Biophysics/Introduction

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Welcome to the Biophysics Project and the Department of Biophysics!

Soliton Wave animation by Dr. Danko Georgiev


Département de Biophysique

"La biophysique est l'étude des phénomènes physiques intervenant chez les êtres vivants."

Faculté de Biologie

Département de Biologie Moléculaire

"La biologie moléculaire est une discipline scientifique au croisement de la génétique, de la biochimie et de la physique, dont l'objet est la compréhension des mécanismes de fonctionnement de la cellule au niveau moléculaire. La biochimie est la discipline scientifique qui étudie les réactions chimiques ayant lieu au sein des cellules."

Languages: (en),(fr), (ro)

"Biophysics is the study of physical phenomena that occur in living beings"... , but without a definition of Life, or of the "living", the subject of Biophysics would remain only vaguely pointing at functional organisms. Determining what Life is also remains, therefore, in the domain of Biophysics--specifically of Mathematical biophysics or Relational Biology. In other words, one is asking:
What are the fundamental relations among the components and processes, and also <relations> among relations occurring in an organism that distinguish the latter from a simple or complex physical system, such as a crystal, a stone, a machine or automaton, a robot, a computer, and so on ?
A related question is that of the underlying operational logics of an organism (which is not Boolean, and it is not perhaps even a quantum logic), and of its defining axioms.
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Welcome to an International Biophysics Course !

Syllabus

Up-to-date descriptions of the background, methods and techniques of protein crystallography, including the mathematical concepts and tools needed to understand X-ray and neutron diffraction, as well as 2D-FT NMR determination of molecular structure in solution. (See also a simple introduction to Proton (H-1) NMR (fr))

Protein crystallography is a multidisciplinary area of research that overlaps in part with several subfields of biochemistry, structural molecular biology, bioinformatics, biophysics, biochemistry and organic chemistry.
XRD Structure Determination Steps

Lecture 15:Examples of crystal lattices: fcc, bcc, diamond; Miller indices of crystal lattice planes.

A- and B- DNA X-ray Diffraction Patterns compared
Wikiversity Topic:Photosynthesis
The Lessons in the
Photosynthetic Mechanisms ORIENTATION


Overall Chemical Reactions for Plant Photosynthesis

Learning materials and introductory articles

Carbon Fixation and Photorespiration in Plants
  1. w:C4 carbon fixation: trace experiments with radioactive labels
  2. Quantum physics aspects of w:Photosynthesis
  3. Photosynthetic systems: w:PSI and w:PSII coupling
  4. w:aquaporin
  5. Specific w:chloride channels
  6. w:Hydronium ion
  7. Specific w:Hydronium ion
  8. Beta counting
    1. w:Regulation of metabolic pathways
  9. Specific inhibitors of photosynthesis, such as hydroxylamine (NH2OH) and uncouplers
    1. Gas chromatography and mass spectrometry
    2. Gamma counting
    3. w:Enzyme assays
    4. w:Micronutrients
      1. Manganese ions' role(s) in photosynthesis
        1. Neutron activation analysis of Mn contents in purified, active thylakoid (photosynthetic) membranes and PSII-particles
    5. w:Enzymes
    6. Krebs' cycle
    7. w:Pyruvate decarboxylation
    8. The ATP cycle and its coupling to photosynthetic processes
    9. w:Oxidative phosphorilation
    10. w:Calvin Cycle
    11. Dickens-Horecker cycle
    12. Hexose interconversions
    13. w:Neoglucogenesis
    14. w:Glycogenesis
    15. w:Glycogenolysis
    16. w:Cori cycle
    17. w:fatty acids
    18. Essential fatty acids
      1. poly-unsaturated fatty acids (w:PUFA);
      2. w:eicosanoids: w:prostaglandins, w:thromboxanes, w:prostacyclin and w:leukotrienes.
    19. The w:lipid bilayer, item, and transport across the bilayer through pores, channels, etc.
    20. w:PCR

Selected Examples

Solutions of the Bessel differential equation.
  1. Bessel functions arise in many mathematical models such as those for vibrating surfaces. Such functions also occur in the analysis of X-ray Diffraction patterns of helical molecules such as certain proteins and also nucleic acids (DNAs, RNAs.)

