FA/0260 - BIOCHEMISTRY AND BIOCHEMISTRY LABORATORY
Academic Year 2021/2022
Free text for the University
ANTONELLA FAIS (Tit.)
- Teaching style
- Lingua Insegnamento
|[60/76] BIOTECHNOLOGY||[76/20 - Ord. 2018] Farmaceutico||12||108|
The course of Biochemistry for the Class Biotechnology is aimed to the acquisition of fundamental information and concepts in structural and functional biochemistry. Therefore, it gives basic biochemical knowledge for a first-level degree in Biology, and moreover it is preparatory to further learning courses, implying the knowledge of such fundamentals.
The Laboratory Module consolidates the manual skills already acquired in previous courses and adds new ones, especially the ability to manipulate protein and enzyme solutions, and to carry out the most common analytical determinations on them.
Knowledge and Understanding:
Understanding the Life molecular logic and the primordial abiotic chemistry.
Knowing structures and properties of the main biological compounds such as proteins, glucides, and lipids. Being able to graphically represent their molecules.
Understanding the structural and functional features of those compounds and their localization in cells and tissues.
Knowing and understanding structure/function relationship of the proteins, and their modulation: the case of respiratory proteins.
Knowing the modes of production, storage, use of metabolic energy, and understanding the related thermodynamics.
Knowing the main metabolic pathways and their molecular tools: enzymes, coenzymes, cofactors, effectors, inhibitors.
Understanding metabolic homeostasis and the general integration of metabolic pathways.
Knowing the main laboratory techniques.
Understanding the theoretical and practical bases for the study of macromolecules.
Applying Knowledge and Understanding:
The students will be able to:
- take advantage from structure formulas getting the main reaction mechanisms applied to biochemistry for both catalysis and metabolic sequences;
- correctly put the various metabolic pathways within the frame of physiological and eventually pathological mechanisms to get conclusions about material and energy balances;
- apply the acquired knowledge to the study of Molecular Biology, Genetics, Physiology, Microbiology.
- apply the laboratory practices also to contexts other than biochemical ones;
- apply the theoretical-practical knowledge acquired for standard analysis of biological matrices.
Students will be able to:
- distinguish among main and secondary topics, finding the logics lying under the study of Biochemistry, and avoiding a memory-based study;
- autonomously find and explain retrohinibition, cycles, and futile cycles, anaplerotic reactions;
- individuate the basic concepts to apply them to other disciplines along the Biology course.
- be able to organize a laboratory experiment by choosing the most suitable technique for the type of analysis to be carried out;
- correctly interpret the laboratory analytical data obtained to draw correct and consistent conclusions.
The students will be able to discuss the topics of the course by using the language and vocabulary typical for Biochemistry. They will interact with the teacher arguing the main points of the study program with the required detail. Owing to the expert tutorage they will also positively interact with their colleagues, possibly forming study groups.
Student/teacher interaction, auto-evaluation tests, slides and booklets will give the students the required tools for profitable and aware learning.
The students must have a sound basic knowledge of both Inorganic and Organic Chemistry. In particular:
Atomic and molecular orbitals;
Molecules and ions, polarity and polarizability;
Chemical bonds: ionic, covalent, dative, coordinative, hydrogen;
Acids and bases following the various definitions, pH, pKa;
Chemical equilibrium, equilibrium constants, mass action law, Le Chatelier principle;
Oxidizers and reductants, electrochemical potential;
Speed of chemical reactions, order and molecularity of reactions, speed constants;
Basic organic chemistry, aliphatic and aromatic compounds, mesomerism, I and M effects; nucleophilic, electrophilic, and radical substitutions, and their mechanisms.
Main functional groups and their reactivity.
It is mandatory to have taken the exams considered preparatory.
The course divided in two learning units: 1) Structural Biochemistry, and 2) Functional Biochemistry.
Biochemistry (6 CFU; 48 hours):
-Aminoacids and peptides, fibrous proteins: 8 hours;
Aminoacids: definition and classification, main physicochemical features. Aminoacids as electrolytes. Essential aminoacids. Peptides. Protein classification and structural levels. The main fibrous proteins.
