2010-11 Academic Year
Biochemistry I (20329)
Qualification/course: Bachelor's Degree in Human Biology
Year: 1
Term: 2
Number of ECTS credits: 6 credits
Number of study hours: 150 hours
Course Language(s):
Teaching staff: Antonio García de Herreros
1. Presentation of the course
The subject coordinator is Antonio García de Herreros The lecturers Francesc Posas, Eulàlia de Nadal, Víctor Diaz (in charge of laboratory practicals), Josep Antoni Pascual, Rosa Ventura, Carme Solé, Montserrat Porta and Javier Jiménez, Urko Martínez and Elena Carnero will also be involved in the teaching of this subject.
2. Competences to be achieved
3. Content
THEORY CLASSES (30 sessions of 1 hour)
1. Presentation of the course
Biochemistry as an experimental science. Weak interactions in aqueous media. Characteristics of water.
2. Energetics of life
Chemical potential. Free energy change. Coupled reactions. Phosphate compounds as chemical energy reserves. Central role of ATP.
3. Amino acids and peptides
Nomenclature. Amino acids as dipolar ions: forms in solution. Chirality. Specific properties. Modifications of amino acids. Peptide linkage. Determination of the amino acid composition of a peptide. Working methods: ion-exchange chromatography. Peptide synthesis.
4. Structural levels of proteins
Methods for analysing proteins: absorption, fluorescence. Determination of molecular weight: electrophoresis, mass spectrometry. Determination of primary structure: Edman degradation, mass spectrometry. Proteases. Comparison of protein sequences. Secondary structure. Possible peptide conformations: Ramachandran plot. Alpha-helix, beta sheet Statistical coil. Structure of collagen and other fibrous proteins. Methods for studying the secondary structure: circular dichroism, X-ray diffraction. Supersecondary structures. Tertiary structure of globular proteins: structural and functional domains. Quaternary structure of oligomeric proteins. Multi-protein complexes. Analytical techniques: Immunoprecipitation, Western blot. Thermodynamic aspects of protein folding: leading interactions. Denaturing. Protein solubility. Kinetic aspects of protein folding: role of chaperones.
5. Oxygen transport proteins
Hemoglobin and myoglobin. Structure. The heme group. Oxygen binding mechanism. Myoglobin: saturation curve. Calculation of the saturation function for hemoglobin. Hill coefficient. Bohr effect. Role of 2,3-diphosphoglycerate. Allosteric regulation of oxygen binding to hemoglobin. Models of cooperativity.
6. Enzymes and enzyme kinetics
Enzymes as catalysts. Activation energy. Active site. Specificity. Enzyme-substrate interaction. Cofactors: Coenzymes, prosthetic groups, metal ions. Catalysis mechanisms: application in proteases. Reaction velocity. Michaelis-Menten equations. Meaning of Km and Vmax. Exchange constant. Representation methods. Kinetics of multi-substrate reactions. Enzyme inhibition. Competitive and non-competitive inhibition: graphical representation. Irreversible inhibition.
7. Regulation of enzyme activity
Study methods: use of isotopes in the determination of enzyme activities. Allosteric regulation of enzyme activity. Regulation of enzyme activity by covalent modification: phosphorylation, proteolysis (proenzymes). Formation and dissociation of complexes. Cellular compartmentalisation. Study methods: immunofluorescence.
8. Carbohydrates and polysaccharides
Monosaccharides: classification. Configurations and conformations. Derivatives. Disaccharides. Structural polysaccharides. Storage polysaccharides. Glucosaminoglycans.
9. Composition and structure of biological membranes
General properties of lipid compounds. Phospholipids. Saturated and unsaturated fatty acids. Triglycerides. Sphingolipids. Steroid compounds. Glucolipids. Properties of the lipid bilayer. Structure of the membrane: properties. Membrane proteins: integral proteins. Determination of topology: membrane markers. Glucoproteins. O-glycosylation and N-glycosylation. Carbohydrates incorporated into proteins. Techniques for working with membrane proteins.
