3213111    ชีวโมเลกุล    Biomolecules

หลักการของอุณหพลศาสตร์ในวิทยาศาสตร์ชีวภาพ โครงสร้างทางเคมี การจำแนกชนิดและหน้าที่ของชีวโมเลกุล เมแทบอลิซึมของชีวโมเลกุล ตัวอย่างของสารชีวโมเลกุลที่สำคัญ

(Principles of thermodynamics in life sciences; chemical structures; classifications and functions of biomolecules; metabolism of biomolecules: examples of important biomolecules.)

(3213111 จุฬาลงกรณ์มหาวิทยาลัย)

3304606    ชีวโมเลกุลกับการพัฒนายา    Biomolecules on Drug Development

ประโยชน์ของสารชีวโมเลกุลในการวิจัยและพัฒนายา สารชีวโมเลกุลที่ใช้ประโยชน์ทางการแพทย์ จำแนกตามโครงสร้าง ข้อมูลโครงสร้างและคุณสมบัติทางกายภาพของสารเหล่านี้ที่มีผลต่อความคงตัวและกระบวนการแยกสารให้บริสุทธิ์ ฤทธิ์ทางชีวภาพหรือการใช้เป็นตัวนำส่งยา/ เป็นเป้าหมายของการใช้ยา ปฏิกิริยาโมเลกุลในการรักษาบำบัดอาการของโรคให้ดีขึ้น ปัญหาที่เกี่ยวข้องกับการพัฒนายา รวมทั้งการผลิต การทำให้บริสุทธิ์ การวิเคราะห์ การนำส่งและการพัฒนารูปแบบยา

(The application of biomolecules in drug discovery and drug development research and drug development research; biomedical compounds classification according to structues, information on structure and physical properties relevent to stability, purification of biomolecules, theeir biological function/effects, or their uses in drug delivery/drug targetting, molecular interactions or approaches which these biomolecules being used to improve pathological conditions in diseases; problems related to the drug development including production, purification, assay, drug delivery and formulation.)

(3304606 จุฬาลงกรณ์มหาวิทยาลัย)

3341751    เคมีของเภสัชชีวโมเลกุล    Chemistry of Pharmaceutical Biomolecules

เคมีและการประยุกต์ใช้ทางเภสัชเคมีของคาร์โบไฮเดรต โปรตีน ไขมัน กรดนิวคลีอิก วิตามิน และสารปฏิชีวนะ

(Chemistry and pharmaceutical applications of carbohydrates, proteins, lipids, nucleic acids, vitamins and antibiotics.)

(3341751 จุฬาลงกรณ์มหาวิทยาลัย)

3341752    ปัญหาพิเศษทางเภสัชเคมีและผลิตภัณฑ์ธรรมชาติ    Special Problems in Pharmaceutical Biomolecules

ปัญหาเฉพาะเรื่องที่น่าสนใจทางเภสัชเคมีและผลิตภัณฑ์ธรรมชาติ

(Special problem of intcrestin the field of pharmaceutical chemistry and natural product.)

(3341752 จุฬาลงกรณ์มหาวิทยาลัย)

Found a great metabolic pathways chart (created by Roche Applied Science) that has been around a while, online today!It really illustrates wonderfully the complexity that many life science fields have to get to grips with and indeed add to!I definatly experienced again a sense of awe at what we know and  it made me proud to be scientist!(not that i wasn’t proud before!)The online chart is useful too as you can click in to various parts of the image to see specific sections in detail and save your poor eyes from having to squint.

Metabolic Pathways Chart available at http://www.expasy.ch/cgi-bin/show_thumbnails.pl

The Expasy Proteomics Server is incidentally an extremely useful bioinformatics resource for the study of proteins.It has tools such as ProtParam for computing physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, isoelectric point, extinction coefficient, etc.),PeptideCutter to predict potential protease and cleavage sites and sites cleaved by chemicals in a given protein sequence and also tools for pattern and profile searches,post translational modification prediction and primary to quaternary protein structure analysis/prediction.

Yes, yes, yes — the scientific and practical applications are awesome, but I’m still not past the incredible images:

From the link:

Now Matthias Germann and buddies at the University of Zurich have a different approach. Instead of high energy electrons, they’ve created holograms of DNA strands using a coherent beam of low energy electrons (although why this approach hasn’t proved fruitful in the past isn’t clear).

Their results show that at certain energies, DNA strands are remarkably robust to low energy electrons. “DNA withstands irradiation by coherent low energy electrons and remains unperturbed even after a total dose of at least 5 orders of magnitude larger than the permissible dose in X-ray or high energy electron imaging,” say the team.

Yep, that’s five orders of magnitude more.

What this suggests is that if you choose electron beams of just right energy–Germann and co say 60eV does the trick–then it becomes possible to take decent snapshots of DNA molecules without destroying them.

