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Ribosome

2015-10-22T14:02:12Z

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A ribosome<ref>http://www.proteopedia.org/wiki/index.php/Ribosome</ref> is the particle upon which [[MRNA|mRNA]] from [[DNA|DNA]] [[Transcription|transcription]] is translated to a [[Polypeptide|polypeptide]] with a specific [[Amino acid|amino acid]] sequence defined by the genetic code. The size of the ribosome in eukaryotes and prokaryotes are slightly different. Prokaryotes has a 70S ribosome that is comprised of 2 subunits:

30S unit: This is the smaller unit which consists of 21 [[Proteins|proteins]] and a [[16S RNA molecule|16S RNA molecule]] . It is involve in initiating translation by selecting a AUG or alternative start codon via the 30S ribosomal subunit. This acts as the starting point for the rest of the translation process.

50S unit: This is the larger unit which consists of 34 [[Proteins|proteins]] and 2 RNA molecules, 23S and 5S <ref>Berg JM, Tymoczko JL, Stryer L: Biochemistry 6th (2007), WH Freeman and Company, New York. Pg 866</ref>

The 2 units together form the complete ribosome, known as the 70S unit. S refers to the [[Svedberg unit|Svedberg unit]], which is a measure of rate at which a compound moves when centrifuged. It is used as a measure of size of a molecule but is not directly proportional to molecular weight <ref>Berg JM, Tymoczko JL, Stryer L: Biochemistry 6th (2007), WH Freeman and Company, New York. Pg 76</ref>.

As ribosomes contain [[RNA|RNA]] (also referred to as [[RRNA|ribosomal RNA]]-[[RRNA|rRNA]]) and [[Proteins|proteins]], they are also referred to as [[Ribonucleoproteins|ribonucleoproteins]]. Ribosomes translate [[MRNA|mRNA]] in triplets ([[Codon|codons]]) by aligning complementary triplets found in [[TRNA|tRNA]] molecules ([[Anticodons|anticodons]]). Each [[TRNA|tRNA]] is assigned a specific anticodon and [[Amino acid|amino acid]] and therefore translation leads to the formation of a [[Protein|protein]] by forming [[Peptide bonds|peptide bonds]] between adjacently aligned [[Amino acids|amino acids]] <ref>Berg JM, Tymoczko JL, Stryer L: Biochemistry 6th (2007), WH Freeman and Company, New York. Pg 872</ref>.

Ribosomes have three [[TRNA|tRNA]] binding sites in the 30S subunit - the A-site ([[Aminoacyl|aminoacyl]] site), the P-site ([[Peptidyl|peptidyl]] site) and the E-site (empty site) - which allow peptide bonds to form between adjacent [[Amino acids|amino acids]]. They are in order A, P, E from the 3' to 5' end or the [[MRNA|mRNA]] strand and are involved in the elongation process of [[Translation|translation]]. The first charged tRNA attaches to the start [[Codon|codon]] in the P-site and is joined by a second, charged tRNA molecule adjacent in the A-site. A peptide bond forms between the two amino acids and the first amino acid is released from its tRNA. The uncharged tRNA moves along into the E-site, whilst the second charged tRNA moves from the A-site and into the P-site. The A-site becomes occupied by the next charged tRNA molecule. This process continues and the polypeptide continues to grow until complete and termination occurs<ref>Berg JM, Tymoczko JL, Stryer L. Biochemistry 7th ed.(2012), WH Freeman and Company, New York. Pg 934</ref>.

Ribosomes are small structures found in all living cells. They can be free in the [[Cytoplasm|cytoplasm]] or attached to [[Endoplasmic Reticulum|endoplasmic reticulum]] (ER), making [[Rough Endoplasmic Reticulum|Rough ER]]. They can differ in size and number, according to whether they are found in [[Bacteria|bacteria]], [[Archaea|archaea]] or in [[Eukaryotes|eukaryotes]]. There are a large number of ribosomes in cells. In [[Eukaryotes|eukaryotes]], there can be millions in one cell alone. As ribosomes are so small, (it has a diameter of 25-30 nm approximately) <ref>Becker, Wayne M., Kleinsmith, Lewis J., Hardin, Jeff., Bertoni, Gregory Paul. (2009) The World of the Cell, 7th Edition, San Francisco: Pearson Benjamin Cummings. P95.</ref>, an [[Electron Microscope|electron microscope]] is needed to see it. Ribosomes are made up of two subunits, one larger than the other. The two subunits join together when attached to [[MRNA|mRNA]] to make a [[Protein|protein]] in [[Protein synthesis|protein synthesis]]. Ribosomes are also found in [[Mitochondria|mitochondria]] and [[Chloroplasts|chloroplasts]] and carry out [[Protein synthesis|protein synthesis]], specifically for these [[Organelles|organelles]].

