Amino acids

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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 isomers, however they can extist as D-isomers in isolated examples, e.g. some bacterial cell walls contain D-isomers.  
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Amino acids are the building blocks of [[Proteins|proteins]] - they create the proteins [[Primary structure|primary structure]]. There are 20 naturally occurring amino acids. Amino acids exist in [[Protiens|proteins]] as L-[[Optical isomers|optical isomers]], however, they can exist as D-isomers in isolated examples, e.g. some [[Bacteria|bacterial]] cell walls contain D-isomers. When two amino acids join they form a [[Peptide bond|peptide bond]]. This bond works as a partial double bond causing the amino acids to have cis/trans [[Isomers|isomers]]. Although most commonly found in trans. All amino acids are&nbsp;amphoteric meaning they can act as both a base and an acid due to their amino and carboyxl groups respectively<ref>Amino Acids [Internet]. Biology LibreTexts. 2013 [cited 4 December 2018]. Available from: https://bio.libretexts.org/LibreTexts/University_of_California_Davis/BIS_105%3A__Biomolecules_and_Metabolism_%28Murphy%29/Proteins/Amino_Acids#Characteristics</ref>.  
  
Amino acids can also be characterized as [[Polar amino acids|polar]] or [[Non-polar amino acids|non-polar]], these dictate the amino acid function. There are 10 non-polar amino acids, these are found in [[Protein|protein]] core. There are also 10 polar amino acids, these have [[Enzyme|enzymatic]] roles, they 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. These amino acids have to be supplied to the body via digested proteins. 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.  
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Amino Acids are the [[Monomers|monomers]] that make up proteins by joining in [[Condensation Reaction|condensation reactions]] to form [[Peptide bond|peptide bonds]] between themselves. When an Amino Acid is part of a protein it is known as an Amino Acid residue, it has the same side chain but it's alpha Amino and carboxyl groups are now part of peptide bonds. All amino acids have an alpha [[Carboxylic acid|carboxylic acid]] group, an alpha [[Amine|amine]] group and a [[Hydrogen|hydrogen]] atom bonded to a central carbon along with a fourth variable group. This group varies in the 20 essential amino acids and generally allows amino acids to exhibit [[Stereoisomerism|sterioisomerism]] to create [[Optical isomerism|optical isomers]] D and L. The only exception to this being the simplest amino acid [[Glycine|glycine]] with its variable group being another hydrogen atom. This prevents [[Stereoisomerism|sterioisomerism]] as there aren't four different groups then bonded to the central carbon - there is no [[Chiral_centre|chiral centre]]<ref>Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto, Jr., Lubert Stryer, Biochemistry 8th edition Freeman</ref>.&nbsp;
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Amino acids can also be characterised 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 occurring [[Ligans|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|histidine]], [[Leucine|leucine]], [[Isoleucine|isoleucine]], [[Lysine|lysine]], [[Methionine|methionine]], [[Valine|valine]], [[Phenylalanine|phenylalanine]], [[Tyrosine|tyrosine]] and [[Tryptophan|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 such as how serine is synthesised from glycine<ref>Kapalka G. Anxiety Disorders. Nutritional and Herbal Therapies for Children and Adolescents. 2010;:219-258.</ref>.  
  
 
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).  
 
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]]:'''  
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'''The table below lists the 20 Amino acids, their 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"
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{| width="357" style="height: 460px; width: 357px" border="1" cellspacing="1" cellpadding="1"
 
|-
 
|-
 
| '''Amino acid'''  
 
| '''Amino acid'''  
| '''single&nbsp;letter code'''  
+
| '''Single Letter Code'''  
| '''three&nbsp;letter code'''  
+
| '''Three Letter Code'''  
| '''charge'''  
+
|  
| '''polarity'''
+
'''Charge'''  
 +
 
