Base pair and Green chemistry: Difference between pages

Revision as of 11:24, 13 September 2005

Revision as of 11:24, 13 September 2005

Line 1:

'''Green Chemistry''' is the design of chemical products and processes that reduce or eliminate the use and generation of hazardous substances. Whereas [[environmental chemistry]] is the chemistry of the natural environment, and of pollutant chemicals in nature, green chemistry seeks to reduce and prevent [[pollution]] at source. In [[1990]] the [[Pollution Prevention Act]] was passed. This act helped create a ''modus operandi'' for dealing with pollution in an original and innovative way.

In [[molecular biology]], two [[nucleotide]]s on opposite [[complementarity (molecular biology)|complementary]] [[DNA]] or [[RNA]] strands that are connected via [[hydrogen bond]]s are called a '''base pair''' (often abbreviated bp). As DNA is usually double-stranded, the number of base pairs in the dsDNA strand equals the number of nucleotides in one of the strands. In DNA, [[adenine]] and [[thymine]], as well as [[guanine]] and [[cytosine]], can be a base pair. In RNA, [[thymine]] is replaced by [[uracil]].

Paul Anastas and John C Warner of the [[Environmental Protection Agency|EPA]] have developed 12 principles to green chemistry [http://www.epa.gov/greenchemistry/principles.html]:

The following abbreviations are commonly used to describe the length of a DNA/RNA molecule:

* kbp = kilo base pairs = 1,000 bp

* Mbp = mega base pairs = 1,000,000 bp

* Gbp = giga base pairs = 1,000,000,000 bp

# ''Prevent waste:'' Design [[chemical synthesis|chemical syntheses]] to prevent [[waste]], leaving no waste to [[waste treatment|treat]] or clean up.

In case of single stranded DNA/RNA we talk about [[nucleotide]]s, abbreviated nt (or knt, Mnt, Gnt), rather than base pairs, as they are not paired.

# ''Design safer [[chemical]]s and products:'' Design chemical products to be fully effective, yet have little or no [[toxicity]].

# ''Design less hazardous chemical syntheses:'' Design syntheses to use and generate substances with little or no toxicity to humans and the [[environment (biology)|environment]].

# ''Use [[renewable]] [[feedstock]]s:'' Use [[raw materials]] and feedstocks that are renewable rather than [[depletion|depleting]]. Renewable feedstocks are often made from [[agriculture|agricultural]] products or are the wastes of other processes; depleting feedstocks are made from [[fossil fuels]] ([[petroleum]], [[natural gas]], or [[coal]]) or are [[mining|mined]].

# ''Use [[catalyst]]s, not [[stoichiometric]] [[reagent]]s:'' Minimize waste by using [[catalysis|catalytic reaction]]s. [[Catalyst]]s are used in small amounts and can carry out a single reaction many times. They are preferable to stoichiometric reagents, which are used in excess and work only once.

# ''Avoid chemical derivatives:'' Avoid using blocking or protecting groups or any temporary modifications if possible. Derivatives use additional reagents and generate waste.

# ''Maximize [[atom economy]]:'' Design syntheses so that the final product contains the maximum proportion of the starting materials. There should be few, if any, wasted atoms.

# ''Use safer [[solvent]]s and [[reaction]] conditions:'' Avoid using solvents, [[separation of mixture|separation]] agents, or other auxiliary chemicals. If these chemicals are necessary, use innocuous chemicals. If a solvent is necessary, water is usually the best medium.

# ''Increase [[energy]] [[efficiency]]:'' Run chemical reactions at [[ambient temperature]] and [[atmospheric pressure|pressure]] whenever possible.

# ''Design chemicals and products to [[biodegradation|degrade]] after use:'' Design chemical products to break down to innocuous substances after use so that they do not accumulate in the environment.

# ''Analyze in real time to prevent [[pollution]]:'' Include in-process [[real-time]] monitoring and control during syntheses to minimize or eliminate the formation of byproducts.