-Globular proteins: 4 hours;
Main physicochemical features. Globular proteins as amphoionic polyelectrolytes. Glycoproteins. Immunoglobulins. Stability and denaturation of globular proteins.
-Glucides: 4 hours;
Definition and classification, main physicochemical features. Anomerism, mutarotation, glycosides. Mono-, oligo-, and polysaccharides.
- Nucleotides and nucleic acids. The purinic and pyrimidinic bases. The nucleotides.
-Lipids: 4 hours;
Definition, classification, main physicochemical features. Simple and complex lipids, lycolipids, phospholipids, sphingolipids. Isoprenoids.
Functional Biochemistry (26 hours);
Porphyrins, metalloporphyrins, heme, hemoproteins and their main physicochemical features.
Myoglobin and hemoglobins, oxygenation and deoxygenation, cooperativity and its logical models. Other respiratory proteins: 6 hours;
-Enzyme kinetics: 4 hours;
Catalysis and biocatalysis, enzymes. Molecularity and reaction order of enzymatic reactions. Michaelis and Menten hypothesis and its developments. Enzyme activity inhibition and modulation.
-Enzymatic catalysis: 4 hours;
Physicochemical background of affinity and catalysis. Theory of the activated complex and enzymatic catalysis. Biocatalytic mechanisms.
-Vitamins and coenzymes: 2 hours;
Definition and classification. Hydrosoluble vitamins, coenzymes and cofactors.
-Metabolism and energy metabolism: 2 hours;
Definition and concepts: metabolism, anabolism, catabolism, biosynthesis, biodegradation. Aerobic and anaerobic metabolism. Metabolic paths and cycles, energy production, transportation, storage of metabolic energy: ATP and analogues.
Glucidic metabolism: 6 hours;
General concepts, glycolysis, lactic and alcoholic fermentations. Citrate and glyoxylate cycles.
-Lipid metabolism: 2 hours;
General concepts, beta-oxidation, particular cases, AcetylCoa fate, ketogenesis.
-Protein metabolism: 2 hours;
General concepts, transamination, deamination, ammonia fate, ornithine cycle.
-Respiratory chain: 2 hours;
General concepts, constituents, dioxygen reduction logics, consequences and purposes.
-Oxidative phosphorylation: 2 hours;
general concepts, ATP synthase and its mechanism, respiratory control, uncoupling agents.
Methods (60 hours):
Lecture syllabus (24 hours)
Purification of protein. Homogenate preparation. Fractional precipitation with ammonium sulfate, organic solvents and precipitation heat. Centrifugation. Dialysis. Ultrafiltration. 4 hours.
Chromatographic techniques: general principles. Ion-exchange, exclusion, adsorption and affinity chromatography. HPLC. 6 hours.
Spectrophotometry UV/VIS: principles, instruments and applications. Lambert-Beer law. Fluorescence analysis: principles, instruments and applications. 6 hours.
Electrophoretic Techniques: general principles. PAGE and SDS-PAGE. Methods of detection and quantitative assessments. Isoelectric focusing (IEF). Western blot. 8 hours.
Laboratory syllabus (36 hours)
Determination of protein concentration by using Bradford method. 5 hours
SDS-PAGE and determination of the molecular weight of a protein. 6 hours
Enzymatic activity on PAGE. 5 hours
Zymogram with SDS-PAGE. 5 hours
Enzymatic activities using spectrophotometric assays and calculation of kinetic parameters (Km e IC50). Chromogen substrates. 10 hours
Assay for the evaluation of antioxidant activity of a solution.
The lessons are carried out using slides made with Power Point, which also allow the use of animations to visualize the reaction mechanisms, and 3D molecular models.
Teaching will be delivered mainly face to face, integrated and "augmented" with online strategies, in order to guarantee its use in an innovative and inclusive way. Depending on the availability of the classrooms and the number of students who will opt for the attendance mode, there may be a shift for actual classroom access.
As regards laboratory activities, on the basis of the contextual conditions linked to the Covid-19 pandemic, online shifts and / or replacement activities may be envisaged.
The teacher will provide individual explanations during the office hours by appointment.
To assist the study, the teacher will provide the slides of the lessons in pdf or ppt format.
Verification of learning
Examinations are aimed to a correct and unbiased evaluation of the preparation degree reached by students, i.e. the achievements of the formative targets required in the course.
