Wordless Time in The World: Julai 2010

Sabtu, 31 Julai 2010

Sakit Gigi

Muka tembok.
Tiba-tiba aku jadi anak ganung.
ke Anak Ganung Mega Gathering.

Pantai Balok.
Pasir dia sangat unik.
Tak boleh nak fikir camne bleh jadi gitu.

Ada playground.
Ada orang kempunan nak main buaian.

Khamis, 29 Julai 2010

Hari Ini & Semalam

Wah.wah.wah. Tajuk bukan main aku ni...

Hari Jumaat?
Jogging 1k to 2 k steps.
Wahai para doktor, okey tak tu?

Physical Science Building, KOS.

Satu je kafe kat KOS!
Cafe at Physical Science Building.

Tak ada kelas
Pergi library la.
Kami yang rajin! Hahaha...

Creating Graphical Objects

Introduction about ACD/ChemSketch

ACD/ChemSketch is a software that make the works of drawing structures of chemical structures of atoms and compounds easier. It consist a lot of useful buttons.

As a basic, we learn to draw chemical bonds (single, double and triple) and atoms using the buttons in the Structure toolbar and general toolbar. For instance, we are being familiarize with Draw Normal tool, Set Bond Vertically button, Undo and Redo buttons, Polymers button and others buttons’ functions. Apart from that, we learn about the cleaning process and also how to flip and make the structures more organized using Clean Structure buttons.

From the basic, we continue to learn how to draw more complex structures using ACD/Chemsketch. We use Table of Radicals to choose the respective structure such as octahydro-1H-indene structure. Furthermore, Markush Bond tools is used to make the selected atom, for example Br, to appear connected to any of the carbon atoms in cyclic structures. ACD/ChemSketch also allows us to generate stereo descriptors for chiral and pseudo chiral centers, and for a double-bond configuration.In addition, using this ACD/ChemSketch, we also can draw the set up of apparatus as required for experiments.

In conclusion, ACD/ChemSketch is a useful software program for students, lecturers, chemists, scientists and everyone who related to chemistry and biology studies for reports and presentations.

Creating Graphical Objects

Energy of Reaction Diagram

p-orbital, d-orbital & pi orbital.

Vacuum Distillation Apparatus

Two chain DNA strand

Lipids & Micelle

Drawing Simple Structures

Bonds, Polymers & Pseudo Atoms

1,3-difluoro-1-(3-phenylpropyl)-5-(8,8,8-trifluorooctyl)cyclononane

Drawing more complex structures

Cation, Anion& Free Radical

Radical Cation, radical anion & triplet radical.

Markush Bond

Markush Bond with Added or Removed Fragment

(2Z)-4-chloropent-2-ene, (2E)-4-chloropent-2-ene & 1,4-dimethylcyclohexane with Stereo Descriptors

{1-(methoxy-κO)-2-[2-(methoxy-κO)ethoxy-κO]ethane}(phenyl)lithium

Delocalized Charges and Curves

2-methyl-1-[2-(phenyldiazenyl)phenyl]butan-2-ol, spatial arrangement of atoms, delocalization of double bonds, tautomeric or aromatic structure & organometallic complex

Isnin, 26 Julai 2010

3-D Macromolecule

[Side 1]

Primary Citation
Crystal structure of LexA: a conformational switch for regulation of self-cleavage.

Authors: Luo Y, Pfuetzner RA, Mosimann S, Paetzel M, Frey EA, Cherney M, Kim B, Little JW, Strynadka NC.

Journal: (2001) Cell(Cambridge,Mass.) 106: 585-594

PubMed: 11551506

PubMed Abstract: LexA repressor undergoes a self-cleavage reaction. In vivo, this reaction requires an activated form of RecA, but it occurs spontaneously in vitro at high pH. Accordingly, LexA must both allow self-cleavage and yet prevent this reaction in the absence of a stimulus. We have solved the crystal structures of several mutant forms of LexA. Strikingly, two distinct conformations are observed, one compatible with cleavage, and the other in which the cleavage site is approximately 20 A from the catalytic center. Our analysis provides insight into the structural and energetic features that modulate the interconversion between these two forms and hence the rate of the self-cleavage reaction. We suggest RecA activates the self-cleavage of LexA and related proteins through selective stabilization of the cleavable conformation.

Related Structures:
Primary Citation of: 1JHC 1JHE 1JHF 1JHH Also Cited By: 1Z0L

Organizational Affiliation:
Department of Biochemistry and Molecular Biology, University of British Columbia, 2146 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3, Canada.

[Side 2]

Molecular Description

Classification : Hydrolase
Structure Weight : 29848.40
Molecule : LEXA REPRESSOR
Polymer : 1
Type : Polypeptide (L)
Length : 135 residues
Chains : A, B
EC Number : 3.4.21.88

Fragment : C-Terminus, Residues 68-202
Mutation : L89P, Q92W, E152A, K156A

Source

Polymer : 1
Scientific name : Escherichia coli
Expression System : Escherichia coli

[Side 3]

Experimental Details

Method: X-RAY DIFFRACTION

Experimental Data:

[ EDS

]

Resolution[Å]:	2.50
R-Value:	0.220 (work)
R-Free:	0.284
Space Group:	C 2

Unit Cell:
	Length [Å]	Angles [°]
	a = 124.70	α = 90.00
	b = 43.70	β = 109.50
	c = 49.50	γ = 90.00

-------------------------------------------------

Related PDB Enteries

Id	Details
1JHC	LEXA S119A C-terminal tryptic fragment
1JHF	LEXA G85D MUTANT
1JHH	LEXA S119A MUTANT

Derived Data

SCOP Classification v1.75 - (2 Domains)
CATH Classification v3.3.0 - (2 Domains)
PFAM Classification - (2 Domains)
GO Terms - (10 Terms)

Source : RCSB PDB
3-D molecules can be viewed using RasWin software.

Ahad, 25 Julai 2010

hari yg penat

Hari Ahad?
Berjogging ke KOP

Taken at level 2, KOP
Administration Building & Kuliyyah of Medicine (KOM)

Taken at level 5, KOP
Girls' Mahallahs' Area

Akhirnya, berjogging ke Pintu Gerbang IIUM Kuantan,
sebelum menuju ke Stadium Tertutup, Majlis Sukan Pahang kat depan.

...What a great and tiring day, Sunday is...