Monday, May 30, 2011

IB Biology, IB Chemistry, Uncertainty, Standard deviation and Error Analysis

IB Chemistry,Uncertainty, Error Analysis, Standard Deviation
Uncertainty Calculation for Rate and Concentration of reaction.
Rate = 1/time, Time for X to disappear. ( Iodine Clock Reaction)
3 Methods for Uncertainty Calculation for Rate (0.10M) KI.
Average time is (5.28 + 4.75 + 4.47) / 3 =  4.83


1) % Uncertainty Method
  • Uncertainty time = Uncertainty stop watch + reaction time, ( 0.01 + 0.09 ) = ( 0.10 )
  • Time  = 4.83 ±( 0.10 )
2) Max-min range Method
  • Uncertainty time = (Max time - Min time)/2, = ( 5.28 - 4.47 )/2 = 0.41
  • Time = 4.83 ±0.41




1) %Uncertainty Method
Uncertainty time = (4.83 ± 0.10)
Rate = 1/ time, 1/ 4.83 = 0.207


2) Max-min range Method
Uncertainty time = ( 4.83 ± 0.41)
Rate = 1/time, 1/ 4.83 = 0.207




1) % Uncertainty Method


%Uncertainty time = (0.1/4.83) x100 %=2.07
%Uncertainty Rate = %Uncertainty time
%Uncertainty Rate = 2.07%
Rate = 0.207 ± 2.07 %
Rate = 0.207 ± 0.004




2) Max-min range Method
% Uncertainty time = (0.41/ 4.83) x 100% = 8.48%
% Uncertainty Rate = % Uncertainty time
%Uncertainty Rate = 8.48%
Rate = 0.207 ± 8.48%
Rate = 0.207 ± 0.017
3) Max /Min Rate Method


Max Rate = 1/ Minimum time, 1/ 4.47 = 0.220
Min Rate = 1/ Maximum time, 1/ 5.28 = 0.190
Ave rate = 1/ Ave time, 1/ 4.83 = 0.207
Uncertainty Rate = 0.207 ± ( 0.220 --- 0.190 )



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Uncertainty Cal for Conc, 30ml 0.1M KI (2 Methods used)
1) % Uncertainty Method
Pipette uncertainty  =  ± 0.4 and Total Volume used = 30ml


1) % Uncertainty Method
%Uncertainty Conc = %Uncertainty Vol of KI + %Uncertainty Vol Water
%Uncertainty Vol KI = (0.4/ 30) x100%=1.3%
%Uncertainty Conc = % Uncertainty Vol KI
%Uncertainty Conc = 1.3%








Calculation Absolute Uncertainty
Conc = 0.10 ± 1.3%
Conc = 0.100 ± 0.001



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2) Max/Minimum Method
Preparing 0.053M from 0.1M KI using pipette.
Pipette uncertainty = ± 0.4
Max Conc KI = Max Vol KI and Min Vol of water used
M x V (dil) = M x V (conc)
M x (15.8 + 14.2) = 0.1 x (15.8)
M = 0.1 x ( 15.8 ) / ( 15.8+ 14.2 )
M = 0.053


Max Conc KI=Max Vol KI + Min Vol water 
Max Vol KI = 15.8 ± 0.4 = 16.2
Min Vol water = 14.2 ± 0.4 = 13.8


M x V (dil) = M x V (conc)
Max Conc KI =  (0.1 x 16.2) / ( 16.2 + 13.8 )
Max Conc = 0.054

Min Conc  = Min Vol KI and Max Vol water used
Min Vol KI = 15.8 ± 0.4 = 15.4
Max Vol water = 14.2 ± 0.4 = 14.6


M x V (dil) = M x V (conc)
M x (15.4 + 14.6)  = 0.1 x (15.4)
M = 0.1 x ( 15.4 ) / ( 15.4 + 14.6 )
M = 0.051
Min Conc = 0.051
Uncertainty Conc = 0.053 ± ( 0.054 --- 0.051)
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Uncertainty Cal, 2 fold Serial dilution using 3% H2O2
2 Methods using 
1st % Uncertainty Method
For 1.5%, Total % Uncertainty is 1.6%, Answer = 1.5 ± 1.6%, Propagation of error involved

Absolute Uncertainty for 1.5 ± 1.6% = (1.50 ± 0.02)%
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2nd, Max/ Min Method 
For 2 fold Serial dilution on 3% H2O2
M x V (dil) = M xV (conc)
M x (1.5 +1.5) = 3% x 1.5
M = 1.5%

