BIOCHEMISTRY AND MOLECULAR BIOLOGY
Academic year and teacher
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- Versione italiana
- Academic year
- 2022/2023
- Teacher
- NICOLETTA BIANCHI
- Credits
- 12
- Didactic period
- Secondo Semestre
Training objectives
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Modulo: 002617 - MOLECULAR BIOLOGY
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The goal of the Integrated Course of Biochemistry and Molecular Biology is to provide students with the basic knowledge applied to structure and function of biological macromolecules (proteins, lipids, carbohydrates and nucleic acids), to the analysis of catalytic mechanisms involved in the main metabolic pathways, and to molecular mechanisms underlying the flow of genetic information. Students will be guided through the course to understand how the provided base knowledge can be applied for purposes related to the biomedical field, with particular attention to innovative approaches for the investigation of proteins and nucleic acids.
KNOWLEDGE AND UNDERSTANDING
The student:
- knows the proper biochemistry and molecular biology terminology;
- knows the biochemical and molecular bases governing biological systems and processes;
- knows the mechanisms and the different layers of integrated control of the main metabolic pathways as well as of the gene expression;
- knows the main experimental approaches to study proteins and nucleic acids.
ABILITY TO APPLY KNOWLEDGE AND UNDERSTANDING
The student is able to:
- use the proper biochemistry and molecular biology terminology;
- understand and evaluate the impact of mechanisms of modulation of biochemical and metabolic processes, as well as of gene mutations/variations on the different processes regulating gene expression;
- exploit the knowledge of techniques to investigate nucleic acids to plan a basic experimental research;
- has the ability to understand biochemical and molecular approaches to investigate biochemical and molecular processes, even for therapeutic or biotechnological approaches.
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Modulo: 28121 - BIOCHIMISTRY
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The goal of the Integrated Course of Biochemistry and Molecular Biology is to provide students with the basic knowledge applied to structure and function of biological macromolecules (proteins, lipids, carbohydrates and nucleic acids), to the analysis of catalytic mechanisms involved in the main metabolic pathways, and to molecular mechanisms underlying the flow of genetic information. Students will be guided through the course to understand how the provided base knowledge can be applied for purposes related to the biomedical field, with particular attention to innovative approaches for the investigation of proteins and nucleic acids.associated with them. Student know how to correctly use the terms of Biochemistry; know the biochemical basis of biological systems and processes; know the molecular basis of biological systems and processes; know the main metabolic pathways and their integrations; know the basic techniques for the study of proteins.
MOLECULAR BIOLOGY
Molecular Biology is a branch of the life sciences that deals with living organisms at the level of molecular mechanisms governing their physiological processes, with a focus on interactions among macromolecules and particularly between proteins and nucleic acids (DNA/RNA). These mechanisms, finely modulating the genetic information flow, are certainly one the main topics.
Students will be guided through the course to understand the mechanisms underlying the control of gene expression at the different levels, from transcription to translation and beyond. Moreover, the students will be guided to apply this knowledge on gene expression modulation also for biotechnological purposes.
KNOWLEDGE AND UNDERSTANDING
The student:
- knows the proper molecular biology terminology;
- knows the molecular mechanisms governing the biological processes;
- knows the different molecular mechanisms regulating gene expression, and their integration;
- knows the main experimental approaches to study nucleic acids.
ABILITY TO APPLY KNOWLEDGE AND UNDERSTANDING
The student is able to:
- use the proper molecular biology terminology;
- understand and evaluate the impact of gene mutations/variations on the different processing that regulate gene expression
- understand and design approaches to modulate gene expression for biotechnological or therapeutic purposes;
- exploit the knowledge of techniques to investigate nucleic acids to plan a basic experimental research.
KNOWLEDGE AND UNDERSTANDING
The student:
- knows the proper biochemistry and molecular biology terminology;
- knows the biochemical and molecular bases governing biological systems and processes;
- knows the mechanisms and the different layers of integrated control of the main metabolic pathways as well as of the gene expression;
- knows the main experimental approaches to study proteins and nucleic acids.
