What's the difference between diesel and biodiesel?
I'm glad you asked!
AUS-e-TUTE has just added new resources (tutorial, game, test, exam) to help you learn how to synthesize and characterize biodiesel, as well as to distinguish between diesel and biodiesel.
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If you are not an AUS-e-TUTE Member, there is a "free-to-view" biodiesel temporarily available at http://www.ausetute.com.au/biodiesel.html for evaluation purposes.
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Sunday, October 18, 2015
Sunday, October 11, 2015
Reaction Schemes
When is a flow chart not a flow chart?
When it's a reaction scheme.
Want to learn about reaction schemes used in organic (carbon chemistry) ?
Good, because AUS-e-TUTE has just added a new tutorial, game, test, and exam to help you learn and understand.
AUS-e-TUTE Members should log-in to use the new resources.
If you are not an AUS-e-TUTE Members, there is a "free-to-view" tutorial currently available for evaluation purposes at:
http://www.ausetute.com.au/schemaorg.html
Want find out more about the benefits of AUS-e-TUTE Membership?
Go to http://www.ausetute.com.au/membership.html
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When it's a reaction scheme.
Want to learn about reaction schemes used in organic (carbon chemistry) ?
Good, because AUS-e-TUTE has just added a new tutorial, game, test, and exam to help you learn and understand.
AUS-e-TUTE Members should log-in to use the new resources.
If you are not an AUS-e-TUTE Members, there is a "free-to-view" tutorial currently available for evaluation purposes at:
http://www.ausetute.com.au/schemaorg.html
Want find out more about the benefits of AUS-e-TUTE Membership?
Go to http://www.ausetute.com.au/membership.html
Ready to become an AUS-e-TUTE Member?
Go to http://www.ausetute.com.au/register.html
Got a question for AUS-e-TUTE?
Go to http://www.ausetute.com.au/contact.html
Friday, October 9, 2015
2015 Nobel Prize in (Bio)chemistry?
The 2015 Nobel Prize in Chemistry was awarded to Tomas Lindahl, Paul Modrich and Aziz Sancar for "mechanistic studies of DNA repair".
Cells have developed mechanisms to repair damaged DNA. Four of these mechanisms are:
Photoreactivation
In the 1920s Hermann Muller found that X-rays could mutate and kill cells.
In the 1940s Albert Kelner found that visible light could stimulate growth recovery after damage caused by UV light, and this was called photoreactivation.
In 1944 Oswald Avery and co-workers showed that DNA is the material of heredity, and in the 1950s it was recognised that DNA became damaged when exposed to UV light.
Renato Dulbecco suggested photoreactivation was an enzymatic reaction dependent on light, which was demonstrated by Stanley Rupert.
In 1978 Aziz Sancar cloned the E. coli photolyase gene, an enzyme responsible for DNA repair in escherichia coli.
In the 1980s Aziz Sancar showed that photolyase can convert the energy of an absorbed photon into chemistry that produces a localised free radical that initiates thymine dimer splitting.
Dark repair (nucleotide excision repair)
In the 1960s Jane Setlow and Richard Setlow showed that thymine dimers inactivated transforming DNA in Hemophilus influenzae and that this was responsible for the biological effect of UV light.
In 1964 Richard Setlow discovered that thymine dimers disappeared from the irradiated, high molecular weight genomic DNA shortly after exposure to UV light and appeared in the low molecular weight fractions, that is, thymine dimers are excised (removed) from the DNA. This mechanism became known as nucleotide excision repair (NER).
In the 1970s Aziz Sancar working with W. Dean Rupp, developed the Maxicell technique for the rapid identification of proteins.
In 1983 Aziz Sancar used purified proteins to reconstitute essential steps in the nucleotide excision repair (NER) pathway, a "cut and patch" method for DNA repair.
Two proteins (UvrA and UvrB) track along the DNA, UvrA recognises damage and causes UvrB to stop tracking and begin unwinding the effected DNA section. Another protein, UvrC, causes the damaged section to be cut out, and then another protein UvrD, causes UvrB to bind and bridge the gap while it is repaired by resynthesising the removed segment via Pol I.
Base excision repair
In the 1970s Tomas Lindahl showed that DNA has limited chemical stability and that modification of the bases of DNA increased the risk of mutations. High levels of spontaneous cytosine deamination leads to the formation of uracil.
Uracil forms base pairs with adenine, so, high levels of cytosine demanination pose a risk of depleting the genetic material from cytosine-guanine base pairs and replacing them with thymine-adenine.
He identified the E. coli uracil-DNA glycosylase (UNG) as the first repair protein which we now know is one member of a large family of proteins that orchestrate base excision repair (BER).
