84259 - GENERAL BIOCHEMISTRY

Conoscenze e abilità da conseguire

Understand the structure, properties, and functional role of the four main classes of biological macromolecules (carbohydrates, lipids, proteins and nucleic acids). Define mechanism, kinetics and regulation of enzyme reactions, and their role in biochemical processes. Describe the thermodynamic basis and mechanisms of cellular bioenergetics.

Contenuti

GENERAL BIOCHEMISTRY- MODULE 1

COURSE CONTENT

Nucleotides and Nucleic Acids:

• Structure and nomenclature of nucleotides.
• Phosphodiester Bonds.
• Three-dimensional structure of DNA (A, B, and Z forms of DNA).
• RNA structures.
• Denaturation of nucleic acids.
• Nucleases: types and mechanisms of action.
• Mutations and polymorphisms.

  Genes and Chromosomes:

• Genes and genome.
• Introns and Exons.
• DNA organization, supercoiling and topoisomerases, nucleosomes and histones.
• Mitochondrial DNA.

  DNA metabolism:

• DNA replication: rules and their meanings, mechanism of reaction.
• Functional characteristics of DNA polymerases and other enzymes and proteins involved in DNA replication (helicases, ligases); catalytic mechanism of ligases and phases of the replicative process.
• DNA repair.
• DNA recombination.
• Telomeres and telomerases.
• DNA genetic engineering with CRISPR/Cas9 technology.

  RNA metabolism:

• RNA polymerases.
• DNA-dependent synthesis of RNA (transcription).
• Transcription in prokaryotes and in eukaryotes.
• Pomoters and transcription regulators.
• Post-transcriptional modifications: significance and molecular mechanisms of splicing and of 5’-cap and polyA insertion; ribozymes.
• mRNA degradation.
• Reverse transcriptase.
• microRNAs and other non-coding RNAs: biogenesis, function, mechanisms of action and involvement in cancer.

  Protein Synthesis:

• The genetic code and its natural variations (mtDNA).
• Structure of ribosomes and peculiarity of tRNA.
• Protein synthesis: aminoacyl-tRNA synthase reaction; initiation, elongation, termination, folding and post-translational processing.
• Protein targeting and degradation (ubiquitin, proteases and proteasome)
• Protein synthesis through the DNA recombinant technology.

GENERAL BIOCHEMISTRY- MODULE 2

COURSE CONTENT

Biological macromolecules

• Lipids: classification; biological role [Nov 22nd, 9-10].
  

• Carbohydrates: classification; biological role; glycoconjugates [Nov 22nd, 10-11].

• Aminoacids: classification, chemical structure and acid-base properties [Nov 26th, 9-11].
  

• Peptides and proteins: general characteristics; the 4 structures of proteins; denaturation and folding [Nov 27th, 9-11].
  

Enzymes and enzymology [Nov 27th, 16-18 + Nov 29th, 9-11]

• Classification.

• Effects on reaction rate and thermodinamics.

• Enzyme kinetics and inhibition.

• Allosterism.

Bioenergetics [Nov 30th, 9-11 + Dec 3rd, 14-16]

• The second law of thermodinamics and free energy.

• Common biochemical reactions.

• Phosphoryl group and ATP.

• Biological redox reactions.

Oxygen binding proteins: myoglobin and hemoglobin [Dec 13th, 9-11]

Testi/Bibliografia

PowerPoint presentations integrated by personal notes can give a useful outline of the course. It is warmly suggested to support the above-mentioned material with some textbook that could help the student also in the study of the Chemistry course and the Biochemistry courses present in the following semester.

Lehninger Principles of Biochemistry, 7th edition - International Edition

D. L. Nelson, M. M. Cox

W. H. Freeman - Macmillan learning

ISBN: 978-1-319-10824-3.

The last textbook is equivalent to the standard 7th edition, whose ISBN code is: 978-1-4641-2611-6

Copies of the textbook, mostly in the previous editions, are available to consultation and borrow at the following University libraries:

• Biblioteca Biomedica Centrale (link [https://acnpsearch.unibo.it/library/BO303] );
• Biblioteca di Fisica (link [https://acnpsearch.unibo.it/library/BO405] ).

In particular, the course will focus on the following chapters:

• Chapter 1 - The fundamentals of Biochemistry (only reading in order to revise some basic concepts propaedeutic to the course).
• Chapter 2 - Water (only reading in order to revise some basic concepts propaedeutic to the course).

