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Proline

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Proline is an [[Imino acid|imino acid]]. It has a molecular weight of 115.13 and its molecular formula is C5H9NO2. It is also classified as a hydrophobic amino acid. 

Proline has an [[Aliphatic|aliphatic]] side chain, which is bonded to the nitrogen atom and the [[Alpha-carbon|alpha-carbon]] [[Atom|atom]]. It influences [[Protein|protein]] architecture, because it's structure makes it more conformationally restricted than other [[Amino acids|amino acids]] <ref>Biochemistry 6th ed. 2006, J.Berg et al</ref>.

[[Image:Proline.png]]

=== References ===

<references />

Tryptophan

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[[Image:Tryptophan.png]]

Tryptophan is an essential [[Amino acids|amino acid]] that must be obtained from the human diet. It has the single amino acid code W (see [[Single letter amino acid codes|single letter amino acid codes]]) and the 3 letter code Trp. It is coded for in the [[Genome|genome]] by the [[Nucleotide|nucleotide base sequence]] UGG <ref>https://www.dna20.com/codontablewheel.php</ref>. 

=== Medical Uses ===

Tryptophan is also a drug which is used to treat depression, when other antidepressants have been otherwise uneffective.

=== References ===

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Glutamine

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[[Image:Glutamine.png]]

Glutamine is one of the 20 naturally occuring [[Amino acids|amino acids]]. It can be abbreviated to three letters: Gln or one letter: Q. It is a [[Polar|polar]] molecule meaning that it has an [[Enzyme|enzymatic]] role and can bind [[Ligand|ligands]] and other [[DNA|DNA]]. [[Polar amino acids|Polar amino acids]] are found buried in a [[Protein|protein]] and can be [[Hydrogen bonds|hydrogen-bonded]] to other [[Polar amino acids|polar amino acids]] or to the [[Polypeptide|polypeptide]] backbone <ref>Molecular biology of the cell, Alberts, 5th edition, chapter 3, page 126-129.</ref>.

=== References ===

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Asparagine

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Asparagine is a non-essential amino acid. Its abbreviations are Asn or N, and its codons are AAU or AAC.

It provides an important site for asparagine-linked glycosylation (N-glycosylation) within peptides <ref>Kenneth W. Joy, Robert J. Ireland and Peter J. Lea, 'Asparagine Synthesis in Pea Leaves, and the Occurrence of an Asparagine Synthetase Inhibitor' Plant Physiology (1983) 73:165-168</ref>.

 '''Synthesis'''

'''                          '''(transaminase)                                (asparagine synthase)

Oxaloacetate                   ⇒                        Aspartate                  ⇒                     Asparagine

                 glutamate   →  alpha-ketoglutarate               glutamine  →     glutamate

                                                                                     ATP   →  AMP + PPi

 

[[Image:Asparagine.png]]

=== References ===

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Glutamic acid

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Glutamic acid (also known as [[Glutamate|Glutamate]]) is a negatively charged [[Amino acid|amino acid]] with an [[Acidic side chain|acidic side chain]]. It is a vital component in the excitatory pathways of the nervous system in mammals with it's [[Gated ion channel|gated ion channels]] being the most common [[Ion channels|ion channels]] found in the [[Brain|brain]]. Glutamate ion channels found in the [[Hippocampus|hippocampus]] are responsible for most of the depolarizing currents of [[Excitatory postsynaptic potential|Excitatory PostSynaptic Potentials]] (EPSPs)<ref>ALBERTS, B. (2008). Molecular biology of the cell. New York [etc.], Garland Science. p691</ref>.

Furthermore, Glutamic acid (Glutamate) is involved in [[Long Term Potentiation|Long Term Potentiation]] (LTP). LTP is an example of synaptic plascitity.  Glutamate is firstly released from the pre-synaptic neuron. Glutamate then binds to 2 inotropic receptors AMPA and NMDA (the NMDA at this point is currently blocked by [[Magnesium|magnesium]] ions though.) 

The [[AMPA receptor|AMPA receptor]] is a Na+ channel so an EPSP is triggers. The EPSP is converted to an action potential is the threshold value (-55mV) is reached.  The depolarization caused as a result trigges the Mg2+ to be ejected from the [[NMDA receptor|NMDA receptor]]. This causes the NMDA receptor to open. As a result, Ca2+ ions flow through the NMDA receptor. 