Kelvin Probe Force Microscopy schematic

Surface charges play a key role in determining the structure and function of proteins, DNA and larger biomolecular structures. For example, negatively charged DNA strands electrostatically interact with histone proteins, transcription factors, or polymerases thereby influencing the read-out of genetic information and the development of cancer. Similarly, the central process of protein folding and protein interaction, often governed by charges, is the major factor in protein-folding diseases such as Alzheimer’s or Parkinson’s Disease. However, thus far there have been no experimental methods to spatially resolve the electrostatic surface potential of individual biological molecules. In general, the investigation of individual molecules can shed light on their dynamic behaviour or on static heterogeneity which is masked in ensemble measurements.

A collaborative effort between researchers from the London Centre for Nanotechnology (Bart W Hoogenboom), King’s College London (Carl Leung, Patrick Mesquida) and UCL Chemistry (Stefan Howorka, Helen Kinns) has led to the first measurements of the electrostatic surface potential of individual DNA and avidin molecules with nanometre resolution using Kelvin Probe Force Microscopy (KPFM) in air.

Kelvin Probe Force Microscopy (KPFM) can measure surface charges by contactless recording of the electrostatic force between a conductive Atomic Force Microscope tip and a biomolecule on a support. To achieve this, the AFM tip is simultaneously excited at its mechanical resonance frequency and by an electrical (AC) voltage. This periodic electrical voltage on the tip leads to a force between the tip and the charges on the biomolecule, which is recorded by means of a lock-in amplifier and nullified by the Kelvin mode feedback by applying a separate DC voltage (not shown). The polarity and magnitude of this DC voltage corresponds to the local surface charge profile (in mV) which is recorded simultaneously with the topography of the biomolecule.

The investigation led at the London Centre for Nanotechnology also show, for the first time, the surface potential of buffer salts shielding DNA molecules on a surface, which would not be possible with conventional ensemble techniques. It is anticipated that the ability to visualize the electrostatic surface potentials of individual proteins and DNA at molecular resolution will be an important tool in fundamental biophysical research and in the fields of biosensing and bio-nanoelectronics.

Original Publication:

Leung C, Kinns H, Hoogenboom BW, Howorka S, Mesquida P. (2009): Imaging surface charges of individual biomolecules.  Nano Lett. 2009 Jul;9(7):2769-73.

 http://www.london-nano.com

Here’s the class presentation – click the shadowed images for animations.

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For more information on condensation and hydrolysis reactions:

Simple explanation by Terry Brown

Collection of examples from North Harris College

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Carbohydrates:

Explanation and animation from National Louis University

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Proteins:

Life Cycle of a Protein from Sumanas

Making polypeptides from John Kyrk

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Lipids:
Structures of Fats from HHMI

Lipids (and condensation animation) from National Louis University

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Grâce à une certaine Valérie P., le premier semestre de L1 de sciences du vivant est soumis au contrôle continu, exclusivement au contrôle continu, à raison d’un contrôle par semaine.

Derrière nous, il y a 7 contrôles. Devant nous, il y a l’examen de l’UE “des biomolécules à l’organisme”. Cette UE est ma préférée. Elle parle de bio cell, bio moléculaire, physio. Mais…

Mais un contrôle par semaine, ça commence à faire lourd.

Je ne sais pas où trouver la motivation de bouger. Le temps est froid, liquide sur les bords, par-dessus la ville ; et le temps manque, quant à lui. Dans mon sac, il y a Moon Palace de Paul Auster, pour les cours de lettres. Il y a “Les métamorphose du valet”, en littérature comparée. Mais il y a les contrôles, contrôles, contrôles, sans cesse. Pas le temps de lire. Plus précisément, pas la volonté. Alors, on se dit qu’en décembre, oui, en décembre, on en lira, des trucs, et on en fera, du latin, de la grammaire, jusqu’au dégoût total.

Alors on va faire comme d’habitude, on va forcer au dernier moment, avaler des pages de cours, faire des schémas bilans, regretter de ne pas s’y être mis plus tôt. Et obtenir une note moyenne, valider, et se dire qu’on fera fichtrement mieux au deuxième semestre.

Et pourtant, cette UE, c’est mon UE préferée.

Some time ago I posted breaking news about solved structure of usher pore. And few days ago it was deposited into PDB as 2VQI (publication appeared in Cell, here’s the abstract). The structure is a beatiful dimer (see above) of 24 stranded beta-barrel, the first of its kind. The paper contains also structures of the whole complex reconstructed based on cryo-EM data.

Interestingly, while the structure of the native dimer is symmetrical, the function of the units is not. Both of twinned pores are involved in alternating recruitment of chaperone:pili-subunit complexes, but only one actually transports pili subunits out. Overall, given large amount of detailed studies on the mechanistic properties of pili transport and formation, this is the best understood translocation process at a structural level.

Read the paper and draw your own conclusions, but for me it changes the way of thinking about protein translocation in bacteria. We learnt a lot on bacterial secretion by observing how similar proteins are involved in fundamentally different processes (for example DNA export and toxin secretion may use the same system). Similarly, usher pore is going to serve as an exemplar for newly found translocation elements.