Amino acids: Difference between revisions
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=== '''Amino acid structure''' === | === '''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]] (NH<sub>2</sub>). The core amino acid structure is:<br> | 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:<br> | ||
NH<sub>2</sub>-----C(H)(R)----COOH | NH<sub>2</sub>-----C(H)(R)----COOH | ||
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where (R) is the side chain unique to each different amino acid. | 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 backbone there is flexible rotation around the peptide bond and there is rigid planar peptide which is caused by 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|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. | 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 backbone there is flexible rotation around the peptide bond and there is rigid planar peptide which is caused by 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|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 [[Structural isomerism|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 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 [[Structural isomerism|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>. | ||
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=== Proline === | === Proline === | ||
[[Proline|Proline]] is also known as imino acid. Unlike other amino acids that exist in the trans-form 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.<ref>http://www.biology.arizona.edu/biochemistry/problem_sets/aa/proline.html</ref> Proline is the only cyclic amino acid. Because Proline has an odd, cyclic structure, when it forms peptide bonds, it induces a bend into the amino acid chain. Therefore, proline is also known as [[ | [[Proline|Proline]] is also known as imino acid. Unlike other amino acids that exist in the trans-form 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.<ref>http://www.biology.arizona.edu/biochemistry/problem_sets/aa/proline.html</ref> Proline is the only cyclic amino acid. Because Proline has an odd, cyclic structure, when it forms peptide bonds, it induces a bend into 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> | ||
=== Amino acids in Translation === | === Amino acids in Translation === | ||
Revision as of 12:25, 4 December 2015
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. When two amino acids join they form a peptide bond. This bond works as a partial doluble bond causing the amino acids to have cis/trans isomers. Although most commonly found in trans.
Amino acids can also be characterized 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 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 [1]. 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[2]. 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 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:
| Amino acid | single letter code | three letter code | charge | 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 |
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 [3]. Amino acids contain both a carboxyl group (COOH) and an 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 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 rigid planar peptide which is caused by 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 [4]. 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 [5].
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 [6].
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 moelcule. [7]
The common amino acids are grouped according to their side chains.[8] For example, acidic, basic, uncharged polar, and non-polar.
For basic side chains, the amino acids are: Lysine, Arginine and Histidine.
For acidic side chains, the amino acids are: Aspartic acid and Glutamic acid (formed by the addition of a proton to the amino acids aspartate and glutamate).
For uncharged polar side chains, the amino acids are: Asparagine, Glutamine, Serine, Theonine and Tyrosine.
For non-polar side chains, the amino acids are: Alanine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Methionine, Tryptophan, Glycine and Cysteine.
Proline
Proline is also known as imino acid. Unlike other amino acids that exist in the trans-form 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.[9] Proline is the only cyclic amino acid. Because Proline has an odd, cyclic structure, when it forms peptide bonds, it induces a bend into the amino acid chain. Therefore, proline is also known as alpha helix breaker ( the other alpha helix breaker is Glycine)[10]
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 producing a polypeptide chain. The 30S subunit binds to the mRNA first, and the 50S subunit binds second to form the 70S initiatior complex [11].
Cysteine
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, tyrosine and tryptophan. 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.[12]
References
- ↑ Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg650.
- ↑ Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg650.
- ↑ Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. (Page 59)
- ↑ J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) Biochemistry, 6th edition, New York: W.H.Freeman and company (page 27).
- ↑ Berg J. Tymoczko J. Stryer L., Biochemistry Sixth Edition (2007, WH Freeman, New York (page 27)
- ↑ J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) Biochemistry, 6th edition, New York: W.H.Freeman and company (page 27)
- ↑ http://www.sciencedaily.com/terms/peptide_bond.htm
- ↑ Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science.(Page 127)
- ↑ http://www.biology.arizona.edu/biochemistry/problem_sets/aa/proline.html
- ↑ https://www.khanacademy.org/test-prep/mcat/biomolecules/amino-acids-and-proteins1/v/special-cases-histidine-proline-glycine-cysteine
- ↑ Berg J, Tymoczko J, Stryer L (2007) Biochemistry sixth edition, New York: W. H. Freeman and Company (page 34)
- ↑ University of Arizona. (2003). Aromatic amino acids. Available: http://www.biology.arizona.edu/biochemistry/problem_sets/aa/aromatic.html. Last accessed 1st Dec 2015.