84259 - General Biochemistry

Learning outcomes

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.

Course contents

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

• Aminoacids: classification, chemical structure and     acid-base properties.

• Peptides and proteins: general characteristics; the 4 structures of proteins; denaturation and folding.

• Oxygen binding proteins: myoglobin and hemoglobin.

• Carbohydrates: classification; biological role; glycoconjugates.

• Lipids: classification; biological role;

        Enzymes and enzymology

• Classification.

• Effects on reaction rate and thermodinamics.

• Enzyme kinetics and inhibition.

• Allosterism.

        Bioenergetics

• The second law of thermodinamics and free energy.

• Common biochemical reactions.

• Phosphoryl group and ATP.

• Biological redox reactions.

Readings/Bibliography

PowerPoint presentations integrated by personal notes can give a useful outline of hte 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.

General, Organic and Biochemistry, 9th edition

K. J. Denniston, J. J. Topping, D. R. Quirk Dorr, R. L. Caret

Mc Graw Hill Education

ISBN: 978-0-07-802154-1

 

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

Teaching methods

Traditional lecture-based teaching based on Power Point presentations.

Assessment methods

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:

WORK IN PROGRESS

A sample exam can be found on AMS Campus.

Teaching tools

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

A sample of the written exam (with solutions) will also be uploaded on AMS Campus, together with other files containing similar questions and/or exercises.

Office hours

See the website of Michele Di Foggia

See the website of Muller Fabbri