• Chapter 3 - Amino Acids, Peptides, and Proteins

- paragraphs 3.1 and 3.2 are important;

- paragraphs 3.3 and 3.4 only reading to know about biochemical techniques;

• Chapter 4 -The 3-D Structure of Proteins
• Chapter 5: Protein Function

- only paragraph 5.1 - Reversible Binding of a Protein to a Ligand: Oxygen-Binding Proteins

• Chapter 6 - Enzymes
• Chapter 7 - Carbohydrates and Glycobiology

- paragraphs 7.1, 7.2 and 7.3 are important;

- paragraphs 7.4 and 7.5 only reading.

• Chapter 10 - Lipids

- paragraphs 10.1, 10.2 and 10.3 are important;

- paragraph 10.4 only reading.

Chapter 13 - Bioenergetics and Biochemical Reaction Types

Metodi didattici

Traditional lecture-based teaching based on Power Point presentations.

Attendance to learning activities is mandatory; the minimum attendance requirement to be admitted to the final exam is 66% of lessons. This teaching is a part of the Chemistry and Bichemistry Integrated Course (IC), therefore the 66% attendance requirement refers to the total amount of IC lessons. Students who fail to meet the minimum attendance requirement will not be admitted to the final exam of the course, and will have to attend relevant classes again during the next academic year.

Professors may authorise excused absences upon receipt of proper justifying documentation, in case of illness or serious reasons. Excused absences do not count against a student’s attendance record to determine their minimum attendance requirement.

Modalità di verifica e valutazione dell'apprendimento

The assessment of the course contents is based on a final examination only; no midterm exams are scheduled. The final examination consists of a single written exam, having a maximum duration of three hours.

During the examination, only the use of ordinary stationery (i.e., pencils, pens, rubber, rulers, etc.) and of a calculator is allowed. The periodic table (which sample copy is available on AMS Campus) and any other supplementary material will be directly attached to the exam papers. During the examination, students are not allowed to leave the classroom, unless they accept to definitively deliver all their exam papers and do not enter the classroom anymore. During the exam, the presence of electronic devices, other than a simple watch and the aforementioned calculator, is strictly forbidden.

In order to take the exam, students must sign up through AlmaEsami within the indicated deadlines. All the activities associated to the “Biochemistry Laboratory” must be completed and approved, before considering to take the exam. During the examination, students must have an ID document and their university badge.

The overall exam score is 34.00 points, equally divided in 17.00 points for the “Chemistry” part and 17.00 points for the “Biochemistry” one. Each single written exam will include both the “Chemistry” and the “Biochemistry” part and cannot be split.

The exam is passed by achieving at least 9.00 points (out of 17.00) in both parts. The final mark is calculated by summing the points obtained in both the above mentioned parts and rounding it to the nearest integer.

Examples:

• Chemistry: 10.50 pts + Biochemistry: 8.50 pts
  ---> FAILED
• Chemistry: 11.00 pts + Biochemistry: 13.75 pts
  ---> 24.75 pts ---> PASSED WITH 25/30.

If a student obtains an overall score of 31 points or more, 30L is assigned.

The exam results will be published online on AlmaEsami. If the exam is passed, the associated mark will be officially registered only after the student's confirmation to be sent to the integrated course coordinator (i.e., Prof. Michele Di Foggia, michele.difoggia2@unibo.it), using the student institutional email (e.g., name.surname@studio.unibo.it).

The registration of a successful examination is permitted no later than 6 months from the date of the exam; after this deadline, the result achieved and not confirmed will expire.

If a student decides to take the exam again, regardless of the associated outcome, the result obtained in the previous examination will automatically be cancelled. The exam can be repeated at any exam session.

The exam contents are:

• 10 multiple choice questions, each awarding 0.25 points; maximum score: 2.5 points.

- 3 questions on lipids and carbohydrates;

- 3 questions on proteins/amino acids/oxygen binding proteins;

- 2 questions on Enzymes;

- 2 questions on Bioenergetics.

• 4 open questions, each awarding 1.5 points; maximum score: 6 points.

- 1 question of carbohydrates/lipids/proteins;

- 1 question on oxygen binding proteins;

- 1 question on Enzymes;

- 1 question on Bioenergetics.

Strumenti a supporto della didattica

All the lectures will be supported by PowerPoint presentations, downloadable from iol.unibo before the beginning of each lecture.

Samples of the written exam (with solutions) will also be uploaded on iol.unibo together with other files containing similar questions and/or exercises.

Orario di ricevimento

Consulta il sito web di Michele Di Foggia

Consulta il sito web di Muller Fabbri