ABILITY TO APPLY KNOWLEDGE AND UNDERSTANDING
The student is able to:
- use the proper biochemistry and molecular biology terminology;
- understand and evaluate the impact of mechanisms of modulation of biochemical and metabolic processes, as well as of gene mutations/variations on the different processes regulating gene expression;
- exploit the knowledge of techniques to investigate nucleic acids to plan a basic experimental research;
- has the ability to understand biochemical and molecular approaches to investigate biochemical and molecular processes, even for therapeutic or biotechnological approaches. Prerequisites
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Modulo: 002617 - BIOLOGIA MOLECOLARE
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No formal prerequisites are required. However, basic knowledge of chemical bonds, and functional groups in inorganic and organic molecules, as well as knowledge of basic notions of cell biology, with particular attention to animal cells, such as the structure of the cell, of cellular compartments, and of function of main organs and tissues, with properties of language and scientific mastery.
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Modulo: 28121 - BIOCHIMICA
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No formal prerequisites are required. However, basic knowledge of chemical bonds, and functional groups in inorganic and organic molecules, as well as knowledge of basic notions of cell biology, with particular attention to animal cells, such as the structure of the cell, of cellular compartments, and of function of main organs and tissues, with properties of language and scientific mastery Course programme
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Modulo: 002617 - BIOLOGIA MOLECOLARE
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1. BIOCHEMISTRY
PROTEINS: water in biological systems; structure and function of proteins: myoglobin and hemoglobin, actin and myosin, immunoglobulins. Molecular chaperons; post-translational modifications. The extracellular matrix. The coagulation cascade. Enzymatic methods used for diagnosis. Main protein analysis techniques.
ENZIMOLOGY: general principles, catalytic strategies, kinetics and mechanisms of regulation and inhibitors.
BIOENERGY: biological reactions, catabolism and anabolism. High energy compounds and ATP production mechanisms. Redox systems. Gradients across the membrane and transport mechanisms.
METABOLISM OF CARBOHYDRATES: metabolism of glucose and other sugars; glucose transporters and glucose control systems, glycolysis, gluconeogenesis, glycogenesis and glycogenolysis, pentose phosphate pathway; pyruvate in aerobic and anaerobic conditions, Cori cycle; synthesis of Acetyl-CoA: the pyruvate dehydrogenase complex. Citric acid cycle and its amphibolic functions. The role of hormones in carbohydrate metabolism. Oncometabolites. Main carbohydrate analysis techniques.
ELECTRON TRANSPORT AND OXIDATIVE PHOSPHORILATION: complexes of the respiratory chain; the mitochondrion: mitochondrial pathologies; ATP synthase, ATP and ADP transport. Shuttle systems. Thermogenin or uncoupling protein.
LIPID METABOLISM: intestinal transport and plasma lipid homeostasis; their metabolic role. Fatty acid oxidation. Ketone bodies. Biosynthesis of lipid and cholesterol. LDL. The role of hormones in lipid metabolism.
METABOLISM OF AMINO ACIDS: nitrogen metabolism; urea cycle and regulation; transamination, degradation and biosynthesis of amino acids. Amino acid derivatives; heme biosynthesis and degradation. Clinical significance (diagnostic and prognostic) of transaminases.
METABOLISM OF NUCLEOTIDES: purine and pyrimidine nucleotides: biosynthesis, degradation and regulation. Synthesis of deoxyribonucleotides.
METABOLISM INTEGRATION (CELLULAR AND TISSUE LEVELS): tissue-specific metabolism and metabolic interrelationships. Hormonal regulation. Mechanism of action of protein and steroid hormones. The meaning of the second messengers. Fasting-feeding cycle.
2. MOLECULAR BIOLOGY
-NUCLEIC ACID STRUCTURE: physical and chemical properties of DNA and RNA:, B, A and Z forms. DNA topology and topoisomerases; structure of the genome: nucleosomes and chromatin; chromatin remodeling, role of histone tail modification and functional implications.
-DNA REPLICATION: DNA polymerases (prokaryotic and eukaryotic); replisome and components of the replicative fork; DNA replication in prokaryotes and eukaryotes.
Overview on recombinant technologies: restriction enzymes, recombinant plasmids (features and manipulation), cloning; the polymerase chain reaction (PCR); electrophoresis; DNA sequencing.
-DNA REPAIR AND RECOMBINATION: mismatch repair system; DNA damage; direct DNA repair; base excision repair (BER); nucleotide excision repair (NER), glycosylases; double strand break and non-homologous end joining (NHEJ); homologous recombination and description of the prokaryotic and eukaryotic molecular machines involved; overview of site-specific recombination.