Max Conc H2O2 when
Max Vol H2O2 used = 1.51
Min Vol water used = 1.49


Min Conc H2O2 when
Min Vol H2O2 used  = 1.49
Max Vol water used = 1.51


Max Conc H2O2                                         Min Conc H2O2                              


M x V (dil) = M x V (conc)                         M x V (dil) = M x V (conc)                           
M x (1.51 + 1.49)  = 3% x ( 1.51 )               M x (1.51 + 1.49)  = 3% x ( 1.49 )
M = 3% x ( 1.51 )/ ( 1.51 + 1.49 )                 M = 3% x ( 1.49 )/ ( 1.51 + 1.49 )
M = 1.51%                                                M = 1.49%
Max Conc = 1.51%                                    Min Conc = 1.49%
Uncertainty Conc H2O2 = 1.50 ± (1.51%---1.49%)
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Uncertainty Cal for Rate Using Vernier Sensor.
How changing conc of H2O2 affect the rate of decomposition of H2O2 (catalase) measured using pressure sensor?

Initial Rate for 1.5% = slope/ gradient of curve
Perform 3 trials at 1.5% and take Average rate
Average Rate by taking average for 3 trials
Uncertainty for Rate = Standard deviation
Use Excel to calculate Std deviation


















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Video, adding uncertainty, error bar, Std deviation into Excel
Keynotes from video
Video tutorial on how to add standard deviation into our data point in Excel
  • Adding horizontal/vertical error bar/ uncertainty or Std deviation
  • Follow notes provided in powerpoint
Video on adding Std deviation into Excel

Saturday, May 28, 2011

IB Biology, IB Chemistry on Antibiotics, Penicillin, Medicine, Drugs, Option D

IB Chemistry, Antibiotics, Penicillin, Medicine, Drugs, Option D


1928
Fleming discovered Penicillin from a fungi Penicillium notatum 
1940
Florey, Chain injected mice with bacteria, then with Penicillin
1945
Fleming, Florey, Chain awarded Nobel Prize (Medicine)

Keywords

  • Beta lactam Ring, inhibit enzyme in peptidoglycan cell wall synthesis
  • R side chain



Types of penicillin.

  • Natural, Penicillin G
  • Semi-synthetic, Penicillin V, Amoxicillin, Ampicillin
  • Antibiotic Resistant Bacteria produce enzyme penicillinase/beta-lactamases to destroy the ring.
  • Penicillinase resistant antibiotics, Methicillin, Oxacillin, Cloxacillin









Penicillin/ Cephalosporin, similar in function
  • Destroy cell wall
  • Beta lactam ring
  • Different side chains
  • From mould/fungi
  • Disrupt the synthesis of peptidoglycan
  • Ampicillin against Gram -ve
  • 1st to 4th generation drugs
  • 4th generation, strongest drug


Click HERE on types of antibiotics

Source taken from
http://jac.oxfordjournals.org/content/60/1/107/F1.large.jpg
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Video, History/ How Penicillin Works


Broad and Narrow Spectrum of Antibiotics
Keywords are
  • Narrow spectrum (specific), Penicillin and Sulfa drugs
  • Broad spectrum (wide range), Tetracyclines and Cephalosporin
  • Narrow is preferred
  • Bacteria develop resistance ( no inhibition zone )
Click HERE to get in 
Source from http://www.jyi.org/news/nb.php?id=555
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Bacteria Fight back with MRSA
Keywords
  • Bacteria develop resistance/mutate
  • Hospital-acquired infections caused by Methicillin Resistant Staphylococcus Aureus (MRSA).
  • MRSA are resistant to Penicillin, oxacillin, amoxicillintetracycline,erythromycin.
Source and picture taken from
http://www.medicinenet.com/mrsa_infection/article.htm
http://www.knowabouthealth.com/extremely-resistant-superbug-triggers-global-concern/5338/
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MRSA to NDM1( SuperBug )



New Delhi metallo-ß-lactamase(NDM-1) a gene carried by bacteria, thus resistant to carbapenem ( powerful antibiotics )


Discovered in Dec 2009 in New Delhi, now detected in Pakistan, UK, States, Canada and Japan

Gut (E.coli) and lungs (Klebsiella), carry NDM1  gene



Carbapenems are beta-lactam antibiotics, developed to overcome antibiotic resistance.