=== References ===

<references />

Enzyme

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Enzymes are biological macromolecule also known as protein. It <ref>Molecular Biology of the Cell 5th ed (2007) Alberts et.al. 159-169</ref> act as specific [[Catalysts|catalysts]] and is very sensitive to changes in the chemical and physical environment. That is to say each enzyme accelerates one or more specific chemical reactions without affecting the final [[Equilibrium|equilibrium]] concentrations of reactants and products, in addition the enzyme is never used up during the reaction it catalyses, and so is always available to catalyse more of the same reaction if needed. In [[Thermodynamics|thermodynamic]] language, enzymes reduce the [[Activation energy|activation energy]] of a reaction but do not affect the [[Free energy|free energy]] change of the overall reaction. Many enzymes are so effective that they will [[Catalyse|catalyse]] intracellular reactions which are too slow to be observed at all under comparable conditions in the absence of enzyme catalysis. Enzyme make and break covalent bond in a cell. It increases the reaction rate to 106 - 1012 times faster. Enzymes are often highly specific, both for the [[Molecule|molecules]] they will accept as [[Substrate|substrates]] and for the precise chemical changes that they will catalyse, and the presence of active enzymes is essential to form most of the [[Molecule|molecules]] in the [[Cell|cell]].In general, an enzyme regulates the biochemical reaction pathway. 

Enzyme reactions can be either [[Anabolic|anabolic]] or [[Catabolic|catabolic]] in nature <ref>Nigel P. O. Green (1989). Biological Science. 2nd ed. Cambridge: Cambridge University Press. p.167.</ref>.  

Enzymes and substrates must first interact to form an [[Enzyme-substrate complex|enzyme-substrate complex]] before any reaction can occur. This happens through molecular motions where all of the molecules in a cell are constantly moving and colliding; however only a few collisions will result in a reaction. Enzymes will remain unchanged after catalysing the reaction. The rate of encounter between the enzyme and the substrate is primarily dependant on the concentration on the substrate; meaning that, to increase the enzyme activity you must increase the substrate concentration. 

=== The mechanism of Enzyme Action: ===

Enzymes increase the rate of reaction between 2 reactants in various possible ways:

*They improve the Proximity of the substrate being that they increase the local concentration of the substrate
*They affect the orientation and hold the [[Atom|atoms]] in positions that favour the reaction
*They produce strain distortion; they put strains on the bonds that are associated with the reaction
*In acid-base catalysis they aid in the exchange of H+ or generation of –OH <ref>Molecular Biology of the Cell 5th ed (2007) Alberts et.al. 159-169</ref>
*They provide an alternative route of reaction with a lower activation energy

=== Specificity ===

Enzymes are specific to the point of being able to distinguish between optical isomers.

The [[Amino acids|amino acids]] forming the active site mainly determine the specificity of the enzyme; a change in only a few [[Amino acids|amino acids]] in this region can result in a large change in the shape of the active site and this could then vastly change to affinity for the substrate or even change the substrate the enzyme is specific for. 

The specificity of enzymes is exhibited in the ‘Lock and Key’ mechanism: 

 

[[Image:Lock and key.jpg]] 

 

Taken from [http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=stryer&part=A1031 http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=stryer&part=A1031] <ref>http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=stryer</ref>

This illustrates the Lock and Key mechanisms and how the shape of the substrate is exactly complememtary to the shape of the active site. However the lock and key model doesn't fully explain enzymatic activity. The model indicates that the enzyme and substrate are unable to change shape.

A modification to the Lock and Key Model of enzymes is the Induced Fit Hypothesis, also known as the "Hand-shake Model" <ref>http://www.portlandpress.com/pp/books/online/glick/searchresdet.cfm?Term=induced-fit%20theory%20%28rack%20model%29</ref>. This hypothesis states that the structure of both the enzyme and substrate can change on binding. In essence the enzyme can wrap itself around the substrate molecule, untill the substrate is completley bound. This produces an enzyme-substrate complex, which places strain on a particular bond, therefore weakening said bond; to a point where it can interact with the enzyme amino acid groups, further non-organic groups or further bound substrates.

The change in the shape of the enzyme is known as a conformational change; the purpose of which is two fold:

#As mentioned above, the conformational change places strain on the desired bond, allowing for a more efficient reaction to take place,
#The new conformation brings amino acid groups essential to the enzyme reaction, which in the unbound conformation may distant from the active site, into the active site. These groups ensure the catalytic reaction will be optimal <ref>The World of the Cell, 3rd Edition, (1996) Becker et.al. p146, p147</ref>. The most common groups to be brought into the Active Site of the Enzyme are those relating to Acid/Base chemistry - therefore promoting the reaction and ensuring optimal conditions <ref>The World of the Cell, 3rd Edition, (1996) Becker et.al. p146</ref>.

=== Substrates and the Active Site ===

Whether an enzymatic reaction will occur is dependant on the substrate colliding and binding to the active site. Once a substrate binds onto the active site, it is held there by a variety of interactions. These interactions take place between charged residual groups of the amino acids in the conformed active site. Hydrogen Bonds and Ionic bonds generally occur - however they are very weak. These weak interactions are of the order of '''3 - 12 kcal mol-1 (12.5 - 50.2 kJ mol''''''-1'''''') '''<ref>Royal Society of Chemistry [RSC]fckLRfckLRhttp://www.rsc.org/ebooks/archive/free/SP9780851869209/SP9780851869209-FP015.pdf</ref> this is of the order of 1/10th the strength of an, on average, single covalent bond <ref>The World of the Cell, 3rd Edition, (1996) Becker et.al. p146</ref>. 

This ensures that enzyme-substrate formation is a reversible process.

=== Allostery ===

An allosteric enzyme couples the effector levels to enzyme activity; it couples signal to functionality. Allosteric enzymes have multiple binding sites (allosteric sites) and show cooperative binding <ref>J.Mol.Biol. (2004) 336, 263-273</ref>.

