84259 - General Biochemistry

Course Unit Page

Academic Year 2022/2023

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

  • Carbohydrates: Monosaccharides. Cyclic structures. Constitutional, configurational and conformational isomers. The glycosidic bond. Disaccharides and polysaccharides. Glycosaminoglycans. (Lehningher chapter 7- slides)
  • Lipids: Saturated, unsaturated and essential fatty acids. Triglycerides. Glycerophospholipids, sphingolipids, glycolipids. Cholesterol. Waxes. (Lehningher chapter 10- slides)
  • Aminoacids and proteins: classification, chemical structure and acid-base properties. Peptides and proteins: Structure, classification and properties of protein amino acids. Essential amino acids. The peptide bond. Primary, secondary, tertiary and quaternary structure of proteins. Denaturation and folding. Globular and fibrous proteins. Glycoproteins. Proteoglycans. (Lehningher chapters 3 and 4 - slides)
  • Oxygen binding proteins: myoglobin and hemoglobin (Lehningher chapter 5 - slides)
  • Enzymes and enzymology : Classification. Effects on reaction rate and thermodinamics. Enzyme kinetics and inhibition. Allosterism. (Lehningher chapter 6 - slides)

GENERAL BIOCHEMISTRY- MODULE 2

COURSE CONTENT

Nucleotides and Nucleic Acids (Lehningher chapter 8 - slides):

  • 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 (Lehningher chapter 24 - slides):

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

    DNA metabolism (Lehningher chapter 25 - slides):

  • 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 (Lehningher chapter 26 - slides):

  • RNA polymerases.
  • DNA-dependent synthesis of RNA (transcription).
  • Transcription in prokaryotes and in eukaryotes.
  • Promoters 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 (Lehningher chapter 27 - slides):

  • 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.

Readings/Bibliography

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, Ed. David L. Nelson & Michael M. Cox, 8th Edition, 2021

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

This 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] ).

Teaching methods

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.

Assessment methods

The exam will focus on the topics covered in class. The assessment of the course contents is based on a final examination consisting of a single written exam, having a maximum duration of 1:15 hours (online) and 1:25 hours (in classroom).

During the examination, only the use of ordinary stationery (i.e., pencils, pens, erasers, rulers, etc.) and of a scientific calculator is allowed. During the examination, students are not allowed to leave the classroom, unless they agree to relinquish all of their exam paperwork and not to re-enter the classroom anymore. During the examination, the presence of any electronic devices is strictly forbidden, with the exception of a simple watch and the aforementioned calculator.

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

The overall exam score is 33.00 points, equally divided into 11.00 points for “Chemistry”, 11.00 points for “Biochemistry-Module 1”, and 11.00 points for “Biochemistry-Module 2”. Each single written examination will include both the “Chemistry” and the “Biochemistry” parts and cannot be split, unless differently indicated by the Professors.

The examination will be structured according to the following general guidelines :

For « Chemistry »: 8 true/false questions ; 8 Multiple choice, 3 possible answers (0.25 point for each correct answer); 2 exercises (1.5 point for each correct exercise).

For each « Biochemistry » module: 8 true/false questions; 10 Multiple choice; 1 open question.

The exam is passed by achieving at least 6.00 points (out of 11.00) in each one of the three modules (Chemistry, Biochemistry-Module 1, and Biochemistry-Module 2). The grade obtained (necessarily greater than or equal to 18) is calculated by summing the points obtained in each of the above mentioned parts, and rounding it to the nearest integer.

Examples:

  • Chemistry: 5 pts

Biochemistry-Module 1: 8.50 pts

Biochemistry-Module 2: 8.50 pts
---> FAILED

  • Chemistry: 11 pts

Biochemistry-Module 1: 6.75 pts

Biochemistry-Module 2: 6.75 pts
---> 24.5 pts ---> PASSED WITH 25/30.

If a student obtains an overall score of 31 points or more, the examining commission will take into consideration whether to confer 30 cum laude (30L) or not. Only a unanimous consensus by the examining commission will result in the final grade of 30 cum laude (30L) and this decision will be not subject to any further discussion.

The exam final grades will be published online on Virtuale. If the exam is passed, the associated grade will be officially registered only after the student's confirmation using the student institutional email (e.g., name.surname@studio.unibo.it [mailto:name.surname@studio.unibo.it].

The registration of a successful examination is allowed no later than 6 months from the date of the examination; after this deadline, the not confirmed grade will expire.

If a student decides to re-take the exam, the outcome of the previous examination will be automatically cancelled, regardless of the previous grade. The exam can be repeated at any available exam session.

Grade Summary and Meanings

Insufficient: Lack of Preparation. Serious and repeated conceptual errors. The student did not provide sufficient evidence of having learnt the most basic concepts of the subject.

18-19: Knowledge of the basic concepts as a whole acceptable, without serious gaps in the preparation and sufficient exposition of concepts.

20-24: Knowledge of the basic concepts without gaps. Ability to analyze and describe chemical and biochemical concepts, reactions and problems with discreet use of proper terminology and scientific rigor.

25-29: Good to Very Good preparation, in some cases even Excellent preparation but with some inaccuracies that prevent full marks. Ability to analyze and describe chemical and biochemical concepts, reactions and problems with good to very good use of proper terminology and scientific rigor.

30-30L: Excellent to Outstanding preparation, consolidated and without inaccuracies on the topics covered in the course. Ability to promptly frame the topic. Ability to analyze and describe chemical and biochemical concepts, reactions and problems with excellent use of proper terminology and scientific rigor. Proven ability to use independent thinking to solve chemical and biochemical problems.

Teaching tools

All the lectures will be supported by PowerPoint presentations, downloadable from virtuale.unibo. Kahoot! App and Jove App will be used for a learning auto-evaluation in the end of each topic.

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

Office hours

See the website of Cristiana Caliceti

See the website of Muller Fabbri