SuperBug NDM1 is now resistant to carbapenems


Source from




Video on Emergence of NDM 1 Superbug
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MRSA to NDM1 to CRKP
What is CRKP Superbug?
From CNN and Healthland
Emergence of Carbapenem Resistant Klebsiella Pneumoniae (CRKP),  found in West, LA. In seven months (2010), there were 356 cases of CRKP.
 CRKP are resistant to most antibiotics including carbapenem cause they produce carbapenemase enzyme.
Video on CRKP Superbug from ABC News

More video on CRKP
Click HERE to get to ABC News


Key notes on CRKP from CDC
  • Spread in health care + hospital, 40% die usually from pneumoniae
  • Prevention by washing hand
  • Hospital acquired infection, called Klebsiella ( gram-negative )
  • Klebsiella enter respiratory tract cause pneumoniae or blood to cause bloodstream infection.
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Bacteria are resistant and why we are losing the battle


World Health Day – 7 April 2011 was declared to combat drug resistance

Antimicrobial resistance: no action today, no cure tomorrow

Key notes from World Health Day,

  • World on brink of losing miracle cures.
  • Resistance is natural process and selective pressure is main cause
  • Evolution of bacterial genome under selective antibiotic pressure is the main cause for multi resistant strains.
  • Bacteria evolve/mutate and become resistant to the antibiotics. 
  • Drugs are dispensed too liberally
  • Overuse of antibiotics in animal feedstock and development of resistance strains
  • Over prescription of drugs by doctors
  • Use of 3rd generation, cephalosporins is linked to Gram -ve bacteria lactamase resistance
  • Bacteria develop resistance as quickly as we've been able to develop new antibiotics.
More Video for antibiotics. Click HERE to get in
Latest Outbreak killed 10 in Germany ( 29 May 2011 )
Shigatoxin/Vero toxin producing Escherichia coli (STEC/VTEC) causes haemolytic uraemic syndrome (HUS). E. coli are harmless found in gut/ faeces of animals
From MRSA to NDM1 to CRKP to STEC/VTEC
Sources from 
International Journal of Antimicrobial Agents 17 (2001) 357–363, World Health Day, Healthland
http://www.who.int/world-health-day/2011/en/

Thanks to all pictures and videos contributor for the above post

Friday, May 27, 2011

IB Biology IA, IB Chemistry IA, EE Biology, EE Chemistry

IB Biology IA , IB Chemistry IA, EE Biology and EE Chemistry 
IA and EE on Vitamin C quantification 


1. Ammonium Oxalate, prepared by dissolving 0.08g ammonium oxalate in 100ml pH 5 buffer
2. Vit C (0.001M ), prepared by dissolving 0.018g of Vit C in 100ml ammonium oxalate solution
3. Perform 2 fold dilution on 0.001M Vit C.
4. Add 1 ml Vit C into a quartz cuvette and 2ml of ammonium oxalate ( as a stabiliser )
5. Leave for 10 mins
6. Prepare a blank with 1ml water and 2 ml ammonium oxalate
7. Set up UV spectrophotometer at 266nm and quantify.
Result shown below
Latest journal published last month, accurate way to quantify Vit C. 
Click HERE to get in
* Oxalate solution used as  stabiliser and pH around 5 as both affect the stability of Vitamin  C
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IA and EE on Glucose Quantification
1. 1% glucose std was prepared ( 1g in 100ml )
2. Perform 2 fold serial dilution ( 1%, 0.5%, 0.25%, 0.125% )
3. Add 2 ml of 1% glucose + 2 ml of DNS (3,5 dinitrosalicylic acid) into a 50ml test tube.
4. Repeat step 1 to 3 for different glucose concentration
5. Place all tubes in boiling water bath for 5 mins for colour formation. ( red brown)



6. Transfer 1 ml of solution from tube to cuvette and added 2ml of water to dilute it
7. Set visible spectrophotometer at 487nm.
8. Prepare a blank containing 1ml DNS + 2ml water.




