage and mutations.
Mechanisms of damage repair: direct, indirect, double-strand break repair mechanisms.
RNA transcription in eukaryotes: characteristics of RNA polymerases, formation of the initiation complex, elongation, termination of transcription.
Characteristics of prokaryotic and eukaryotic promoters.
Regulation of gene expression in eukaryotes.
RNA maturation: capping, splicing, tailing, editing.
Notes on RNA interference.
From RNA to proteins: mechanisms and enzymes of messenger RNA translation. The genetic code.
Translation of messenger mRNA: molecules and enzymes involved.
t-RNA, ribosomes, aminoacyl-tRNAsynthetase
Stages of translation: initiation, elongation, termination.
Drugs that interfere with the protein translation process.
Bibliography
Nelson DL, Cox MM: I principi di Biochimica di Lehninger, Zanichelli, Bologna.
JD Watson et al.: Biologia Molecolare del gene. Zanichelli, Bologna.
G. Capranico, E. Martegani, G. Musci, G. Raugei, T. Russo, N. Zambrano, V. Zappavigna. Edises
Lieberman, Marks: Biochimica Medica, un approccio clinico. Casa Editrice Ambrosiana, Milano.
Devlin TM: Biochimica con aspetti clinici. Wiley-Liss, New York.
Garrett RH, Grisham CM: Biochimica. Piccin, Padova.
Murray RK, Granner DK, Mayes PA, Rodwell VW; Harper Biochimica, McGraw-Hill Libri Italia srl, Milano.
Voet D, Voet JG: Biochimica John Wiley & Sons, USA.
Teaching methods
Lectures will be held on-site in compliance with the health safety protocols adopted by the University of Parma.
Lectures will be supported by slide presentations and videos, promoting the molecular approach which will be available to students on Elly platform.
Assessment methods and criteria
The exam consists in a written test with closed answers, made of 30 multiple choice questions, twenty of which concerning the program of Biochemistry and the remaining ten on the Molecular Biology program. Time allowed for the test is 60 minutes; in the first 20 minutes the students are allowed to quit, returning the test to the commission. Each positive answer contributes with 1 point to the final grade (0-30/30). There is no penalty for incorrect answers. In case of a positive result, you can choose whether to proceed with the recording of the grade or to take an oral exam.
Students with SLD / BSE must first contact Le Eli-che: support for students with disabilities, D.S.A., B.E.S. (https://sea.unipr.it/it/servizi/le-eli-che-supporto-studenti-con-disabilita-dsa-bes).
Other information
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