Download Course Guide

Course Guide
33132 Macromolecular Structure and Enzymology
COURSE DATA
Data Subject
Código
Name
Cycle
ECTS Credits
Curso académico
33132
Macromolecular Structure and Enzymology
Grade
7.5
2015 - 2016
Study (s)
Degree
Center
1109 - Grado de Bioquímica y Ciencias
Biomédicas (2015)
FACULTY OF BIOLOGICAL
SCIENCES
Subject-matter
Degree
1109 - Grado de Bioquímica y Ciencias
Biomédicas (2015)
Subject-matter
8 - Bioquímica
Acad. Period
year
2
Character
Obligatory
SUMMARY
"Structure of macromolecules and enzymology" is a compulsory course taught in the first quarter of the
second year of the degree in Biochemistry and Biomedical Sciences with 7.5 ECTS credits. After
completing this course is intended that students learn the biochemical principles of the structure of
biological macromolecules and understand the main forces that stabilize them and allow specific
interactions with other molecules. Also, students must understand the mechanisms of enzymatic
reactions, kinetics and regulation.
PREVIOUS KNOWLEDGE
Relationship to other subjects of the same degree
There are no specified enrollment restrictions with other subjects of the curriculum.
Other requirements
OUTCOMES
33132 Macromolecular Structure and Enzymology
1
Course Guide
33132 Macromolecular Structure and Enzymology
1101 - Grado de Bioquímica y Ciencias Biomédicas
- Conocer los principios de la estructura de las macromoléculas biológicas DNA, RNA y Proteínas, y
de las fuerzas que las estabilizan.
- Relacionar la estructura de las macromoléculas con su función.
- Conocer las interacciones que se establecen entre diferentes tipos de macromoléculas biológicas.
- Conocer los mecanismos de las reacciones enzimáticas. Cinética enzimática.
- Conocer los principios de activación e inhibición enzimática: efectos alostéricos y cooperativos.
- Conocimiento y aplicación de los métodos experimentales y tecnología de enzimas. Análisis
enzimático.
- Aplicación de los conocimientos sobre estructura tridimensional de proteínas al estudio de la función
de máquinas moleculares transductoras de energía.
LEARNING OUTCOMES
To understand the chemical and physical principles that determine the conformation of macromolecules.
Knowing the molecular interactions that determine the properties and dynamics of macromolecules to
form complexes with each other or with small ligands.
Knowing the current models on the mechanisms of folding.
To learn the main methodologies used for structural analysis of biological macromolecules.
To understand databases and applications needed for the structural analysis of macromolecules.
To understand the concept of enzyme and to know its general characteristics.
Understanding the mechanisms of action for some model enzymes.
Understanding the kinetic aspects and the mechanisms underlying its activity.
Understanding the mechanisms of enzymatic regulation, mainly through reversible binding of ligands and
the concepts of cooperativity and allosterism.
Knowing the standard procedures used by scientists in the field of molecular biosciences to generate,
transmit and disseminate scientific information
Understanding the experimental approaches and their limitations and interpret scientific results.
DESCRIPTION OF CONTENTS
1. Introduction
Structural Biology: connections to other disciplines. Chemical composition of life. Biological polymers and
macromolecular complexes. Weak interactions in aqueous media. Methods in Structural Biology
2. Protein Structure (I)
Structure and classification of amino acids: hydrophobicity scales. The peptide bond. Structural levels of
proteins. Determining the primary structure of proteins: peptide sequencing. Properties of the peptide
bond. Conformational constraints of the peptides. Ramachandran plot. Secondary structure: α
helix, β sheet and turns. Determination of secondary structure. Secondary structure prediction.
33132 Macromolecular Structure and Enzymology
2
Course Guide
33132 Macromolecular Structure and Enzymology
3. Protein Structure (II)
Tertiary and quaternary structure of proteins. Structural classification of proteins. Fibrous proteins: alphakeratin, collagen and fibroin. Globular proteins. Supersecundary structures: motifs. Structural domains.
Protein-proein interactions and cuaternary structure. Proteins α and β proteins. Structure
determination by X-ray diffraction, nuclear magnetic resonance and electron microscopy. Tertiary
structure prediction.
4. Protein Stability
Main interactions protein stability. Concept of folding in vitro: hydrophobic effect. Native and denatured
state. Thermodynamic stability of proteins. Protein folding. Transition states and intermediates (molten
globule). Protein folding in the cell: molecular chaperones. Pathologies related to protein misfolding:
Alzheimer's, Parkinson's and spongiform encephalopathies.
5. Macromolecular complexes
Cylindrical assemblies: the proteasome and others. Nuclear pore complex. Protein filaments.