10. Membrane transport
Permeability. Facilitated diffusion transport system. Transporters: analogy with enzymes. Channels. Ionophores. Active transport systems. Coupled transport.
11. Structure of nucleic acids
Nucleotides: composition. Puric and pyrimidine bases. Nucleosides and nucleotides. Nucleotide triphosphates. Oligonucleotides. Chemical properties. Synthesis of oligonucleotides. Structure of DNA. Watson and Crick model: B-DNA. Other helices: A-DNA and Z-DNA. Interactions that stabilise the double helix: base-stacking. Denaturing and renaturing. Supercoiling. DNA polymerases. Requirements. DNA amplification. DNA purification methods: electrophoresis. Analysis by Southern blot. RNA: types. Primary and secondary structure of messenger RNA. RNA polymerases. RNases. Analytical methods: Northern blot. Maturation of messenger RNA. Transfer RNA. Secondary structure. Processing. Modification of bases. Ribosomal RNA: processing. RNA as a catalyst.
ADDITIONAL CLASSES
Four different types of these classes will be given:
2 sessions (2 hours) of consolidation of chemical concepts (A1 and A2)
4 sessions (4 hours) of reinforcement of theoretical concepts (A4, A7, A9 and A12)
5 sessions (10 hours) of problem solving (A3, A5, A8, A10 and A13)
2 sessions (2 hours) of practicals in the computer room (A6 and A11)
PRACTICAL LABORATORY CLASSES
(6 sessions of 4 hours)
1. Electrometric pH measurement. Preparation of buffers. Titration. Concept and expression of dilution. Preparation of solutions diluted from mother solutions. Preparation of buffers of different pH. Measuring pH. Titrating a solution. Checking the buffering capacity.
2. Spectrophotometric quantification of proteins. Understanding the concept of absorption spectra as a basis for colorimetric methods of quantification. Comparison and evaluation of different protein quantification methods.
3. Enzyme kinetics. Quantification of the enzyme activity of phosphatase: determination of Km for p-nitrophenyl phosphate and Ki for inhibition by phosphate.
4-5. Purification of proteins: ion-exchange chromatography, affinity and molecular exclusion chromatography. Purification of enzymes via protein extraction using these techniques and analysis of specific activity.
6. Electrophoresis of proteins under denaturing conditions. Dyeing with specific colours. Making up denaturing polyacrylamide gels and resolving samples of these gels. Detection of proteins in the gel by dyeing with Coomassie blue.
4. Assessment
Before presenting him or herself for assessment, the student must have handed in the answers to the problems raised in class. These answers have a maximum value of 0.5 points towards the final mark. It is essential for the student to pass the practical classes of the course in order to pass the course as a whole. These practicals also have a weight of 0.5 points towards the final mark.
The final grade will depend on two exams:
a) A test comprising between 25 and 30 multiple choice questions (marks out of 5). A minimum mark of 1.4 is required to pass the course.
b) A written exam where four or five problems are solved, using information provided by the lecturer (marks out of 4). A minimum mark of 1.3 is required to pass the course.
5. Bibliography and teaching resources
5.1. Basic bibliography
Textbooks
MATHEWS, C. K.; VAN HOLDE, K. E.; AHERN, K.G Bioquímica. 3a. edició. McGraw-Hill/Interamericana, 2002.
BERG, J. M.; TYMOCZKO, J. L.; STRYER, L. Bioquímica. 6a. edició. Reverté, 2007.
Reference books
VOET. D.; VOET, J. G.; PRATT, C. W. Fundamentos de bioquímica. 2a. edició. Ed. Médica Panamericana, 2007.
McKEE, T.; McKEE, J. R. Bioquímica. 1a. edició. McGraw-Hill/Interamericana, 2003.
CAMPBELL, M. K.; FARRELL, S. O. Bioquímica. 4a. edició. Thomson, 2004.
GARRETT, R. H.; GRISHAM, C. M. Biochemistry. 2a. edició. Harcourt Brace, 1999.
6. Methodology
7. Programme of activities