 +
'''(+/-/ neutral)'''
 +
 
 +
| '''Polarity'''
 
|-
 
|-
 
| [[Alanine|alanine]]  
 
| [[Alanine|alanine]]  
 
| A  
 
| A  
| ala
+
| Ala
 
| neutral  
 
| neutral  
 
| nonpolar
 
| nonpolar
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| [[Arginine|arginine]]  
 
| [[Arginine|arginine]]  
 
| R  
 
| R  
| arg
+
| Arg
 
| +ve  
 
| +ve  
 
| polar
 
| polar
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| [[Asparagine|asparagine]]  
 
| [[Asparagine|asparagine]]  
 
| N  
 
| N  
| asn
+
| Asn
 
| neutral  
 
| neutral  
 
| polar
 
| polar
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| [[Aspartate|aspartate]]  
 
| [[Aspartate|aspartate]]  
 
| D  
 
| D  
| asp
+
| Asp
 
| -ve  
 
| -ve  
 
| polar
 
| polar
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| [[Cysteine|cysteine]]  
 
| [[Cysteine|cysteine]]  
 
| C  
 
| C  
| cys
+
| Cys
 
| neutral  
 
| neutral  
 
| polar
 
| polar
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| [[Glycine|glycine]]  
 
| [[Glycine|glycine]]  
 
| G  
 
| G  
| gly
+
| Gly
 
| neutral  
 
| neutral  
 
| nonpolar
 
| nonpolar
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| [[Glutamine|glutamine]]  
 
| [[Glutamine|glutamine]]  
 
| Q  
 
| Q  
| gln
+
| Gln
 
| neutral  
 
| neutral  
 
| polar
 
| polar
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| [[Glutamate|glutamate]]  
 
| [[Glutamate|glutamate]]  
 
| E  
 
| E  
| glu
+
| Glu
 
| -ve  
 
| -ve  
 
| polar
 
| polar
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| [[Histidine|histidine]]  
 
| [[Histidine|histidine]]  
 
| H  
 
| H  
| his
+
| His
 
| +ve  
 
| +ve  
 
| polar
 
| polar
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| [[Isoleucine|isoleucine]]  
 
| [[Isoleucine|isoleucine]]  
 
| I  
 
| I  
| ile
+
| Ile
 
| neutral  
 
| neutral  
 
| nonpolar
 
| nonpolar
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| [[Leucine|leucine]]  
 
| [[Leucine|leucine]]  
 
| L  
 
| L  
| leu
+
| Leu
 
| neutral  
 
| neutral  
 
| nonpolar
 
| nonpolar
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| [[Lysine|lysine]]  
 
| [[Lysine|lysine]]  
 
| K  
 
| K  
| lys
+
| Lys
 
| +ve  
 
| +ve  
 
| polar
 
| polar
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| [[Methionine|methionine]]  
 
| [[Methionine|methionine]]  
 
| M  
 
| M  
| met
+
| Met
 
| neutral  
 
| neutral  
 
| nonpolar
 
| nonpolar
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| [[Phenylalanine|phenylalanine]]  
 
| [[Phenylalanine|phenylalanine]]  
 
| F  
 
| F  
| phe
+
| Phe
 
| neutral  
 
| neutral  
 
| nonpolar
 
| nonpolar
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| [[Proline|proline]]  
 
| [[Proline|proline]]  
 
| P  
 
| P  
| pro
+
| Pro
 
| neutral  
 
| neutral  
 
| nonpolar
 
| nonpolar
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| [[Serine|serine]]  
 
| [[Serine|serine]]  
 
| S  
 
| S  
| ser
+
| Ser
 
| neutral  
 
| neutral  
 
| polar
 
| polar
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| [[Threonine|threonine]]  
 
| [[Threonine|threonine]]  
 
| T  
 
| T  
| thr
+
| Thr
 
| neutral  
 
| neutral  
 
| polar
 
| polar
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| [[Tryptophan|tryptophan]]  
 
| [[Tryptophan|tryptophan]]  
 
| W  
 
| W  
| trp
+
| Trp
 
| neutral  
 
| neutral  
 
| nonpolar
 
| nonpolar
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| [[Tyrosine|tyrosine]]  
 
| [[Tyrosine|tyrosine]]  
 
