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Methionine

2012-11-30T15:34:54Z

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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]].

Proline

2012-11-30T15:32:56Z

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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. 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 amino acid. 

=== References ===

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Valine

2012-11-30T15:32:22Z

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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>.

== '''References''' ==

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Leucine

2012-11-30T15:31:16Z

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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>.

=== References: ===

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Leucine

2012-11-30T15:30:40Z

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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 [[Non-polar amino acid|non-polar ]]and hydrophobic 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>.

=== References: ===

<references />

Amino acids

2012-11-30T15:23:24Z

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Amino acids are the building blocks of proteins. There are 20 naturally occurring amino acids. Amino acids exist in proteins as L-optical [[Isomer|isomers]], however they can extist as D-isomers in isolated examples, e.g. some bacterial cell walls contain D-isomers.

Amino acids can also be characterized as [[Polar amino acids|polar]] or [[Non-polar amino acids|non-polar]] and these dictate the amino acid function. There are 10 non-polar amino acids found in [[Protein|protein]] core, and there are 10 polar amino acids. These have [[Enzyme|enzymatic]] roles and can be used to bind [[DNA|DNA]], metals and other naturally occuring ligands. There are essential amino acids and non-essential amino acids. Essential amino acids are the ones that the body cannot synthesise on its own. The essential amino acids in humans are: histidine, leucine, isoleucine, lysine, methionine, valine, phenylalanine, tyrosine and tryptophan.<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg650.</ref> These amino acids have to be supplied to the body via digested proteins that are then absorbed in the intestine and transported in the blood to where they are needed<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg650.</ref>. The digestion of cellular proteins is also an important source for amino acids. Non-essential amino acids can be synthesised from compounds already existing in the body.

Amino acids have been abbreviated into a 3 letter code as well as a 1 letter code. For example, [[Glycine|glycine]] has the 3 letter code 'Gly' and is assigned the letter 'G' (see single letter amino acid codes).

'''List of the 20 Amino acids, single letter code, three letter code, their charges, and side chain [[Polarity|polarity]]:'''

{| style="width: 357px; height: 460px" border="1" cellspacing="1" cellpadding="1" width="357"
|-
| '''Amino acid'''
| '''single letter code'''
| '''three letter code'''
| '''charge'''
| '''polarity'''
|-
| [[Alanine|alanine]]
| A
| Ala
| neutral
| nonpolar
|-
| [[Arginine|arginine]]
| R
| Arg
| +ve
| polar
|-
| [[Asparagine|asparagine]]
| N
| Asn
| neutral
| polar
|-
| [[Aspartate|aspartate]]
| D
| Asp
| -ve
| polar
|-
| [[Cysteine|cysteine]]
| C
| Cys
| neutral
| polar
|-
| [[Glycine|glycine]]
| G
| Gly
| neutral
| nonpolar
|-
| [[Glutamine|glutamine]]
| Q
| Gln
| neutral
| polar
|-
| [[Glutamate|glutamate]]
| E
| Glu
| -ve
| polar
|-
| [[Histidine|histidine]]
| H
| His
| +ve
| polar
|-
| [[Isoleucine|isoleucine]]
| I
| Ile
| neutral
| nonpolar
|-
| [[Leucine|leucine]]
| L
| Leu
| neutral
| nonpolar
|-
| [[Lysine|lysine]]
| K
| Lys
| +ve
| polar
|-
| [[Methionine|methionine]]
| M
| Met
| neutral
| nonpolar
|-
| [[Phenylalanine|phenylalanine]]
| F
| Phe
| neutral
| nonpolar
|-
| [[Proline|proline]]
| P
| Pro
| neutral
| nonpolar
|-
| [[Serine|serine]]
| S
| Ser
| neutral
| polar
|-
| [[Threonine|threonine]]
| T
| Thr
| neutral
| polar
|-
| [[Tryptophan|tryptophan]]
| W
| Trp
| neutral
| nonpolar
|-
| [[Tyrosine|tyrosine]]
| Y
| Tyr
| neutral
| polar
|-
| [[Valine|valine]]
| V
| Val
| neutral
| nonpolar
|}

=== '''Amino acid structure''' ===

All amino acids have a carboxyl terminus and an amino terminus, but they differ in their residual groups. Amino acids are bonded together by a [[Covalent|covalent]] linkage called a [[Peptide bond|peptide bond]] <ref>Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. (Page 59)</ref>. Amino acids contain both a [[Carboxyl group|carboxyl group]] (COOH) and an [[Amino group|amino group]] (NH2). The core amino acid structure is: 

              NH2-----C(H)(R)----COOH

where (R) is the side chain unique to each different amino acid.

Large amino acids form the rigid region of the polypeptide backbone while the small amino acids form the flexible regions of the [[Polypeptide|polypeptide]] allowing the protein to fold into it's three dimensional shape. This is what allows the polypeptides primary sequence to fold to an alpha helix which is one strand coiled. A beta strand is two strands coiled to an antiparallel helix. The core of the polypeptide is made up of the [[Hydrophobic|hydrophobic]] amino acids like [[Phenyalanine|phenyalanine]], [[Tyrosine|tyrosine]], and [[Tryptophan|tryptophan]] <ref>J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) Biochemistry, 6th edition, New York: W.H.Freeman and company (page 27).</ref>. These three amino acids are also aromatic and are the largest amino acids. The other hydrophobic amino acids, but are not aromatic, are: proline, valine, isoleucine, leucine and methionine.