The Ca2+ activates secondary messenger pathways, and so post-synaptic cell becomes more sensitive to glutamate. The release of Ca2+ causes enhanced neurotransmitter release (so enhanced glutatmate from the pre-synaptic cell.) For example, the Ca2+ can trigger a phorphorylation cascade, causing the phosphorylation of the glutamate receptor channels (AMPA and NMDA.) 

LTP leads to an increase in the quality (and quantity) of synaptic transmission <ref>(not mentioned). (2013). The Molecular Basis of Learning and Memory. Available: http://www.learner.org/courses/biology/textbook/neuro/neuro_9.html. Last accessed 27th November, 2013.</ref>. 

=== [[Image:Glutamate.png]] ===

===   ===

=== References ===

<ref>Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.</ref>

Aspartate

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Aspartate also known as [[Aspartic acid|Aspartic ]][[Aspartic acid|Acid]] is an α-[[Amino acid|amino acid]] which contains two acidic side chains making it one of the two negativley charged amino acids (the other being [[Glutamic Acid|Glutamic Acid]]) <ref>Berg, J. Stryer, L. Tymoczko, J. (2011) Biochemistry, 7th Edition, New York: W.H Freeman and Company. Chapter 2, Page 31.</ref>.

'''Single Letter Code: '''D

'''Three Letter Code: '''Asp 

[[Image:Aspartic acid.gif]][[Image:Aspartate5.gif]]

=== [[Image:Aspartate.png]] ===

=== ===

=== References ===

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Histidine

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Histidine (commonly abbreviated to His or H) <ref>^ IUPAC-IUBMB Joint Commission on Biochemical Nomenclature. "Nomenclature and Symbolism for Amino Acids and Peptides". Recommendations on Organic and Biochemical Nomenclature, Symbols and Terminology etc. Retrieved 2007-05-17.</ref>  is one of the twenty naturally-occurring [[Amino acids|amino acids]]. Of these amino acids it is one of ten [[Polarity|polar]] and one of three positively-charged amino acids <ref name="Amino Acid Chart">http://www.detectingdesign.com/images/Abiogenesis/Amino%20Acid%20Chart.jpg</ref>.  The [[Codon|codons]] of His are CAU or CAC. 

Histidine is an [[Aromatic_ring|aromatic]] amino acid, which acts as an [[acid|acid]] when [[Proton|protonated]]. When unprotonated it has a positively charged [[imidazole|imidazole]] functional group and acts as a general base. It plays an important role in stabilising the folding structures of proteins and active sites of [[enzymes|enzymes]] <ref>http://www.biology.arizona.edu/biochemistry/problem_sets/aa/histidine.html</ref> . This ability is due to its binding properties with metals and the basic properties of the nitrogen [[atoms|atoms]] in the ring. It is only found as an L- isomer and it plays an important role in growth and repair of tissues in the body.

[[Image:Histidine.png]]

=== References ===

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Arginine

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=== Abbreviation ===

Arg

=== Single Letter Code ===

R

=== Infomation ===

Arginine is one of the twenty [[Amino acids|amino acids]]. It is most commonly found in its stereotypical L-isomeric formation and is a polar, positively charged molecule.

Due to the [[Molecule|molecule's]] charge, it can sometimes be found located in the functional part of a [[Proteins|protein]] conforming a pore<ref>The Biology Project,Department of Biochemistry and Molecular Biophysics, University of Arizona. 2003</ref>.

Arginine displays basic properties in most basic, acidic and neutral environments due to the nature of its side chain or R-group. Its side chain contains a complex guanidinium cap on an aliphatic 3 [[Carbon|carbon]] chain. Multiple [[Hydrogen bonds|H-bonds]] are able to form due to the conjugation of [[Double bond|double bonds]] and [[Lone pair|lone pairs]] on the [[Nitrogen|nitrogen]] atoms.