| Y  
 
| Y  
| tyr
+
| Tyr
 
| neutral  
 
| neutral  
 
| polar
 
| polar
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| [[Valine|valine]]  
 
| [[Valine|valine]]  
 
| V  
 
| V  
| val
+
| Val
 
| neutral  
 
| neutral  
 
| nonpolar
 
| nonpolar
 
|}
 
|}
  
=== '''Amino acid structure''' ===
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= Amino acid structure  =
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All amino acids have a carboxyl terminus (called the C-terminus) and an amino terminus (called the N-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]] (NH<sub>2</sub>). The core amino acid structure is:
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[[Image:Amino acid.jpg|left|325x200px|Amino acid.jpg]]
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Image: See ref<ref>http://www.nutrientsreview.com/proteins/amino-acids</ref>.
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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 its three-dimensional shape. On the [[Peptide|peptide backbone there]] is flexible rotation around the peptide bond and there is a rigid planar peptide which is caused by a partial double bond. This is what allows the [[Polypeptides|polypeptides]] primary sequence to fold to an [[DNA|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.
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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 Levorotatory [[Structural isomerism|L isomer and]] the Dextrotatory 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>.
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Amino acids in solution at neutral pH exist predominantly as dipolar ions, or [[Zwitter Ion|zwitterions]]. In the dipolar form, the [[Amino group|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>. A series of amino acids joined by [[Peptide bond|peptide bonds]] form a [[Polypeptide|polypeptide]] chain, and each amino acid unit in a peptide is called a residue. Two amino acids can undergo a [[Condensation reaction]] to form a dipeptide, accompanied by the loss of a water molecule<ref>http://www.sciencedaily.com/terms/peptide_bond.htm</ref>.
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The common amino acids are grouped according to their side chains<ref>Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science.(Page 127)</ref>. For example, acidic, basic, uncharged polar, and non-polar.
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 +
For basic side chains, the amino acids are: Lysine (K), Arginine (R) and Histidine (H).
 +
 
 +
For acidic side chains, the amino acids are: Aspartic acid (D) and Glutamic acid (E) (formed by the addition of a proton to the amino acids aspartate and glutamate).
 +
 
 +
For uncharged polar side chains, the amino acids are: Asparagine (N), Glutamine (Q), Serine (S), Threonine (T) and Tyrosine (Y).
 +
 
 +
For non-polar side chains, the amino acids are: [[Alanine|Alanine]] (A), [[Valine|Valine]] (V), [[Leucine|Leucine]] (L), [[Isoleucine|Isoleucine]] (I), [[Proline|Proline]] (P), [[Phenylalanine|Phenylalanine]] (F), [[Methionine|Methionine]] (M), [[Tryptophan|Tryptophan]] (W), [[Glycine|Glycine]] (G) and [[Cysteine|Cysteine]] (C).
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 +
=== Proline (P) ===
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 +
[[Proline|Proline]] is also known as an amino acid. which is commonly found in animal proteins. It is not essential to the human diet since it can be synthesized in the body from glutamic acid<ref>glutamic acid</ref>. Unlike other amino acids that exist in the transform in [[POLYPEPTIDES|polypeptides]], proline can exist in the cis-form in peptides. Proline is often found at the end of α helix or in turns or loops<ref>http://www.biology.arizona.edu/biochemistry/problem_sets/aa/proline.html</ref>. Proline is the only cyclic amino acid. This is due to Proline having an odd, cyclic structure when it forms peptide bonds, it induces a bend in the amino acid chain. Therefore, proline is also known as [[Alpha helix|alpha helix]] breaker ( the other alpha helix breaker is [[Glycine|Glycine]])<ref name="khanacademy">https://www.khanacademy.org/test-prep/mcat/biomolecules/amino-acids-and-proteins1/v/special-cases-histidine-proline-glycine-cysteine</ref>.
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=== Amino acids in Translation  ===
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 +
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 by forming peptide bonds between the carboxyl group of one amino acid and the amino group of another via a condensation reaction.&nbsp;This produces a polypeptide chain. The 30S subunit binds to the mRNA first, and the 50S subunit binds second to form the 70S initiator complex<ref>Berg J, Tymoczko J, Stryer L (2007) Biochemistry sixth edition, New York: W. H. Freeman and Company (page 34)</ref>.
  