9. Measure absorbance at 487nm
10. Plot std calibration curve
11. Beer's Law works only for diluted solution.
12. Recommended range for glucose ( 1% to 0.01%)
13.Expt will not work if too little glucose is used




Video,Glucose Quantification using DNS with visible spec


Click HERE on glucose quantification and preparation of DNS solution.
* Resulting Glucose/DNS solution must be diluted with water as Beer's Law only applies for diluted solution.
*Experimental Kit can be purchased  for EE and IA work. Click HERE to purchase kit
* Glucose solution range must be around 1% to 0.1% for colour determination.
* All item can be purchased from Carolina Biologicals or Kemtecscience

Sample on IA and EE on glucose quantification using DNS and Visible Spec

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IA and EE on Iron Quantification
Preparation
1. 0.01M iron(II), prepared by dissolving 3.92g of Fe(SO4)2(NH4)2.6H2O in 2M HCI to 1liter.
2. Perform 2 fold serial dilution.
4. Add 1 ml of iron (II) std to cuvette
5. Add 0.5ml 5% trisodium citrate/buffer to cuvette( use pH <6)
6. Add 0.5ml 10% hydroxyammonium chloride (reducing agent  to reduced all iron (III ). Ignore this step if you think iron (II) is not oxidised.
7. Add 1ml 0.01M phenanthroline for colour formation.
8. Leave for 24 hours for iron (II) phenanthroline complex to form ( orange red )
9. Set visible spectrophotometer at 508nm
10.Prepare a blank ( 1 ml water, 0.5ml trisodium citrate, 0.5ml hydroxyammonium chloride, 1ml phenanthroline )
10. Measured absorbance for  iron(II) std in cuvette shown above

Result on iron quantification

2 fold dilution from 0.0001M was done, absorbance was measured after 24 hours.




Std Calibration curve for iron(II) standard at 508nm.
Click HERE, sample EE on iron quantification with visible spec
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IA and EE on Quantification for starch iodine solution 
Starch with iodine solution forms blue black colouration.
1. Prepare 0.01% starch solution ( 0.01g in 100ml )
2. Perform a 2 fold dilution ( 0.01, 0.005, 0.00250, 0.00125, 0.000625%)
3. Add 1ml 0.01% starch to cuvette
4. Add 50ul 1% iodine solution ( adjust volume accordingly to obtain appropriate blue black)
5. Set visible spec at 567nm
6. Prepare a blank ( 1ml water + 50ul iodine ) and calibrate/zeroize it
7. Prepare cuvette (1ml 0.01%starch + 50ul iodine) and measure absorbance at 567nm
8. Repeat step 7 with different starch conc and plot std calibration curve.
Hints and tips 
  • Starch iodine must be diluted with water as Beer's Law, works for diluted solution.
  • Starch solution decomposes over time (Prepare fresh)
  • Volume of 1% Iodine must be adjusted accordingly so a blue black is formed.



Video, Starch Iodine quantification using Visible Spec


IA, digestion of starch using amylase measured using visible spec

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EE and IA on DNA Quantification
1. Prepare 5% DNA by adding 5ul of lambda DNA (stock 0.1mg) to 100ul TE ( DNA buffer ) into microcentrifuge 
2. Perform 2 fold dilution. ( 5, 2.5, 1.25, 0.625, 0.3125%)
3. Add 100ul DNA solution into a quartz cuvette
4. Set UV spectrophotometer at 260nm
5. Prepare blank ( 100ul TE buffer )
6. Measure absorbance at 260 and plot DNA std calibration curve at 260nm

Useful for EE in Biology DNA studies


Click HERE, view EE on DNA quantification

DNA std calibration curve at 260nm.
DNA and TE buffer can be purchased from Carolina








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Suggested IA and EE that can be done by IB Bio/IB Chem
For Vitamin C,
  • EE on the effect of UV radiation (A,B,C ) on the decomposition of Vitamin C quantified using UV spectrophotometer.
  • EE/IA on effect of heat, temperature, pH, presence of transition metal ions on the decomposition of Vit C measured using UV spectrophotometer/iodine titration method
For Glucose Quantification,
  • EE/IA on how changing pH, temperature, inhibitors, ionic salt conc affect the amylase activity measured using visible spectrophotometer. ( by either monitoring the decrease in absorbance of starch/iodine solution over time or by measuring the absorbance of starch/iodine solution after a period of time using the std calibration curve)
For Iron Quantification
  • EE/IA on how temperature affect the amount of iron content in spinach, seaweed, brocolli measured using visible spec
  • EE on the relationship between different part of plants with the amount of iron content measured using visible spec
For DNA Quantification
  • EE on how temperature affect the stability of DNA double strand ( breaking of hydrogen bond ) measured using UV spec
  • EE on how different extraction techniques, using SDS, Proteinase K, Protease, Phenol Chloroform affect the amount of DNA/purity of DNA measured using UV spec
For Starch Quantification
  • EE/IA on how changing pH, temperature, inhibitors, ionic salt conc affect the rate of digestion of amylase on starch/iodine solution measured using visible spec ( by either monitoring the decrease in absorbance of starch/iodine over time or by measuring the absorbance of starch/iodine over a period of time using std calibration curve)
List goes on...............endless Research Questions. 
Most importantly we must establish a sound methodology and a reliable way to quantify.