Allosteric control of enzymes can be positive or negative and can have effects such as up regulate or down regulate activity.

Types of Allosteric control:

#Homotropic - The modulator is a substrate for the target enzyme aswell as the egulator e.g. Oxygen acting on Haemoglobin.
#Heterotropic - The modulator is the regulatory molecule but is not also the enzymes substrate. 

=== Enzyme Types ===

There are many enzymes used in labs, each has it's own unique active site and so will catalyse a specific reaction. Restriction enzymes are one type of enzymes that are frequently used.

Restriction [[Endonucleases|endonucleases]] are used naturally in a wide range of [[Prokaryotes|prokaryotes]] as a self-defence mechanism against foreign [[DNA|DNA]] [[Molecule|molecules]].  The prokaryotes own [[DNA|DNA]] is methylated so it will not be cut by the enzyme.They recognise a specific 4-8 base pair [[Palindromic sequence|palindromic sequence]] and by carrying out a hydrolysis reaction cut at that specific point. They may cut to form a blunt end or a sticky end. A blunt end is when the enzyme cut the [[DNA|DNA]] symmetrically. Asymmetrical cleavage leaves sticky end, these are unpaired bases. These sticky end can anneal to complementary bases on another strand <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman</ref>. 

=== Kinetics ===

Kinetic parameters:

Two important enzyme parameters in a simple enzyme catalysed reaction are the [[Michaelis-Menten constant|Michaelis-Menten constant]] ([[Michaelis-Menten constant|K]][[Michaelis-Menten constant|m]]) and the [[Maximum reaction|maximum reaction]] velocity ([[Maximum reaction|V]][[Maximum reaction|max]])

*Km is the approximate measure of the enzyme affinity for the substrate. This can be calculated from the graph as ½ Vmax. Generally a lower Km value signifies a higher affinity for the substrate.
*Kd is the dissociation constant for substrate binding to enzyme
*Kcat is the turnover number for the enzyme
*Vmax is the maximal activity of the enzyme when all of the active sites are saturated.

The michaelis-menten equation:

 V = Vmax [S]/Km [S]

 To obtain Vmax and Km the enzyme activity must be recorded and then plotted on a double reciprocal plot, a [[Lineweaver-Burk plot|Lineweaver-Burk plot]], and the Michaelis Menten equation is then rearranged to look like this: 1/V = (Km/Vmax)(1/S)+1/Vmax <ref>Molecular Biology of the Cell 5th ed (2007) Alberts et.al. 159-169</ref>.

[[Image:350px-Lineweaver-Burke plot svg.png]] 

Taken from [http://www.search.com/reference/Lineweaver-Burk_plot www.search.com/reference/Lineweaver-Burk_plot] <ref>http://www.search.com/reference/Lineweaver-Burk_plot</ref> A Lineweaver-Burk plot showing all the necessary parameters. 

=== Inhibition ===

Enzymes can be inhibited by denaturing which is when a protein is changed in structure to form a randomly coiled peptide which exhibits none of its usual functions. Denaturing can result from extreme temperatures and [[PH|pHs]], as these alter the bonding in the molecule.

Inhibition can also be initiated by the binding of specific molecules called inhibitors. These can be split into categories:

#Irreversible Inhibitors are molecules that permanently bind to the enzyme's active site or specific side chain, commonly to the serine (CH2OH) or cysteine (CH2SH) by [[Covalent|covalent]] bonds. Thsi inactivates the enzyme so the substrate cannt bind.
#Competitive Inhibitors are competing molecules that will have a very similar structure to that of the natural substrate and thus will be complementary to the enzyme active site. Vmax stays the same, but Km increases This type of inhibition can be overcome by an increase in substrate concentration.
#Non-competitive inhibitors bind to a region on the enzyme other than the active site, causing changes to enzyme shape resulting in disruption of the active site. This decreases the turnover number of the enzyme rather than preventing substrate binding- Vmax decreases but Km stays the same. This cannot be overcome with an increase in substrate concentration.
#Uncompetitive inhibitors only bind to an enzyme-substrate complex; so both Km and Vmax decreaae as it takes longer for the substrate to leave the active site. This also cannot be overcome by an increase in substrate concentration. We are able to distinguish the types of inhibition occurring by looking at the graph of enzyme activity <ref>Biochemistry 6th (2006) Stryer et.al. pg51</ref>.

[[Image:Inhibitor graph.jpg]] Taken from [http://ibhow.files.wordpress.com/2010/06/7-6-4.jpg?w=399&h=275 http://ibhow.files.wordpress.com/2010/06/7-6-4.jpg?w=399&h=275] <ref>http://ibhow.files.wordpress.com/2010/06/7-6-4.jpg?w=399&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;h=275</ref>

Competative Inhibitors show the same Vmax value however we see an increased Km value and non-competitive inhibitors show a decreased Vmax but the same Km. 