A DNA glycosylase recognises and cuts the base-deoxyribose glycosyl bond of a damaged nucleotide. DNA glycosylase kinks the DNA and the abnormal nucleotide flips out and is removed and the section can then be repaired.
Mismatch repair
During the synthesis of a new DNA strand, a non-Watson-Crick base pair may be formed which distorts the double-stranded DNA helix. These types of errors are known as mismatches.
In 1983 Paul Modrich and Matthew Meselson showed that DNA methylation directed strand-specific elimination of mismatches in E. coli. Modrich developed an assay to isolate the products of the different repair genes and identify the proteins.
Further Reading:
http://www.ausetute.com.au/dna.html
http://www.ausetute.com.au/enzymes.html
Suggested Study Questions:
Cells have developed mechanisms to repair damaged DNA. Four of these mechanisms are:
- photoreactivation
- dark repair (nucleotide excision repair)
- base excision repair
- mismatch repair
Photoreactivation
In the 1920s Hermann Muller found that X-rays could mutate and kill cells.
In the 1940s Albert Kelner found that visible light could stimulate growth recovery after damage caused by UV light, and this was called photoreactivation.
In 1944 Oswald Avery and co-workers showed that DNA is the material of heredity, and in the 1950s it was recognised that DNA became damaged when exposed to UV light.
Renato Dulbecco suggested photoreactivation was an enzymatic reaction dependent on light, which was demonstrated by Stanley Rupert.
In 1978 Aziz Sancar cloned the E. coli photolyase gene, an enzyme responsible for DNA repair in escherichia coli.
In the 1980s Aziz Sancar showed that photolyase can convert the energy of an absorbed photon into chemistry that produces a localised free radical that initiates thymine dimer splitting.
Dark repair (nucleotide excision repair)
In the 1960s Jane Setlow and Richard Setlow showed that thymine dimers inactivated transforming DNA in Hemophilus influenzae and that this was responsible for the biological effect of UV light.
In 1964 Richard Setlow discovered that thymine dimers disappeared from the irradiated, high molecular weight genomic DNA shortly after exposure to UV light and appeared in the low molecular weight fractions, that is, thymine dimers are excised (removed) from the DNA. This mechanism became known as nucleotide excision repair (NER).
In the 1970s Aziz Sancar working with W. Dean Rupp, developed the Maxicell technique for the rapid identification of proteins.
In 1983 Aziz Sancar used purified proteins to reconstitute essential steps in the nucleotide excision repair (NER) pathway, a "cut and patch" method for DNA repair.
Two proteins (UvrA and UvrB) track along the DNA, UvrA recognises damage and causes UvrB to stop tracking and begin unwinding the effected DNA section. Another protein, UvrC, causes the damaged section to be cut out, and then another protein UvrD, causes UvrB to bind and bridge the gap while it is repaired by resynthesising the removed segment via Pol I.
Base excision repair
In the 1970s Tomas Lindahl showed that DNA has limited chemical stability and that modification of the bases of DNA increased the risk of mutations. High levels of spontaneous cytosine deamination leads to the formation of uracil.
Uracil forms base pairs with adenine, so, high levels of cytosine demanination pose a risk of depleting the genetic material from cytosine-guanine base pairs and replacing them with thymine-adenine.
He identified the E. coli uracil-DNA glycosylase (UNG) as the first repair protein which we now know is one member of a large family of proteins that orchestrate base excision repair (BER).
A DNA glycosylase recognises and cuts the base-deoxyribose glycosyl bond of a damaged nucleotide. DNA glycosylase kinks the DNA and the abnormal nucleotide flips out and is removed and the section can then be repaired.
Mismatch repair
During the synthesis of a new DNA strand, a non-Watson-Crick base pair may be formed which distorts the double-stranded DNA helix. These types of errors are known as mismatches.
In 1983 Paul Modrich and Matthew Meselson showed that DNA methylation directed strand-specific elimination of mismatches in E. coli. Modrich developed an assay to isolate the products of the different repair genes and identify the proteins.
Further Reading:
http://www.ausetute.com.au/dna.html
http://www.ausetute.com.au/enzymes.html
Suggested Study Questions:
- What does the abbrevaition DNA stand for?
- What do you think when biochemists refer to damaged DNA?
- What is meant by the term enzyme?
- Why do you think enzymes are required in the mechanisms available within a living cell to repair damaged DNA?
- What is a free radical?
- Draw the structural formula of thymine.
- Draw the structural formula for a possible dimer of thymine.
- What is meant by the term nucleotide?
- With reference to DNA, what is meant by a base pair?
- Show how uracil forms a base pair with adenine.
- Draw the structure of a cytosine-guanine base pair
- What do you think is meant by the statement, "cytosine deamination leads to the formation of uracil" (structural formulae may be useful in your explanation but you do not need to include chemical reactions).
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