-TRANSCRIPTION: description of transcription mechanisms in prokaryotes and eukaryotes; gene promoters; RNA editing; the splicing mechanism and the spliceosome; alternative splicing and trans-splicing; the role of ESEs, ESSs, ISSs, ISEs; transcriptional regulation in prokaryotes: activators, repressors and operons (with examples); transcriptional regulation in eukaryotes; DNA-binding and activation domains of transcription factors, combinatorial control, DNA methylation; overview of reporter gene systems; regulatory small RNAs.
-TRANSLATION: recognition of the initiation codon in prokaryotes and eukaryotes; tRNA structure; aminoacyl-tRNA synthetases; ribosomes, structure and determinants; mechanisms of translation in prokaryotes and eukaryotes; the genetic code; translation regulation in prokaryotes and eukaryotes; nonsense- and nonstop-mediated mRNA decay; overview of mechanisms governing protein trafficking and post-translational modifications.
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Modulo: 28121 - BIOCHIMICA
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PROTEINS: water in biological systems; structure and function of proteins: myoglobin and hemoglobin, actin and myosin, immunoglobulins. Molecular chaperons; post-translational modifications. The extracellular matrix. The coagulation cascade. Enzymatic methods used for diagnosis. Main protein analysis techniques.
ENZIMOLOGY: general principles, catalytic strategies, kinetics and mechanisms of regulation and inhibitors.
BIOENERGY: biological reactions, catabolism and anabolism. High energy compounds and ATP production mechanisms. Redox systems. Gradients across the membrane and transport mechanisms, cell signaling.
METABOLISM OF CARBOHYDRATES: metabolism of glucose and other sugars; glucose transporters and glucose control systems, glycolysis, gluconeogenesis, glycogenesis and glycogenolysis, pentose phosphate pathway; pyruvate in aerobic and anaerobic conditions, Cori cycle; synthesis of Acetyl-CoA: the pyruvate dehydrogenase complex. Citric acid cycle and its amphibolic functions. The role of hormones in carbohydrate metabolism. Oncometabolites. Main carbohydrate analysis techniques.
ELECTRON TRANSPORT AND OXIDATIVE PHOSPHORILATION: complexes of the respiratory chain; the mitochondrion: mitochondrial pathologies; ATP synthase, ATP and ADP transport. Shuttle systems. Thermogenin or uncoupling protein.
LIPID METABOLISM: intestinal transport and plasma lipid homeostasis; their metabolic role. Fatty acid oxidation. Ketone bodies. Biosynthesis of lipid and cholesterol. LDL. The role of hormones in lipid metabolism.
METABOLISM OF AMINO ACIDS: nitrogen metabolism; urea cycle and regulation; transamination, degradation and biosynthesis of amino acids. Amino acid derivatives; heme biosynthesis and degradation. Clinical significance (diagnostic and prognostic) of transaminases.
METABOLISM OF NUCLEOTIDES: purine and pyrimidine nucleotides: biosynthesis, degradation and regulation. Synthesis of deoxyribonucleotides.
METABOLISM INTEGRATION (CELLULAR AND TISSUE LEVELS): tissue-specific metabolism and metabolic interrelationships. Hormonal regulation. Mechanism of action of protein and steroid hormones. The meaning of the second messengers. Fasting-feeding cycle.
MOLECULAR BIOLOGY
NUCLEIC ACID STRUCTURE: physical and chemical properties of DNA and RNA:, B, A and Z forms. DNA topology and topoisomerases; structure of the genome: nucleosomes and chromatin; chromatin remodeling, role of histone tail modification and functional implications.
DNA REPLICATION: DNA polymerases (prokaryotic and eukaryotic); replisome and components of the replicative fork; DNA replication in prokaryotes and eukaryotes.
Overview on recombinant technologies: restriction enzymes, recombinant plasmids (features and manipulation), cloning; the polymerase chain reaction (PCR); electrophoresis; DNA sequencing.
DNA REPAIR AND RECOMBINATION: mismatch repair system; DNA damage; direct DNA repair; base excision repair (BER); nucleotide excision repair (NER), glycosylases; double strand break and non-homologous end joining (NHEJ); homologous recombination and description of the prokaryotic and eukaryotic molecular machines involved; overview of site-specific recombination.