=== Targets for drug action ===

We are able to exploit these mechanisms of inhibition to engineer drugs with therapeutic effects. By targeting an enzyme in drug therapy we have the ability to change whole metabolic reactions that are catalysed by that particular enzyme. We can investigate possible new drugs by exploring drug-reaction interactions and drug-pathway interactions <ref>BMC Bioinformatics 2010, 11:501</ref>.  Some examples of Drug Inhibitors:

*Irreversible drug inhibitors: [[Penicillin|Penicillin]] the antibiotic which inhibits transpeptidate in bacteria rendering them unable to synthesise cell walls. Aspirin which decreases the inflammatory response by inhibiting Cyclooxegenase.
*[[Competitive inhibitors|Competitive inhibitors]]: Methotrexate which inhibits dihydrofolate reductase which is involved in the synthesis of [[Purine|purines]] and [[Pyrimidine|pyrimidines]].
*[[Non-competative inhibitor|Non-competitive inhibitor]]: NNRT1 in the treatment of HIV <ref>Biochemistry 6th (2006) Stryer et al.</ref>. 

=== References ===

<references />

Neuraminidase

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140662665: Created page with "Neuraminidase works by removing neuramic acid residue from the surface of the host cell to ease the release stage of the life cycle. This happens when new virions needs to be rel..."

Neuraminidase works by removing neuramic acid residue from the surface of the host cell to ease the release stage of the life cycle. This happens when new virions needs to be release out of the cell to infect new cells.

Myoglobin

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Myoglobin is a compact globular protein consisting of just 153 [[Amino acids|amino acids]]. It is known to have the tertiary structure of protein as it is made up of 1 subunit. The single polypeptide is found in [[Muscle|muscles]] and provides vital stores of [[Oxygen|oxygen]] to the muscle cells when required. Myoglobin, like [[Haemoglobin|haemoglobin]], has a haem group which contains iron and bind to oxygen.[[Haem group|Haem group]] This iron in the haem group gives muscle its red colour. The [[Alpha-helix|alpha helical]] 3D structure of the protein was one of the first to be discovered by John Kendrew who studied myoglobin in sperm whales using [[X-ray crystallography|x-ray crystallography]].

Secondary structure

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Hydrogen bond formation causes the protein secondary structure to be stabilise.There are two main forms of protein secondary structure, the [[Alpha-helix|alpha helix ]] and the [[Beta sheet|beta sheet]], however other forms such as the beta turn and the omega loop are known to exist <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>.

== Alpha helix ==

The structure of the alpha helix, first predicted by Pauling and Corey in 1951 <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>, consists of a coiled helical structure held together by [[Hydrogen bonds|hydrogen bonds ]]<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The helix can be left or right handed, coiling in an anticlockwise or clockwise direction respectively; however the right handed configuration is more energetically favourable due the fact that the side chains of the peptide backbone do not interfere with each other as much <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds that stabilise the structure are formed between the carbonyl oxygen (CO group) of the nth residue and the amide hydrogen (NH group) of the n+4th residue <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. A turn of the helix consists of 3.6 amino acid residues and the rise from one residue to the next is approximately 1.5A<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. 

When it was discovered, the alpha helix was found in the protein α-keratin, which is abundant in skin and its derivatives- hair, nails and horns. Short regions of alpha helix are mainly present in proteins that are embedded in cell membranes such as transport proteins and receptors.<ref> Alberts B., Bray D., Hopkin K., Johnson A., Lewis J., Roff M., Roberts K., Walter P. (2013), Essentials Cell Biology, 4th edition, New York: Garland Science. page 132 </ref>

Sometimes two or three alpha helices will wrap around one another to form a particularly stable structure known as a coiled-coil. This structure forms when the alpha helices have most of their nonpolar side chains on one side so that they can twist around each other with these side chains facing inward- minimizing their contact with the aqueous cytosol. Long, rodlike coiled-coils form the structural framework for many elongated proteins. Examples include α-keratin, which forms the intracellular fibres that reinforce the outer layer of the skin, and [[Myosin]], the motor protein responsible for muscle contraction. <ref> Alberts B., Bray D., Hopkin K., Johnson A., Lewis J., Roff M., Roberts K., Walter P. (2013), Essentials Cell Biology, 4th edition, New York: Garland Science. page 133-134 </ref>

== Beta sheet ==

The beta sheet is the other main secondary structure of proteins, beta sheets are made up of two or more peptide chains called beta strands <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. Hydrogen bonds are formed between two adjacent beta strands <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The side chains of the amino acid residues point out perpendicularly in opposite directions (up and down) to the plain of the peptide backbone of the beta strands<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. 

There are two types of beta sheets, anti-parallel and parallel. Anti parallel beta sheets are formed from adjacent beta strands running in an alternating configurations, if beta strand n runs from the N terminus to the C terminus the beta strand n+1 runs from the C terminus to the N terminus and the strands of the beta sheet alternate in that manner <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds are formed between the amide hydrogen (NH group) and the carbonyl oxygen (CO group) of one beta strand and the carbonyl oxygen (CO group) and the amide hydrogen (NH group) of the adjacent strand respectively <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds in an anti-parallel beta sheet are short and straight making them strong <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The parallel beta sheets are formed from adjacent beta strands running in the same configuration, if beta strand n runs from the N terminus to the C terminus then beta strand n+1 also runs from the N terminus to the C terminus <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds are formed between the amide hydrogen (NH group) of an amino acid residue on beta strand n and the carbonyl oxygen (CO group) of the adjacent strand beta strand, n+1 <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The carbonyl oxygen (CO group) of beta strand n forms hydrogen bonds with the amide hydrogen (NH group) of the amino acid residue two residues further down on the adjacent strand<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds in parallel beta strands are long and angled making them weaker than those found in anti-parallel beta sheet <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>.