Arginine plays an important role in last reaction of the urea cycle. In this metabolic pathway arginine is hydrolysed by the [[Enzyme|enzyme]] [[Arginase|arginase]] in the [[Cytoplasm|cytoplasm]] to form [[Urea|urea]]<ref>Berg, J. Stryer, L. Tymoczko, J. (2011)fckLRBiochemistry, 7th Edition, New York: W.H Freeman and Company. Chapter 23, Pages 709-711</ref>. 

=== [[Image:Arginine.png]] ===

=== References ===

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Lysine

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Lysine is an [[Amino acids|amino acid]] with the single letter code of K and the three letter code of Lys. Lysine is one of three [[Amino acids|amino acids]] that is positively charged <ref>Hernandez,B. et al, 2010,Vibrational analysis of amino acids and short peptides in hydrated media. VI. Amino acids with positively charged side chains: L-lysine and L-arginine,The Journal of Physical Chemistry.B., 114(2),1077-88,Abstract only, Available through: PubMed.gov,(Accessed 12/11/10).</ref>.

[[Image:Lysine.png]]

=== References ===

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Threonine

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[[Image:Threonine.png]]

Threonine is an uncharged, polar [[Amino acids|amino acid]] whose three letter code is Thr and single letter code is T. It interacts with other polar molecules using [[Hydrogen bonds|hydrogen bonds]]. Its [[Hydroxyl group|hydroxyl]] group is polar and its R group is uncharged and is C2H5O <ref>Lodish, H et al., 2008, Molecular Cell Biology, Sixth edition, 42-43, New York,NY:WH Freeman and Company.</ref>.

=== References ===

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Serine

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Serine is a polar [[Amino acid|amino acid]] with an [[Non-polar|non-polar]] side chain of CH2OH. The single letter code for this amino acid is S, and the three letter code is Ser <ref>Lodish, H. et al, 2008.Molecular Cell Biology. 6th edition. New York,NY:WH Freeman and Company.</ref>. 

[[Image:Serine.jpg]] 

[[Image:Serine.png]]

=== References ===

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Tyrosine

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Tyrosine is a non essential white crystalline [[Amino acids|amino acid]] (C9H11NO3) with an uncharged [[Polar|polar]] side chain. Its three letter code is Tyr and its single letter amino acid code is Y. Its side chain consists of an [[Aromatic ring|aromatic ring]] and a [[Hydroxyl group|hydroxyl group]] which is polar <ref>J Biol Chem. 1972 Feb 25;247(4):977-83</ref>. It's formed from the hydrolysis of [[Proteins|proteins]] for example, [[Casein|casein]]. It is also a precursor for [[Epinephrine|epinephrine]], [[Thyroxine|thyroxine]] and [[Melanin|melanin]].

[[Image:Tyrosine.png]]

=== References ===

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Alanine

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Alanine is a [[Hydrophobic|hydrophobic]] [[Amino acids|amino acid]]. 

Three letter code: Ala

One letter code: A

It is a [[Non-polar amino acid|non-polar amino acid]]. It has a side chain of  -CH3 making it the second simplest amino acid (Gylcine is the simplest amino acid with a single hydrogen atom as its side chain.) It has four [[Codon|codons]]: GCA, GCC, GCG and GCU<ref>Berg J., Tymoczko J. and Stryer L (2012) Biochemistry, seventh edition, Basinstoke: W.H.Freeman and Company.</ref>. 

See [[Single letter amino acid codes|single letter amino acid codes]] 

[[Image:Alanine.png]]

=== References ===

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Valine

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Valine is an [[Amino acid|amino acid]] with a large non-polar side chain -CH(CH3)2 <ref>Alberts, Bray, Hopkin, Johnson, Lewis, Raff, Roberts, Walter, 2010, Essential Cell Biology, Third Edition, New York, Garland Science</ref>, with the three letter code Val and the single letter code V. It is a hydrophobic amino acid. The [[Codon|codons]] for valine are GUU, GUC, GUA and GUG <ref>Berg, Tymoczko, Stryer (2007) Biochemistry, 6th Edition, New York: W.H. Freeman and Company.</ref>.