"When mathematically analyzing a vibrating drum the boundary conditions lead to solutions that are harmonic functions. When using cylindrical coordinates, the solutions are sines, cosines or Bessel functions (in the radial direction)".


Notes


"Protéine, macromolécule composée d'acides aminés reliés par des liaisons peptidiques, présente chez les organismes vivants et essentielle à leur fonctionnement. Découvertes en 1838, les protéines sont le principal composant des cellules, représentant plus de 50 p. 100 de leur poids sec. Le mot protéine vient du grec proteios qui signifie « premier ».

La forme des protéines est très variable : elle va des longues fibres présentes dans les tissus conjonctifs et les cheveux aux globules compacts et solubles capables de traverser la membrane des cellules. Les protéines sont des macromolécules dont le poids moléculaire varie de quelques milliers à plus d'un million d'unités. Elles sont spécifiques à chaque espèce vivante et à chaque organe. On estime qu'il existe environ trente mille protéines différentes chez l'Homme, dont 2 p. 100 seulement ont été décrites. Les protéines servent à construire et à entretenir les cellules, et leur dégradation chimique fournit de l'énergie, produisant près de 4 kilocalories par gramme (voir Métabolisme).

Outre leur rôle dans la croissance et l'entretien des cellules, les protéines sont également responsables de la contraction des muscles. Les enzymes digestives sont des protéines, de même que l'insuline et la plupart des autres hormones, ainsi que les anticorps du système immunitaire et l'hémoglobine. Les chromosomes, qui transmettent toutes les caractéristiques héréditaires sous forme de gènes, sont constitués d'acides nucléiques et de protéines (histones)."

Course textbooks

Things remaining to do-Short list

  1. Continue and expand lectures
  2. New Instructor involvement in biophysics courses
  3. Web links to biophysics and protein structure syllabi at several universities
  4. Add other resources (such as: Structure and Genomic Databases, Image libraries and galleries, Library links, and so on.
  5. Develop student Enrollment and student Help pages

See also

Leçons par thèmes = Lectures by subject

Leçons par niveau = Lectures by level

Instructors

If you have knowledge in this field, please post your name here to answer questions from students.

Short list of course consultants and instructors:

External links for the International Biophysics Course

    1. The International System of Units, item
    2. Nomenclature of organic chemistry,item,
    3. w:Logarithms
    4. w:Nuclides
    5. w:Radioactive decay
    6. w:gas laws, Gases and Gas Laws
    7. w:Partial pressure and w:mole fraction
    8. w:Osmosis
    9. w:Diffusion
    10. pH, pKa's and titration
    11. Buffers
    1. w:Nucleic acids
    2. w:Amino acids
    3. w:Protein
    4. w:Carbohydrate
    5. w:Lipid
    1. Simple (glass) laboratory equipment and how to use it
    2. Laboratory safety
    3. w:Size exclusion chromatography
    4. UV-VIS Spectrometry
    5. Centrifugation and w:Ultracentrifugation
    6. w:Electrophoresis
    7. w:Chromatography
      1. w:Decarboxylation
      2. w:Transamination
      3. General amino acid synthesis
      4. General amino acid catabolism
      5. Special amino acid metabolism
      6. Amino acid interconversion
      7. w:Urea cycle, item
      8. Gamma-glutamyl cycle
      9. Associated: w:Gout,w:Maple syrup disease
      1. In vivo nucleic acids synthesis
      2. Nucleic acid degradation, pyrimidine and purine catabolism
      3. w:Peptide bond
      4. In vivo protein synthesis

References

Virtual Labs

Virtual Molecular Biology and Biophysics laboratories
Ion Trap in a Mass Spectrometer

(Schéma d'un analyseur de type trappe ionique (pièges à ions) 3D et trajectoire des ions, en spectrométrie de mass).

NMR spectrometer
COSY 2D-NMR Spectrum
2D-FT (N)MRI Imager
Triple Quadropole Mass Spectrometer
Synchrotron SOLEIL facility near Paris
ISIS Pulsed neutron facility hall
SLAC Synchrotron entrance near Stanford, CA
SLAC Detector

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