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>.&nbsp;Amino acids contain both a [[Carboxyl group|carboxyl group]] (COOH) and an [[Amino group|amino group]]&nbsp;(NH<sub>2</sub>). The core amino acid structure is:<br>
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=== Cysteine (C) ===
  
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;NH<sub>2</sub>-----C(H)(R)----COOH
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The amino acid [[Cysteine|Cysteine]] has many applications and plays an important role in [[Protein structure|protein structure]]. This is mainly due to its thiol group. The thiol (made up of a sulphur and hydrogen atom) is very susceptible to [[Oxidation|oxidation]], allowing cysteine to form [[Disulphide bonds|disulphide bonds]] with other molecules including other cysteines. The resulting product of two linked cysteines is called [[Cystine|cystine]]. When bound to other cysteines, the disulphide bond greatly increases the stability of the protein. However, as this is an oxidation reaction, it is exclusive to [[Extracellular|extracellular]] proteins with a few exceptions. This is because the inside of the cell is highly reducing making the disulphide bond highly unstable.
  
where R is the side chain tha differ in all amino acids.
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=== Aromatic Amino acids ===
  
Large amino acids form the rigid region of the polypeptide backbone while the small amino acids form the flexible regions of the polypeptide allowing the protein to fold into it's three dimensional shape. The core of the polypeptide is made up of the hydrophobic amino acids like phenyalanine, tyrosine, and tryptophan.  
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Aromatic Amino acids are the largest of the amino acids and include; phenylalanine (F), tyrosine (Y) and tryptophan (W). They can all absorb ultra-violet light however some can absorb more than others, tyrosine and tryptophan absorb more than phenylalanine meaning that tryptophan is the main molecule which absorbs light in the protein. Aromatic amino acids are also [[Hydrophobic|hydrophobic]] so are located in the core of the protein ensuring they are not near water. Humans cannot synthesize phenylalanine or tryptophan, and can only make tyrosine from phenylalanine, this means that aromatic amino acids are a vital component of our diet as we require them in certain proteins but do not synthesize them ourselves. Aromatic amino acids contain an aromatic ring<ref>University of Arizona. (2003). Aromatic amino acids. Available: http://www.biology.arizona.edu/biochemistry/problem_sets/aa/aromatic.html. Last accessed 1st Dec 2015.</ref>. Phenylalanine deficiency can cause confusion, depression, lack of energy and decreased alertness. It can be bought in a tablet form to supplement any deficiency<ref>Steven D. Ehrlich, University of Maryland Medical Center, http://umm.edu/health/medical/altmed/supplement/phenylalanine, date accessed 18/10/2016</ref>. An inability to break down excess phenylalanine is called Phenylketonuria. To combat this a low phenylalanine diet is used and avoids aspartame sweeteners which resemble phenylalanine and can break down to produce it.  
  
=== References: ===
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=== References  ===
  
<references />J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) ''Biochemistry, ''6th edition, New York: W.H.Freeman and company (page 27)
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<references />

Latest revision as of 11:30, 6 December 2018

Amino acids are the building blocks of proteins - they create the proteins primary structure. There are 20 naturally occurring amino acids. Amino acids exist in proteins as L-optical isomers, however, they can exist as D-isomers in isolated examples, e.g. some bacterial cell walls contain D-isomers. When two amino acids join they form a peptide bond. This bond works as a partial double bond causing the amino acids to have cis/trans isomers. Although most commonly found in trans. All amino acids are amphoteric meaning they can act as both a base and an acid due to their amino and carboyxl groups respectively[1].