Amino acids are referred to as chiral due to the alpha carbon being connected to four different groups. They can exist as one of two mirror images referred to as the L isomer and the D isomer with only the L form of the amino acid isomer present within proteins. <ref>Berg J. Tymoczko J. Stryer L., Biochemistry Sixth Edition (2007, WH Freeman, New York (page 27)</ref>

Amino acids in solution at neutral pH exist predominantly as dipolar ions, or zwitterions. In the dipolar form, the amino  group is protonated, and the carboxyl group is deprotonated. The ionization state of an amino acid varies with pH.<ref>J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) Biochemistry, 6th edition, New York: W.H.Freeman and company (page 27)</ref>

=== Amino acids in Translation ===

During the [[Translation|translation]] of [[MRNA|mRNA]] amino acids bind to the [[Ribosome|ribosome]] as it reads the mRNA and using the information given it produces a specific amino acid sequence producing a polypeptide chain. The 30S subunit binds to the mRNA first, and the 50S subunit binds second to form the 70S initiatior complex.

=== References ===

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Translation

2012-11-29T14:33:26Z

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Translation in an important, and complex feature of the process of [[Protein synthesis|protein synthesis]]. Genetic information codes for [[Proteins|proteins]] via protein syntheis, this is an essential process as proteins are responsible for the vast majority of cell function and structure. Protein synthesis involves [[MRNA|mRNA]] and [[TRNA|tRNA]] along with other [[Proteins|proteins]] and has three main steps:

#DNA replication
#Transcription
#Translation

Translation is the most complex, it consists of the [[Nucleotide|nucleotide]] sequence of [[MRNA|mRNA]] being translated into the [[Amino acid|amino acid]] secquence of the specific protein. The direction that translation is carried out is very significant; it occurs in the same direction as transcription ( 5'-3') this results in proteins being produced more efficiently as translation can occur during transcription <ref>Berg et al., 2007:869</ref>.

The [[MRNA|mRNA]] and [[TRNA|tRNA]] play very important specific roles during translation; firstly [[MRNA|mRNA]] acts as a template for the production of the polypeptide chain from the genetic code. The genetic code had three important features:

#Triplet code
#Non-overlapping
#Degenerate

The genetic code is degenerate because it has 64 codons but only 20 amino acids, therefore most amino acids are coded for by more than one codon. 61 of these codons are used for amino acids and 3 are used as stop codons which will end translation. Only 1 codon is used for the amino acid Methionine and this is the start codon (AUG).

The [[TRNA|tRNA]] acts as an adaptor molecule to decode the [[MRNA|mRNA]] into the protein, it interacts with the [[MRNA|mRNA]] through its anticodon.The [[TRNA|tRNA]] is also responsible for [[Proof-reading|proof-reading]] the [[Amino acids|amino acid]] chain, this ensures that mistakes are very rare (less than 1 per 10000). This is done by many [[TRNA|tRNA]] having an editing site as well as an activation site. These change or reject [[Amino acids|amino acids]] if they are larger or smaller than they should be.

 

There are 3 main steps in Prokaryotic translation; Initiation, Elongation and Termination. 

''Initiation:''

This involves the initiation factors IF1, IF2, IF3; [[GTP|GTP]] is required for energy. 

IF1 and IF3 bind to the free 30S subunit, releasing it from the 50S subunit. IF2 forms a complex with GTP and binds to the 30S subunit, which attaches to an [[MRNA|mRNA]] molecule. mRNA has a ribosome binding site (RBS), which is adjacent to the stat codon AUG. The start codon is approximately 7-10 nucleotides away from the RBS. It is important to note that the 30S subunit is complementary to the ribosome binding site, so [[Watson-crick base pairing|base pairing]] can occur with the 16S rRNA. A charged initiator tRNA (fMet-tRNAfmet), then binds to this start codon. IF3 is released, allowing a 50S subunit to bind to the 30S complex to form the 70S initiation complex which has a P (peptidyl) and A (acceptor) site . During this formation, IF1 is released and both IF2 and GTP are [[Hydrolysis|hydrolysed]]. GTP--> GDP + Pi.

''Elongation:''

Elongation requires the elongation factors<ref>Stryer, Biochemistry, Seventh edition, 2007: 936</ref> EF-Tu, EF-Ts and EF-G as well as GTP to supply the energy. Elongation describes the process of aminoacyl tRNA molecules binding to the codon. A [[Peptide bond|peptide bond]] is formed between the amino acid of the tRNA in the P site and the amino acid in the tRNA molecule that has just arrived at the A site; the formation of this peptide bond is catalysed by the 23S subunit. The amino acid in the P site is released from its tRNA molecule and the ribosome moves along so as to transfer the tRNA currently in the A site into the P site. This step is known as transloaction. The uncharged tRNA i.e. tRNA without an amino acid, moves into the E (empty) site. <ref>http://rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/translate.htm</ref>

 

''Termination:''

A [[Stop codon|stop codon]] attaches to the A site and the newly synthesised [[Polypeptide|polypeptide chain]] occupies the P site. A release factor binds to the stop codon, initiating the release of the polypeptide chain which is transferred to the cytoplasm<ref>http://staff.jccc.net/pdecell/proteinsynthesis/translation/steps.html</ref> . Several release factors are involved as they recognise different amino acid sequences. These are RF1, RF2 and RF3. RRF (ribosome release/ rec-cycling factor), EF-G and GTP hydrolysis promotes the dissociation of the ribosome from mRNA so the mRNA can be released. 

 

 

=== References ===

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