== References ==

<references />

Secondary structure

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<ref name="hydrogen bond" /> formation causes the protein secondary structure to be stabilise.There are two main forms of protein secondary structure, the [[Alpha-helix|alpha helix ]] and the [[Beta sheet|beta sheet]], however other forms such as the beta turn and the omega loop are known to exist <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>.

== Alpha helix ==

The structure of the alpha helix, first predicted by Pauling and Corey in 1951 <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>, consists of a coiled helical structure held together by [[Hydrogen bonds|hydrogen bonds ]]<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The helix can be left or right handed, coiling in an anticlockwise or clockwise direction respectively; however the right handed configuration is more energetically favourable due the fact that the side chains of the peptide backbone do not interfere with each other as much <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds that stabilise the structure are formed between the carbonyl oxygen (CO group) of the nth residue and the amide hydrogen (NH group) of the n+4th residue <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. A turn of the helix consists of 3.6 amino acid residues and the rise from one residue to the next is approximately 1.5A<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. 

When it was discovered, the alpha helix was found in the protein α-keratin, which is abundant in skin and its derivatives- hair, nails and horns. Short regions of alpha helix are mainly present in proteins that are embedded in cell membranes such as transport proteins and receptors.<ref> Alberts B., Bray D., Hopkin K., Johnson A., Lewis J., Roff M., Roberts K., Walter P. (2013), Essentials Cell Biology, 4th edition, New York: Garland Science. page 132 </ref>

Sometimes two or three alpha helices will wrap around one another to form a particularly stable structure known as a coiled-coil. This structure forms when the alpha helices have most of their nonpolar side chains on one side so that they can twist around each other with these side chains facing inward- minimizing their contact with the aqueous cytosol. Long, rodlike coiled-coils form the structural framework for many elongated proteins. Examples include α-keratin, which forms the intracellular fibres that reinforce the outer layer of the skin, and [[Myosin]], the motor protein responsible for muscle contraction. <ref> Alberts B., Bray D., Hopkin K., Johnson A., Lewis J., Roff M., Roberts K., Walter P. (2013), Essentials Cell Biology, 4th edition, New York: Garland Science. page 133-134 </ref>

== Beta sheet ==

The beta sheet is the other main secondary structure of proteins, beta sheets are made up of two or more peptide chains called beta strands <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. Hydrogen bonds are formed between two adjacent beta strands <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The side chains of the amino acid residues point out perpendicularly in opposite directions (up and down) to the plain of the peptide backbone of the beta strands<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. 

There are two types of beta sheets, anti-parallel and parallel. Anti parallel beta sheets are formed from adjacent beta strands running in an alternating configurations, if beta strand n runs from the N terminus to the C terminus the beta strand n+1 runs from the C terminus to the N terminus and the strands of the beta sheet alternate in that manner <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds are formed between the amide hydrogen (NH group) and the carbonyl oxygen (CO group) of one beta strand and the carbonyl oxygen (CO group) and the amide hydrogen (NH group) of the adjacent strand respectively <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds in an anti-parallel beta sheet are short and straight making them strong <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The parallel beta sheets are formed from adjacent beta strands running in the same configuration, if beta strand n runs from the N terminus to the C terminus then beta strand n+1 also runs from the N terminus to the C terminus <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds are formed between the amide hydrogen (NH group) of an amino acid residue on beta strand n and the carbonyl oxygen (CO group) of the adjacent strand beta strand, n+1 <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The carbonyl oxygen (CO group) of beta strand n forms hydrogen bonds with the amide hydrogen (NH group) of the amino acid residue two residues further down on the adjacent strand<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds in parallel beta strands are long and angled making them weaker than those found in anti-parallel beta sheet <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>.

== References ==

<references />

Hydrogen bonds

2014-11-27T23:16:59Z

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A [[Hydrogen|hydrogen]] bond is an attraction between a [[Hydrogen|hydrogen]] atom and an [[Electronegative|electronegative]] atom, with the most common ones being [[Nitrogen|nitrogen]] (N), [[Oxygen|oxygen]] (O) or [[Fluorine|fluorine]] (F). Hydrogen bonds appear frequently within biological molecules and exist in [[Compound|polar compounds]]. A common example of this is [[Water|water]], where the attractive interaction exists between the [[Oxygen|oxygen]] and [[Hydrogen|hydrogen]] atoms. [[Hydrogen|Hydrogen]] bonding is a type of [[Intermolecular|intermolecular]] force, where the Hydrogen bond is found between different [[Molecule|molecules]], or [[Intramolecular|intramolecular]], where the bond exists between different parts of the same [[Molecule|molecule]] <ref>http://www.chemguide.co.uk/atoms/bonding/hbond.html</ref>.