TRANSCRIPTION: description of transcription mechanisms in prokaryotes and eukaryotes; gene promoters; RNA editing; the splicing mechanism and the spliceosome; alternative splicing and trans-splicing; the role of ESEs, ESSs, ISSs, ISEs; transcriptional regulation in prokaryotes: activators, repressors and operons (with examples); transcriptional regulation in eukaryotes; DNA-binding and activation domains of transcription factors, combinatorial control, DNA methylation; overview of reporter gene systems; regulatory small RNAs.
TRANSLATION: recognition of the initiation codon in prokaryotes and eukaryotes; tRNA structure; aminoacyl-tRNA synthetases; ribosomes, structure and determinants; mechanisms of translation in prokaryotes and eukaryotes; the genetic code; translation regulation in prokaryotes and eukaryotes; nonsense- and nonstop-mediated mRNA decay; overview of mechanisms governing protein trafficking and post-translational modifications. Topics will be discussed with particular attention to sex and gender differences. Didactic methods
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Modulo: 002617 - BIOLOGIA MOLECOLARE
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The course is structured in class lectures on the several topics listed in the previous section. The student is guided through the course even by taking advantage of the “active learning”, allowing a deep understanding of the relationship between structure and function of macromolecules, as well as of the several regulation strategies of metabolic reactions and of the flow of genetic information at the different levels. Students will be actively involved in the discussion of course topics.
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Modulo: 28121 - BIOCHIMICA
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The course is structured in class lectures on the several topics listed in the previous section. The student is guided through the course even by taking advantage of the “active learning”, allowing a deep understanding of the relationship between structure and function of macromolecules, as well as of the several regulation strategies of metabolic reactions and of the flow of genetic information at the different levels. Students will be actively involved in the discussion of course topics. Learning assessment procedures
- The exam is aimed at verifying the achievement of the indicated training objectives. Considering the specific requirements to verify the level of knowledge of the topics, the evaluation process will be organized as separated exams. The evaluation of the integrated course will be given by the average of the score obtained in the partial tests (module of Biochemistry and module of Molecular Biology). The final score is an arithmetic average of the marks obtained in each schedule of Biochemistry and Molecular Biology.
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Modulo: 002617 - MOLECULAR BIOLOGY
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The assessment of the learning will be carried out by means of a written exam with 21 questions (1.5 points for each correct answer) lasting 25 minutes, with the duration of the whole test increased for students with "Specific Learning Disorders". The questions will be formulated with multiple choice questions related to all the training objectives defined above. There will be no penalty for incorrect or unsuccessful answers. The final score will be expressed in thirtieths (minimum grade 18/30).
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Modulo: 28121 - BIOCHIMISTRY
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The assessment of the learning will be carried out by means of a written exam with 25 questions lasting 25 min (Biochemistry schedule). The questions will be formulated with multiple choice questions (5 options for each question) relating to all the training objectives defined above. There will be no penalty for incorrect or unsuccessful answers.
The final score (expressed in thirtieths) will be agreed with the teachers involved and will take into account the weight in terms of CFU of each teacher. The teachers reserve the right to examine students' learning by oral examination. The duration of the whole test will be increased for students with "Specific Learning Disorder". The minimum mark for passing the exam, equal to 18/30, is achieved by those who will answer exactly 14 questions. Reference texts
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Modulo: 002617 - BIOLOGIA MOLECOLARE
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BIOCHEMISTRY
"Biochimica" by Berg-Tynoczko-Stryer, Zanichelli.
"I principi di Biochimica di Lehninger" by Nelson-Cox, Zanichelli.
"Principi di Biochimica" by Garret&Grisham, Piccin.
"Fondamenti di Biochimica" by Voet-Voet-Pratt, Zanichelli.
MOLECULAR BIOLOGY
"Biologia molecolare del gene" di Watson et al, Ottava Edizione, Zanichelli.
“Fondamenti di Biologia Molecolare” di Lizabeth A. Allison, Seconda Edizione, Zanichelli.
"Biologia molecolare" di Amaldi-Benedettii-Pesole-Plevani, Casa Editrice Ambrosiana.
“Biologia molecolare” di G. Capranico et al, Seconda Edizione, EdiSES.
Schemes, videos possibly provided by the teacher and scientific reports.
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Modulo: 28121 - BIOCHIMICA
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BIOCHEMISTRY
"Fondamenti di Biochimica" by Voet-Voet-Pratt, Zanichelli.
"Introduzione alla Biochimica di Lehninger" di Nelson-Cox, Zanichelli.