Ribonucleoprtein complexes: the ribosome, the spliceosome and others. (1 hour)
6. Polysaccharides
Monosaccharides and glycosidic bond. Structure of polysaccharides that function as store fuels: starch
and glycogen. Polysaccharides with structural role: cellulose, chitin, glycosaminoglycans and
peptidoglycans. Glycoconjugates. Molecular recognition and cell communication: the code of sugars and
the role of lectins.
7. Biological membranes
Amphipathic properties of the lipids. Lipid organization in aqueous solution: micelles, vesicles and
bilayers. Composition of biological membranes. Membrane proteins: biosynthesis and folding. Structural
examples: proton pumps, transporters and channels.
8. DNA Composition & Structure
Nucleosides and nucleotides. Properties. Phosphodiester linkages. Determination of DNA secondary
structure. Watson and Crick model of double helix. Detailed conformation of DNA and the sequence
dependence. DNA structural variability. Other types of double helix: DNA B, DNA A DNA Z, H DNA, DNA
G. Deformability and curvature. Triple helices: types. Denaturation and renaturation of the DNA. (5.5
hours)
9. High-order DNA Structure in genomes
DNA in prokaryotes: supercoiling. Organization of the bacterial chromosome. Packaging of DNA in
eukaryotic cells: chromatin. Histones. Nucleosomal structure of chromatin. Posttranslational
modifications of histones. Higher levels of organization. (5 hours)
33132 Macromolecular Structure and Enzymology
3
Course Guide
33132 Macromolecular Structure and Enzymology
10. RNA Structure
RNA types. Secondary and tertiary structure of RNAs. Secondary structure prediction. Riboswitches.
Ribozymes.(1.5 hours)
11. Nucleic acids-protein interactions
Examples. Protein-nucleic acid interactions. Binding to the major groove and minor groove. Examples.
Methods of study. (2 hours).
13. Basic concepts
Protein-ligand interactions: recognition and affinity. Association and dissociation constants. Cooperativity
in ligand binding. Types of enzymes. The enzyme-substrate complex: the active site. Cofactors in
enzyme activity. Classification and nomenclature of enzymes. Catalytic RNAs.
14. Enzyme kinetics
Enzyme-substrate interaction. Energy and entropic effects. Energy profile of an enzymatic reaction:
transition state and reaction intermediates. Effects of orientation and proximity. Mechanisms of
enzymatic catalysis. Examples.
15. Enzyme kinetics: monosubstrate reactions
The Michaelis-Menten equation. Meaning of the kinetic parameters: KM, Vmax and Kcat: efficiency and
specificity. Determination of kinetic parameters. Effect of pH and temperature on reaction rate.
Experimental methods for measuring enzyme activity.
16. Enzyme inhibition
Types of inhibition. Reversible inhibition. Graphic representations. Significance of inhibition constants.
Inhibition by competing substrates. Irreversible inhibitors. Applications of enzyme inhibition.
17. Enzyme kinetics: two or more substrates
Bisubstrate reactions. Mechanisms ordered and random sequential and ping-pong mechanism. Rate
equations.
18. Enzyme regulation
Regulation of enzyme activity. Regulating the amount of enzyme. Isoenzymes. Covalent modification of
enzymes: zymogens and enzymes interconvertible. Enzymatic cascades. Regulation by reversible
binding of ligands: allosterism. Quantitative treatment of cooperativity: the Hill equation. Models of
cooperativity and allosterism.
33132 Macromolecular Structure and Enzymology
4
Guía Docente
42681 Salud y Salud Pública
19. Macromolecular structure: bioinformatic tools
Locally installed programs for analysis and modeling of structures.
Introduction to the use of Swiss-Pdb Viwer and Swiss-Model
Visit the main structural databases.
Sequence Databases.
Databases of 3D structures
Libraries of structural motifs
Libraries of structural families
Libraries of ligands
Tools Available on Web servers.
Sequence alignment
Secondary structure prediction
Prediction of transmembrane segments
Modeling by homology
20. Enzymology: practical lectures
We will be use the computer program Grafit (RJ Leatherbarrow from Erithacus Software Ltd.) which
allows theoretical simulations of chemical and enzyme kinetics, adjustment of experimental data and
kinetic resolution of problems by iterative multiple kinetic equations included in the program. This
program includes several examples of protein-ligand interaction with one or more independent and
equivalent sites, adjustments to the equation of Adair, etc. It also allows adjustment of theoretical kinetic
data and allosteric enzymes, representations of Eadie-Hofstee or Lineweaver-Burk plots for the study of
inhibition or the determination of the contribution of the ionization state, or covalent modification of active
site residues in the enzyme activity.
WORKLOAD
ACTIVITY
Clases de teoría
TOTAL
Hours
24,00
24,00
% To be attended
100
TEACHING METHODOLOGY
EVALUATION
REFERENCES
42681 Salud y Salud Pública
5