# ''Minimize the potential for accidents:'' Design chemicals and their forms ([[solid]], [[liquid]], or [[gas]]) to minimize the potential for chemical accidents including explosions, fires, and releases to the environment.

In 2005 [[Ryoji Noyori]] identified three key developments in green chemistry: use of [[supercritical carbon dioxide]] as green solvent, [[aqueous]] [[hydrogen peroxide]] for clean [[oxidation]]s and the use of hydrogen in [[asymmetric synthesis]] {{ref|1}}. Examples of applied green chemistry are [[Supercritical water oxidation]], [[On water reaction]]s and [[dry media reaction]]s.

<!-- This image is full of errors, please make a new one!

The following figure shows the chemical structures of properly base-paired [[nucleic acid]]s.

<center>

[[Image:DNAbasePairing.png|none|500px|Chemical structure of base pair bonding]]<br />

<small>''Chemical structure of base pair bonding''</small>

</center>

-->

For similar initiatives in other fields, see also [[Green computing]].

The larger nucleic acids, adenine and guanine, are members of a class of doubly-ringed chemical structures called [[purine]]s; the smaller nucleic acids, cytosine and thymine (and uracil), are members of a class of singly-ringed chemical structures called [[pyrimidine]]s. Purines are only complementary with pyrimidines: pyrimidine-pyrimidine pairings are energetically unfavourable because the molecules are too far apart for hydrogen bonding to be established; purine-purine pairings are energetically unfavourable because the molecules are too close, leading to electrostatic repulsion. The only other possible pairings are GT and AC; these pairings are mismatches because the pattern of hydrogen donors and acceptors do not correspond.

==External links==

As [[hydrogen bond]]s are not very strong, the two nucleotides will separate on temperatures higher than 94 [[degree Celsius|°C]].

*[http://www.epa.gov/greenchemistry/whats_gc.html EPA Green Chemistry Website]

*[http://www.epa.gov/greenchemistry/docs/general_fact_sheet.pdf EPA Green Chemistry Fact Sheet]

*[http://www.chemistry.org/greenchemistryinstitute Green Chemistry Institute]

*[http://www.usatoday.com/news/science/2004-11-21-green_x.htm Green chemistry takes root (USA Today)]

*[http://www.greenchemistry.uml.edu Green Chemistry PhD Program at University of Massachusetts Lowell]

*[http://darkwing.uoregon.edu/~greenlab/index.html Green Chemistry Experiments for Education, University of Oregon]

== References ==

Chemical analogs of nucleotides can take the place of proper nucleotides and establish non-canonical base-pairing, leading to errors in [[DNA replication]] and [[Transcription (genetics)|DNA transcription]]. Some analogs are [[carcinogen]]s; others are [[chemotherapy]] drugs.

* {{note|1}}. ''Pursuing practical elegance in chemical synthesis'' Ryoji Noyori Chemical Communications, 2005, (14), 1807 - 1811 [http://www.rsc.org/publishing/journals/CC/article.asp?doi=b502713f Abstract]

[[Category:Environmental chemistry]]

==Intramolecular base pairs==

RNA can form intramolecular base pairs. These form a loop and a chain off the main RNA.

== See also ==

* [[Nucleobase]]

* [[Wobble base pair]]

* [[Hoogsteen base pair]]

[[it:Chimica verde]]

==References==

[[ja:%E3%82%B0%E3%83%AA%E3%83%BC%E3%83%B3%E3%82%B5%E3%82%B9%E3%83%86%E3%82%A3%E3%83%8A%E3%83%96%E3%83%AB%E3%82%B1%E3%83%9F%E3%82%B9%E3%83%88%E3%83%AA%E3%83%BC]]

* Diagram by Martin Chaplin, released under GFDL. [http://www.sbu.ac.uk/water/nucleic.html Link to original] (contains information about the role of water in DNA structure formation and stabilization).

[[pl:Zielona chemia]]

[[zh:&#32511;&#33394;&#21270;&#23398;]]

[[de:Basenpaar]]

[[Category:Genetics]]