Wednesday, May 25, 2011

IB Chemistry in Organic Chemistry, Medicine, Drugs, Option D

IB Chemistry on Medicine, Drugs, Aspirin, Analgesic , Option D
Miracle Drug, Aspirin
Analgesic drugs, Aspirin, salicylate drug acts on enzyme which produces prostaglandins to relieve pain,  antipyretic to reduce fever and anti-inflammatory properties.
Aspirin ( acetylsalicylic acid ) made from salicylic acid and acetic anhydride. 

Active ingredient from Willow Bark ( Salicylic acid ), very acidic due to OH group of phenol. Adding acetyl group changes it to Aspirin (less acidic).
1897---Aspirin synthesized by Felix Hoffmann, at Bayer.
1899-- Aspirin marketed by Bayer.
1900---First water-soluble Aspirin by Bayer.
1915---Aspirin available without prescription.
Video on History, Discovery and Nobel Prize on Aspirin 


1960---Craven's discovered Aspirin prevent platelet aggregation ( prevent blood clot )


1970---Professor Vane discovered aspirin blocks an (COX) enzyme needed for production of  hormones (prostaglandins). 


1982---Professor Vane awarded Nobel Prize, How Aspirin acts by blocking the formation of prostaglandins, giving anti inflammatory/anti pyretic and anti platelet properties.










Video on How aspirin works
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How Aspirin Works
  • Aspirin decrease production of prostaglandins by inhibiting (COX) enzyme. 
  • Works by acetylating (add acetyl gp) to a serine residue on active site of the (COX) enzyme.
  • Aspirin inhibits COX enzyme, decrease prostaglandins (hormone) production -  pain relief, reduce inflammation or swelling



                        
.....................................................................................................................................................
Good and Bad side of Aspirin from CNN
Good side
Aspirin before air travel decrease risk of deep-vein thrombosis (DVT), prevent inflammation, reduce fever, heart attacksstrokes, and blood clot.
Bad side
Aspirin increase the risk of gastrointestinal bleeding, bleeding due to its acidity



Latest discovery on Aspirin from Telegraph and Lancet
Aspirin prevent Cancer and Heart diseaseTaking a quarter of an aspirin with milk before bed could reduce your chance of dying in middle age by a tenth, the biggest study into the drug has found.
Video, latest discovery published in Lancet ( Jan 2011 )
Keywords from study/video

  • 25,570 patients on drug for average 4 years. 
  • Reduced Prostate Cancer  by 10%, Lung Cancer 30%, Bowel Cancer 40%, Throat Cancer  60%.
  • Longer you take aspirin, the greater the benefit, risks ( stomach bleeding) is "trivial" compared with the benefits. More research is required before clear conclusions can be drawn on the implications for clinical practice.
Sources from
http://www.telegraph.co.uk/health/healthnews/8184776/Aspirin-the-wonder-drug-fights-off-cancer-as-well-as-heart-disease.html
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Published in Lancet (2011),  Aspirin could save thousands of lives a year from cancer alone.
Sources from
http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(10)62110-1/abstract
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Timeline for aspirin from 400BC to Jan 2011( Lancet)
Sources from 
http://www.telegraph.co.uk/health/healthnews/8185164/Aspirin-timeline.html
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Aspirin Synthesis in Lab adopted from Carolina

  • Soak 2g of Willow Bark in 100 ml 95% ethanol to extract Salicylic acid.
  • After 20 mins, filter the extract (Salicylic acid)
  • Add 2 ml conc acetic acid to extract (convert it to Aspirin)
  • How to test for Salicylic acid and Aspirin.
  • Test for Salicylic acid, add 100ul of iron (III) chloride, it turn purple (phenol group)
  • Test for Aspirin, add 100ul of iron (III) chloride, it remain orange (no phenol group)
  • Test which is more acidic, Aspirin or Salicylic acid, add universal paper/indicator, Salicylic acid (more acidic), Aspirin ( less acidic ).
Thanks to all Pictures, Video and Carolina contributors for the above post
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