A [[Hydrogen|hydrogen]] bond is a non-covalent bond; they have much stronger attractions than [[Van der waals forces|Van der Waals forces]] and [[Permanent dipole - permanent dipole interactions|permanent dipole-dipole interactions]], but are weaker than [[Ionic bonding|ionic bonding or]] [[Covalent bonding|covalent bonding]]. Evidence for [[Hydrogen|hydrogen]] bonding can be found when comparing the [[Boiling point|boiling points]] of [[Hydrogen|hydrogen]] molecules across groups 5, 6 and 7 of the [[Periodic table|periodic table]]. The compounds where [[Hydrogen|hydrogen]] bonding is present produce a much higher [[Boiling point|boiling point]] as [[Hydrogen|hydrogen]] bonds require more energy to be broken than [[Van der waals forces|Van der Waals forces]] <ref>http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/H/HydrogenBonds.html</ref>.

The distance between two parts of the same [[Molecule|molecule]], or different [[Molecule|molecules]], can vary and this has an effect on the strength of the hydrogen bond. This why the hydrogen bonds are said to be "elastic," the greater the distance between the [[Hydrogen|hydrogen]] [[Atom|atom]] and the electronegative atom the longer the hydrogen bond will be and this results in a weaker hydrogen bond.

A hydrogen bond can be defined as the polar interaction between an electronegative atom ([[Nitrogen]], [[Oxygen|oxygen]] or [[Fluorine|fluorine]]) and a hydrogen atom which is covalently bonded to another electronegative atom that is on the same molecule, or on a different molecule. The bond is strongest when all three of these atoms are arranged in such a way that their bond angles are at a value of 180 degrees. 

Hydrogen bonding is extremely prevalent throughout nature and can be found in [[Water|water]], [[DNA|DNA]] base-pair interactions, protein folding, [[Protein|protein]] structure and protein-ligand binding.

Hydrogen bond formation is due to the attraction of different elements which has variety of electron. The electronegativity series is O > N > C = H.

=== Water ===

A water molecule consists of one oxygen atom attached to two [[Hydrogen|hydrogen]] [[Atom|atoms]]. A hydrogen bond can be formed between two [[Molecules|molecules]] of [[Water|water]] due to the 'unequal distribution of electrons within a water molecule' <ref>Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. p55</ref>. The oxygen has a strong attraction for the electrons and has a negative charge, whereas the hydrogen only has a weak attraction and therefore has a slight positive charge. When these two oppositely-charged regions come close to each other, the result is a hydrogen bond <ref>Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. p55</ref>.

Although water has a low molecular mass, it has an unusually high boiling point. This property can be attributed to the large amount of hydrogen bonds that exists within water. Since these bonds are difficult to break, water’s melting and boiling points are relatively high in comparison to other liquids that are similar but lack the hydrogen bonding.

Another unusual property of water is it has a higher density than it's solid counterpart - ice. This is due to the unique formation of the hydrogen bonds forming a lattice structure whreby the strength and relative regidity of the bonds allows for greater seperation betweeen molecules than in its liquid form where the molecules interact at a greater velocity. 

=== DNA ===

In the [[DNA helix|DNA helix]],the bases: [[Adenine|adenine]], [[Cytosine|cytosine]], [[Thymine|thymine]] and [[Guanine|guanine]] are each linked with their complementary base by hydrogen bonding. Adenine pairs with thymine with 2 hydrogen bonds. Guanine pairs with cytosine with 3 hydrogen bonds.<ref>J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) Biochemistry, 6th edition, New York: W.H.Freeman and company p112</ref>This creates a difference in strength between the two sets of Watson and Crick bases. Guanine and cytosine bonded base pairs are stronger then thymine and adenine bonded base pairs in DNA. This difference in strength is because of the difference in number of hydrogen bonds. This allows researchers to figure out the base content of DNA by observing at what temperature it denatures. The higher the temperature at which DNA denatures the more guanine and cytosine base pairs are present. this variation in the number of hydrogen bonds a nucleic base can make in a watson crick base pair is also pertenant for the designing of primers for [[Polymerase Chain Reaction (PCR)|PCR]]. To ensure both primers anneal proportionally to their binding sites they must be designed such that they produce hydrogen bonds of similar affinity. The greater strength of hydrogen bonding between guanine and cytosine is also utilised during PCR primer design to ensure that primers is thoroughly bound to the target DNA at it's 3' end so that the polymerase can begin reading in the 3' to 5' direction. The inclusion of guanine or cytosine at the 3' end of a primer is known as a GC clamp. 

Protein

*An alpha-helix contains hydrogen bonds that is form between the carbonyl oxygen on residue N to the amide nitrogen on residue N + 4. In an alpha-helix structure there is 3.6 residue per turn. each of the side chains point outwards, 100 degrees apart from one another.Can exist singly,in groups and alson in long coils. Example of alpha helix that exist in long coils is keratins that can be found in the hair and skin. 
*Also the individual, antiparallel strands of the beta-pleated-sheet have hydrogen bonds which connect the peptide bonds of different strands <ref>Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. p137</ref>. All the side chains points alternately up and down at180 degrees per residue. the peptide is fully stretch where there is 3.5A per residue. An example of a beta-pleated sheet is silk which is known for is rigidness. 