Amino Acids are the monomers that make up proteins by joining in condensation reactions to form peptide bonds between themselves. When an Amino Acid is part of a protein it is known as an Amino Acid residue, it has the same side chain but it's alpha Amino and carboxyl groups are now part of peptide bonds. All amino acids have an alpha carboxylic acid group, an alpha amine group and a hydrogen atom bonded to a central carbon along with a fourth variable group. This group varies in the 20 essential amino acids and generally allows amino acids to exhibit sterioisomerism to create optical isomers D and L. The only exception to this being the simplest amino acid glycine with its variable group being another hydrogen atom. This prevents sterioisomerism as there aren't four different groups then bonded to the central carbon - there is no chiral centre[2]

Amino acids can also be characterised as polar or non-polar and these dictate the amino acid function. There are 10 non-polar amino acids found in protein core, and there are 10 polar amino acids. These have enzymatic roles and can be used to bind DNA, metals and other naturally occurring 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[3]. 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[4]. 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 such as how serine is synthesised from glycine[5].

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

The table below lists the 20 Amino acids, their single letter code, three letter code, their charges, and side chain polarity:

Amino acid Single Letter Code Three Letter Code

Charge

(+/-/ neutral)

Polarity
alanine A Ala neutral nonpolar
arginine R Arg +ve polar
asparagine N Asn neutral polar
aspartate D Asp -ve polar
cysteine C Cys neutral polar
glycine G Gly neutral nonpolar
glutamine Q Gln neutral polar
glutamate E Glu -ve polar
histidine H His +ve polar
isoleucine I Ile neutral nonpolar
leucine L Leu neutral nonpolar
lysine K Lys +ve polar
methionine M Met neutral nonpolar
phenylalanine F Phe neutral nonpolar
proline P Pro neutral nonpolar
serine S Ser neutral polar
threonine T Thr neutral polar
tryptophan W Trp neutral nonpolar
tyrosine Y Tyr neutral polar
valine V Val neutral nonpolar

Contents

Amino acid structure

All amino acids have a carboxyl terminus (called the C-terminus) and an amino terminus (called the N-terminus), but they differ in their residual groups. Amino acids are bonded together by a covalent linkage called a peptide bond[6]. Amino acids contain both a carboxyl group (COOH) and an amino group (NH2). The core amino acid structure is:

Amino acid.jpg

Image: See ref[7].

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 allowing the protein to fold into its three-dimensional shape. On the peptide backbone there is flexible rotation around the peptide bond and there is a rigid planar peptide which is caused by a partial double bond. 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 amino acids like phenyalanine, tyrosine, and tryptophan[8]. 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 Levorotatory L isomer and the Dextrotatory D isomer with only the L form of the amino acid isomer present within proteins[9].

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[10]. A series of amino acids joined by peptide bonds form a polypeptide chain, and each amino acid unit in a peptide is called a residue. Two amino acids can undergo a Condensation reaction to form a dipeptide, accompanied by the loss of a water molecule[11].

The common amino acids are grouped according to their side chains[12]. For example, acidic, basic, uncharged polar, and non-polar.

For basic side chains, the amino acids are: Lysine (K), Arginine (R) and Histidine (H).

For acidic side chains, the amino acids are: Aspartic acid (D) and Glutamic acid (E) (formed by the addition of a proton to the amino acids aspartate and glutamate).

For uncharged polar side chains, the amino acids are: Asparagine (N), Glutamine (Q), Serine (S), Threonine (T) and Tyrosine (Y).

For non-polar side chains, the amino acids are: Alanine (A), Valine (V), Leucine (L), Isoleucine (I), Proline (P), Phenylalanine (F), Methionine (M), Tryptophan (W), Glycine (G) and Cysteine (C).

Proline (P)

Proline is also known as an amino acid. which is commonly found in animal proteins. It is not essential to the human diet since it can be synthesized in the body from glutamic acid[13]. Unlike other amino acids that exist in the transform in polypeptides, proline can exist in the cis-form in peptides. Proline is often found at the end of α helix or in turns or loops[14]. Proline is the only cyclic amino acid. This is due to Proline having an odd, cyclic structure when it forms peptide bonds, it induces a bend in the amino acid chain. Therefore, proline is also known as alpha helix breaker ( the other alpha helix breaker is Glycine)[15].