Individual colloquium, also requiring the use of graphics, equations, schemes, flux diagrams. From general to particular, the student will move among basic concepts to proceed in depth within the topic.
The final grade takes into account several factors:
Quality of the knowledge, skills, competences:
a) appropriateness, accuracy and consistency of knowledge
b) appropriateness, accuracy and consistency of abilities
c) appropriateness, accuracy and consistency of ability to apply knowledge and understanding
a) Ability of expression;
b) Proper use of the specific language of the discipline;
c) Logical skills and inherent consequentiality in communicating;
d) Manual and practical skills;
e) Ability to connect different subjects by finding the common points and establish a consistent overall design, i.e. taking care of structure, organization and logical connections of speech;
f) Ability to summarize also through the use of specific symbolism of each discipline and graphic expression of ideas and concepts, for example in form of formulas, schemes, equations.
Availability to exchange and interact with the teacher during the interview.
a) critical thinking;
b) ability of self-evaluation.
Consequently, the judgment can be:
a) Sufficient (from 18 to 20)
The candidate demonstrates little acquisition of theoretical knowledge, superficial level, many gaps. Modest communicative abilities, but still sufficient to support a coherent dialogue, logical capacity and consequentiality in fitting the subjects of elementary level; poor capacity of synthesis and rather stunted ability of graphical expression, scanty interaction with the teacher during the interview.
b) Moderate (21 to 23)
The applicant demonstrates a moderate acquisition of knowledge but lack of expatiation, a few gaps; communicative abilities more than sufficient to support a coherent dialogue; acceptable mastery of the scientific language, logical capacity and consequentiality in fitting the subjects of moderate complexity, good enough capacity of synthesis and acceptable ability of graphical expression.
c) Good (24 to 26)
The candidate demonstrates a rather large wealth of knowledge, moderate in-depth, with small gaps; satisfactory mastery of the communicative abilities and meaningful scientific language; dialogical ability and critical thinking well detectable, good capacity of synthesis and more than acceptable ability of graphical expression.
d) Outstanding (27 to 29)
The candidate demonstrates a very extensive wealth of notions, high in-depth, with marginal gaps; remarkable ability in communicating and high mastery of scientific language; remarkable dialogical capacity, good competence and relevant aptitude for logical synthesis, high capacity of synthesis and graphical expression.
e) Excellent (30)
The candidate demonstrates a wealth of very extensive and in-depth knowledge, irrelevant gaps, high capacity and high mastery in communicating through the scientific language; excellent dialogical ability and marked aptitude to make connections among different subjects, excellent ability to synthesize and very familiar with the graphical expression.
The praise is attributed to the candidates clearly above average, and whose notional, expressive, conceptual, logical limits, if any, as a whole are completely irrelevant.
Since the situation relating to the Covi-19 pandemic is constantly changing, it is specified that the methods indicated above can be replaced by different verification methods.
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- L. Pollegioni, Fondamenti di Biochimica, EdiSES
- Campbell, Farrell, McDougal, Biochimica, EdiSES
- Voet-Voet-Pratt; Fondamenti di Biochimica; Zanichelli
- Jeremy M. Berg, John L. Tymozcko, Gregory J. Gatto, Lubert Stryer, Biochimica; Zanichelli
- Garrett-Grisham; Principi di Biochimica; Piccin
- Mathews-Van Holden-Appling- Anthony Cahill; Biochimica; Piccin
Bonaccorsi di Patti et al., Metodologie Biochimiche, Zanichelli;
Stoppini, Bellotti. Biochimica Applicata. EdiSES
- Prof.ssa Antonella Fais: Department of Life and Environment Sciences, Biomedical Section, Cittadella Universitaria S.S 554 km 0.700 bivio per Sestu, 09042 Monserrato.
Student will be received every working day by appointment.
Link Teams “CdL STCQ-CdL BiotecFarm BIOCHIMICA-Ricevimento studenti”
- Dott.ssa Francesca Pintus, Department of Life and Environment Sciences, Biomedical Section, Cittadella Universitaria S.S 554 km 0.700 bivio per Sestu, 09042 Monserrato.
Student will be received every working day by appointment.