=== References: ===

<references />

Hydrogen bonds

2014-11-27T23:11:24Z

140662665:

Hydrogen bonds

2014-11-27T22:24:06Z

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A [[Hydrogen|hydrogen]] bond is an attraction between a [[Hydrogen|hydrogen]] atom and an [[Electronegative|electronegative]] atom, with the most common ones being [[Nitrogen|nitrogen]] (N), [[Oxygen|oxygen]] (O) or [[Fluorine|fluorine]] (F). Hydrogen bonds appear frequently within biological molecules and exist in [[Compound|polar compounds]]. A common example of this is [[Water|water]], where the attractive interaction exists between the [[Oxygen|oxygen]] and [[Hydrogen|hydrogen]] atoms. [[Hydrogen|Hydrogen]] bonding is a type of [[Intermolecular|intermolecular]] force, where the Hydrogen bond is found between different [[Molecule|molecules]], or [[Intramolecular|intramolecular]], where the bond exists between different parts of the same [[Molecule|molecule]] <ref>http://www.chemguide.co.uk/atoms/bonding/hbond.html</ref>.

A [[Hydrogen|hydrogen]] bond is a non-covalent bond; they have much stronger attractions than [[Van der waals forces|Van der Waals forces]] and [[Permanent dipole - permanent dipole interactions|permanent dipole-dipole interactions]], but are weaker than [[Ionic bonding|ionic bonding or]] [[Covalent bonding|covalent bonding]]. Evidence for [[Hydrogen|hydrogen]] bonding can be found when comparing the [[Boiling point|boiling points]] of [[Hydrogen|hydrogen]] molecules across groups 5, 6 and 7 of the [[Periodic table|periodic table]]. The compounds where [[Hydrogen|hydrogen]] bonding is present produce a much higher [[Boiling point|boiling point]] as [[Hydrogen|hydrogen]] bonds require more energy to be broken than [[Van der waals forces|Van der Waals forces]] <ref>http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/H/HydrogenBonds.html</ref>.

The distance between two parts of the same [[Molecule|molecule]], or different [[Molecule|molecules]], can vary and this has an effect on the strength of the hydrogen bond. This why the hydrogen bonds are said to be "elastic," the greater the distance between the [[Hydrogen|hydrogen]] [[Atom|atom]] and the electronegative atom the longer the hydrogen bond will be and this results in a weaker hydrogen bond.

A hydrogen bond can be defined as the polar interaction between an electronegative atom ([[Nitrogen]], [[Oxygen|oxygen]] or [[Fluorine|fluorine]]) and a hydrogen atom which is covalently bonded to another electronegative atom that is on the same molecule, or on a different molecule. The bond is strongest when all three of these atoms are arranged in such a way that their bond angles are at a value of 180 degrees. 

Hydrogen bonding is extremely prevalent throughout nature and can be found in [[Water|water]], [[DNA|DNA]] base-pair interactions, protein folding, [[Protein|protein]] structure and protein-ligand binding.

Hydrogen bond formation is due to the attraction of different elements which has variety of electron. The electronegativity series is O > N > C = H.

=== Water ===

A water molecule consists of one oxygen atom attached to two [[Hydrogen|hydrogen]] [[Atom|atoms]]. A hydrogen bond can be formed between two [[Molecules|molecules]] of [[Water|water]] due to the 'unequal distribution of electrons within a water molecule' <ref>Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. p55</ref>. The oxygen has a strong attraction for the electrons and has a negative charge, whereas the hydrogen only has a weak attraction and therefore has a slight positive charge. When these two oppositely-charged regions come close to each other, the result is a hydrogen bond <ref>Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. p55</ref>.

Although water has a low molecular mass, it has an unusually high boiling point. This property can be attributed to the large amount of hydrogen bonds that exists within water. Since these bonds are difficult to break, water’s melting and boiling points are relatively high in comparison to other liquids that are similar but lack the hydrogen bonding.

Another unusual property of water is it has a higher density than it's solid counterpart - ice. This is due to the unique formation of the hydrogen bonds forming a lattice structure whreby the strength and relative regidity of the bonds allows for greater seperation betweeen molecules than in its liquid form where the molecules interact at a greater velocity. 

=== DNA ===

In the [[DNA helix|DNA helix]],the bases: [[Adenine|adenine]], [[Cytosine|cytosine]], [[Thymine|thymine]] and [[Guanine|guanine]] are each linked with their complementary base by hydrogen bonding. Adenine pairs with thymine with 2 hydrogen bonds. Guanine pairs with cytosine with 3 hydrogen bonds.<ref>J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) Biochemistry, 6th edition, New York: W.H.Freeman and company p112</ref>This creates a difference in strength between the two sets of Watson and Crick bases. Guanine and cytosine bonded base pairs are stronger then thymine and adenine bonded base pairs in DNA. This difference in strength is because of the difference in number of hydrogen bonds. This allows researchers to figure out the base content of DNA by observing at what temperature it denatures. The higher the temperature at which DNA denatures the more guanine and cytosine base pairs are present. this variation in the number of hydrogen bonds a nucleic base can make in a watson crick base pair is also pertenant for the designing of primers for [[Polymerase Chain Reaction (PCR)|PCR]]. To ensure both primers anneal proportionally to their binding sites they must be designed such that they produce hydrogen bonds of similar affinity. The greater strength of hydrogen bonding between guanine and cytosine is also utilised during PCR primer design to ensure that primers is thoroughly bound to the target DNA at it's 3' end so that the polymerase can begin reading in the 3' to 5' direction. The inclusion of guanine or cytosine at the 3' end of a primer is known as a GC clamp. 