[[Image:Valine.png]]

=== '''References''' ===

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Phenylalanine

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[[Image:Phenylalanine.png]]

Phenylalanine contains a benzyl side chain, giving it a [[Hydrophobic|hydrophobic]] nature that gives it the classification of [[Non-polar|non-polar]]. This alpha amino acid is also known as Phe or F.

'''References'''

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Proline

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Not an [[Amino acid|amino acid]]...........(It is actually an [[Imino acid|imino acid]]!)

Due it being joined to itself back on to the [[Nitrogen|nitrogen]]. Its molecular formula is C5H9NO2.

Proline has an [[Aliphatic|aliphatic]] side chain, which is bonded to the nitrogen atom and the [[Alpha-carbon|alpha-carbon]] [[atom|atom]]. It influences [[Protein|protein]] architecture, because it's structure makes it more conformationally restricted than other [[Amino acids|amino acids]] <ref>Biochemistry 6th ed. 2006, J.Berg et al</ref>. It is also a [[hydrophobic|hydrophobic]] amino acid. 

[[Image:Proline.png]]

=== References ===

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Methionine

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[[Image:Methionine.png]]

Methionine is an alpha [[Amino acids|amino acid]] also known as Met or M. It is classified as a [[Non-polar|non-polar]] and hydrophobic amino acid. It has a [[Molecular weight|molecular weight]] of 149.21 and its [[Molecular formula|molecular formula]] is C5H11NO2S . Methionine is an '[[Essential amino acid|essential amino acid]]' as it is not produced naturally in humans, and therefore must be ingested. The [[Codon|triplet code]] for methionine is AUG, which is always the first codon to be [[Translation|translated]] in an [[Open reading frame|open reading frame]] - thus, [[Methionine|methionine]] is always the first amino acid in a [[Polypeptide|polypeptide chain]]. However, [[Methionine|methionine]] may be removed if the protein is edited in the [[Golgi Apparatus|Golgi Apparatus]]. 

'''References'''
Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Isoleucine

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Isoleucine is a [[Hydrophobic|hydrophobic]] neutral [[Amino acids|amino acid]], the reason why it is [[hydrophilic|hydrophilic]] is because it has an [[Aliphatic|aliphatic]] side chain. Isoleucine has an additional [[Chiral centre|chiral centre]] at [[Carbon|carbon]] 3 <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman</ref>. 

[[Image:Isoleucine.png]]

=== References ===

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Leucine

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Leucine is an [[Amino acids|amino acid]] which has the [[Single letter amino acid codes|single letter amino acid code]] L, and the 3 letter code Leu. It is a hydrophobic and [[Non-polar amino acid|non-polar]] amino acid. It is coded for by the [[Nucleotide|nucleotide]] base sequences: CUU, CUA, CUC and CUG <ref>https://www.dna20.com/codontablewheel.php</ref>.

[[Image:Leucine.png]]

=== References: ===

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Glycine

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Glycine is one of the 20 [[Amino acids|amino acids]].  It's three letter code is Gly, and it's [[Single letter amino acid codes|single letter code]] is G. It is the simplest [[Amino acids|amino acid]], with a [[Hydrogen|hydrogen]] atom as a side chain - this means glycine is the only [[Amino acids|amino acid]] which does not have a [[Chiral carbon|chiral]] [[Carbon|carbon]] [[Atom|atom]] <ref name="Glycine">Priv.-Doz. B. Kirste. (01-23-1998). Glycine. Available: http://www.chemie.fu-berlin.de/chemistry/bio/aminoacid/glycin_en.html. Last accessed 23-11-2010.</ref>, so it does not form [[stereoisomer|stereoisomers]] therefore will not have L or D configurations.

Glycine has a function outside of the [[Cell|cell]]. It plays a vital role in the [[Central nervous system|central nervous system]] as is acts as a [[Neurotransmitter|neurotransmitter]] in chemical synapses <ref>Molecular biology of the cell,4th edition, 2002, Bruce Alberts, Alexander Johnson , Julian Lewis, Martin Raff , Keith Roberts and Peter Walter. Page 764</ref>. 

Glycine has two [[Hydrogen|hydrogens]] attatched to the [[alpha carbon|alpha carbon]] and is found in flexible areas of proteins due to its short side chain <ref>http://www.acnp.org/g4/gn401000008/default.htm</ref>.