Amino acids in Translation

During the translation of mRNA, amino acids bind to the ribosome as it reads the mRNA and using the information given it produces a specific amino acid sequence by forming peptide bonds between the carboxyl group of one amino acid and the amino group of another via a condensation reaction. This produces a polypeptide chain. The 30S subunit binds to the mRNA first, and the 50S subunit binds second to form the 70S initiator complex[16].

Cysteine (C)

The amino acid Cysteine has many applications and plays an important role in protein structure. This is mainly due to its thiol group. The thiol (made up of a sulphur and hydrogen atom) is very susceptible to oxidation, allowing cysteine to form disulphide bonds with other molecules including other cysteines. The resulting product of two linked cysteines is called cystine. When bound to other cysteines, the disulphide bond greatly increases the stability of the protein. However, as this is an oxidation reaction, it is exclusive to extracellular proteins with a few exceptions. This is because the inside of the cell is highly reducing making the disulphide bond highly unstable.

Aromatic Amino acids

Aromatic Amino acids are the largest of the amino acids and include; phenylalanine (F), tyrosine (Y) and tryptophan (W). They can all absorb ultra-violet light however some can absorb more than others, tyrosine and tryptophan absorb more than phenylalanine meaning that tryptophan is the main molecule which absorbs light in the protein. Aromatic amino acids are also hydrophobic so are located in the core of the protein ensuring they are not near water. Humans cannot synthesize phenylalanine or tryptophan, and can only make tyrosine from phenylalanine, this means that aromatic amino acids are a vital component of our diet as we require them in certain proteins but do not synthesize them ourselves. Aromatic amino acids contain an aromatic ring[17]. Phenylalanine deficiency can cause confusion, depression, lack of energy and decreased alertness. It can be bought in a tablet form to supplement any deficiency[18]. An inability to break down excess phenylalanine is called Phenylketonuria. To combat this a low phenylalanine diet is used and avoids aspartame sweeteners which resemble phenylalanine and can break down to produce it.

References

  1. Amino Acids [Internet]. Biology LibreTexts. 2013 [cited 4 December 2018]. Available from: https://bio.libretexts.org/LibreTexts/University_of_California_Davis/BIS_105%3A__Biomolecules_and_Metabolism_%28Murphy%29/Proteins/Amino_Acids#Characteristics
  2. Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto, Jr., Lubert Stryer, Biochemistry 8th edition Freeman
  3. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg650.
  4. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg650.
  5. Kapalka G. Anxiety Disorders. Nutritional and Herbal Therapies for Children and Adolescents. 2010;:219-258.
  6. Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. (Page 59)
  7. http://www.nutrientsreview.com/proteins/amino-acids
  8. J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) Biochemistry, 6th edition, New York: W.H.Freeman and company (page 27).
  9. Berg J. Tymoczko J. Stryer L., Biochemistry Sixth Edition (2007, WH Freeman, New York (page 27)
  10. J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) Biochemistry, 6th edition, New York: W.H.Freeman and company (page 27)
  11. http://www.sciencedaily.com/terms/peptide_bond.htm
  12. Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science.(Page 127)
  13. glutamic acid
  14. http://www.biology.arizona.edu/biochemistry/problem_sets/aa/proline.html
  15. https://www.khanacademy.org/test-prep/mcat/biomolecules/amino-acids-and-proteins1/v/special-cases-histidine-proline-glycine-cysteine
  16. Berg J, Tymoczko J, Stryer L (2007) Biochemistry sixth edition, New York: W. H. Freeman and Company (page 34)
  17. University of Arizona. (2003). Aromatic amino acids. Available: http://www.biology.arizona.edu/biochemistry/problem_sets/aa/aromatic.html. Last accessed 1st Dec 2015.
  18. Steven D. Ehrlich, University of Maryland Medical Center, http://umm.edu/health/medical/altmed/supplement/phenylalanine, date accessed 18/10/2016
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