[[Image:Glycine.png]]

=== References ===

Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.

Glycine

2013-11-29T14:32:12Z

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Glycine is one of the 20 [[Amino acids|amino acids]].  It's three letter code is Gly, and it's [[Single letter amino acid codes|single letter code]] is G. It is the simplest [[Amino acids|amino acid]], with a [[Hydrogen|hydrogen]] atom as a side chain - this means glycine is the only [[Amino acids|amino acid]] which does not have a [[Chiral carbon|chiral]] [[Carbon|carbon]] [[Atom|atom]] <ref name="Glycine">Priv.-Doz. B. Kirste. (01-23-1998). Glycine. Available: http://www.chemie.fu-berlin.de/chemistry/bio/aminoacid/glycin_en.html. Last accessed 23-11-2010.</ref>, so it does not form [[stereoisomer|stereoisomers]] therefore will not have L or D configurations.

Glycine has a function outside of the [[Cell|cell]]. It plays a vital role in the [[Central nervous system|central nervous system]] as is acts as a [[Neurotransmitter|neurotransmitter]] in chemical synapses <ref>Molecular biology of the cell,4th edition, 2002, Bruce Alberts, Alexander Johnson , Julian Lewis, Martin Raff , Keith Roberts and Peter Walter. Page 764</ref>. 

Glycine has two [[Hydrogen|hydrogens]] attatched to the [[alpha carbon|alpha carbon]] and is found in flexible areas of proteins due to its short side chain <ref>http://www.acnp.org/g4/gn401000008/default.htm</ref>.

[[Image:Glycine.png]]

=== References ===

<references /><ref>Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York: W.H. Freeman.</ref>

File:Glutamine.png

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130024257: Structure of Glutamine

Structure of Glutamine

File:Asparagine.png

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130024257: Structure of Asparagine

Structure of Asparagine

File:Glutamate.png

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130024257: Structure of Glutamate

Structure of Glutamate

File:Aspartate.png

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130024257: Structure of Aspartate

Structure of Aspartate

File:Histidine.png

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130024257: Structure of Histidine

Structure of Histidine

File:Arginine.png

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130024257: Structure of Arginine

Structure of Arginine

File:Lysine.png

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130024257: Structure of Lysine

Structure of Lysine

File:Cysteine.png

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130024257: Structure of Cysteine

Structure of Cysteine

File:Threonine.png

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130024257: Structure of Threonine

Structure of Threonine

File:Serine.png

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130024257: Structure of Serine

Structure of Serine

File:Tryptophan.png

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130024257: Structure of Tryptophan

Structure of Tryptophan

File:Tyrosine.png

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130024257: Structure of Tyrosine

Structure of Tyrosine

File:Phenylalanine.png

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130024257: Structure of Phenylalanine

Structure of Phenylalanine

File:Proline.png

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130024257: Structure of Proline

Structure of Proline

File:Methionine.png

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130024257: Structure of Methionine

Structure of Methionine

File:Isoleucine.png

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130024257: Strucure of Isoleucine

Strucure of Isoleucine

File:Leucine.png

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130024257: Structure of Leucine

Structure of Leucine

File:Valine.png

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130024257: Strucutre of Valine

Strucutre of Valine

File:Alanine.png

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130024257: Structure of Alanine

Structure of Alanine

File:Glycine.png

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130024257: Structure of glycine

Structure of glycine

Electroporation

2013-11-23T10:10:42Z

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Electroporation is a method used to insert a recombinant plasmid into a bacterial cell using high voltage electrical pulses. 

 

==== '''References''' ====

1) http://www.lifetechnologies.com/my/en/home/life-science/cell-culture/transfection/transfection-methods/electroporation.html

Electroporation

2013-11-23T10:09:00Z

130024257: Created page with "Electroporation is a method used to insert a recombinant plasmid into a bacterial cell using high voltage electrical pulses.  1) http://www.lifetec..."

Electroporation is a method used to insert a recombinant plasmid into a bacterial cell using high voltage electrical pulses. 

 

 

1) http://www.lifetechnologies.com/my/en/home/life-science/cell-culture/transfection/transfection-methods/electroporation.html