Protein

*An alpha-helix contains hydrogen bonds that is form between the carbonyl oxygen on residue N to the amide nitrogen on residue N + 4. In an alpha-helix structure there is 3.6 residue per turn. each of the side chains point outwards, 100 degrees apart from one another. Can exist singly,in groups and alson in long coils. Example of alpha helix that exist in long coils is keratins that can be found in the hair and skin. 
*Also the individual, antiparallel strands of the beta-pleated-sheet have hydrogen bonds which connect the peptide bonds of different strands <ref>Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. p137</ref>. 

=== References: ===

<references />

Hydrogen bonds

2014-11-27T22:18:05Z

140662665:

A [[Hydrogen|hydrogen]] bond is an attraction between a [[Hydrogen|hydrogen]] atom and an [[Electronegative|electronegative]] atom, with the most common ones being [[Nitrogen|nitrogen]] (N), [[Oxygen|oxygen]] (O) or [[Fluorine|fluorine]] (F). Hydrogen bonds appear frequently within biological molecules and exist in [[Compound|polar compounds]]. A common example of this is [[Water|water]], where the attractive interaction exists between the [[Oxygen|oxygen]] and [[Hydrogen|hydrogen]] atoms. [[Hydrogen|Hydrogen]] bonding is a type of [[Intermolecular|intermolecular]] force, where the Hydrogen bond is found between different [[Molecule|molecules]], or [[Intramolecular|intramolecular]], where the bond exists between different parts of the same [[Molecule|molecule]] <ref>http://www.chemguide.co.uk/atoms/bonding/hbond.html</ref>.

A [[Hydrogen|hydrogen]] bond is a non-covalent bond; they have much stronger attractions than [[Van der waals forces|Van der Waals forces]] and [[Permanent dipole - permanent dipole interactions|permanent dipole-dipole interactions]], but are weaker than [[Ionic bonding|ionic bonding or]] [[Covalent bonding|covalent bonding]]. Evidence for [[Hydrogen|hydrogen]] bonding can be found when comparing the [[Boiling point|boiling points]] of [[Hydrogen|hydrogen]] molecules across groups 5, 6 and 7 of the [[Periodic table|periodic table]]. The compounds where [[Hydrogen|hydrogen]] bonding is present produce a much higher [[Boiling point|boiling point]] as [[Hydrogen|hydrogen]] bonds require more energy to be broken than [[Van der waals forces|Van der Waals forces]] <ref>http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/H/HydrogenBonds.html</ref>.

The distance between two parts of the same [[Molecule|molecule]], or different [[Molecule|molecules]], can vary and this has an effect on the strength of the hydrogen bond. This why the hydrogen bonds are said to be "elastic," the greater the distance between the [[Hydrogen|hydrogen]] [[Atom|atom]] and the electronegative atom the longer the hydrogen bond will be and this results in a weaker hydrogen bond.

A hydrogen bond can be defined as the polar interaction between an electronegative atom ([[Nitrogen]], [[Oxygen|oxygen]] or [[Fluorine|fluorine]]) and a hydrogen atom which is covalently bonded to another electronegative atom that is on the same molecule, or on a different molecule. The bond is strongest when all three of these atoms are arranged in such a way that their bond angles are at a value of 180 degrees. 

Hydrogen bonding is extremely prevalent throughout nature and can be found in [[Water|water]], [[DNA|DNA]] base-pair interactions, protein folding, [[Protein|protein]] structure and protein-ligand binding.

Hydrogen bond formation is due to the attraction of different elements which has variety of electron. The electronegativity series is O > N > C = H.

=== Water ===

A water molecule consists of one oxygen atom attached to two [[Hydrogen|hydrogen]] [[Atom|atoms]]. A hydrogen bond can be formed between two [[Molecules|molecules]] of [[Water|water]] due to the 'unequal distribution of electrons within a water molecule' <ref>Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. p55</ref>. The oxygen has a strong attraction for the electrons and has a negative charge, whereas the hydrogen only has a weak attraction and therefore has a slight positive charge. When these two oppositely-charged regions come close to each other, the result is a hydrogen bond <ref>Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. p55</ref>.

Although water has a low molecular mass, it has an unusually high boiling point. This property can be attributed to the large amount of hydrogen bonds that exists within water. Since these bonds are difficult to break, water’s melting and boiling points are relatively high in comparison to other liquids that are similar but lack the hydrogen bonding.

Another unusual property of water is it has a higher density than it's solid counterpart - ice. This is due to the unique formation of the hydrogen bonds forming a lattice structure whreby the strength and relative regidity of the bonds allows for greater seperation betweeen molecules than in its liquid form where the molecules interact at a greater velocity. 

=== DNA ===

In the [[DNA helix|DNA helix]],the bases: [[Adenine|adenine]], [[Cytosine|cytosine]], [[Thymine|thymine]] and [[Guanine|guanine]] are each linked with their complementary base by hydrogen bonding. Adenine pairs with thymine with 2 hydrogen bonds. Guanine pairs with cytosine with 3 hydrogen bonds.<ref>J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) Biochemistry, 6th edition, New York: W.H.Freeman and company p112</ref>This creates a difference in strength between the two sets of Watson and Crick bases. Guanine and cytosine bonded base pairs are stronger then thymine and adenine bonded base pairs in DNA. This difference in strength is because of the difference in number of hydrogen bonds. This allows researchers to figure out the base content of DNA by observing at what temperature it denatures. The higher the temperature at which DNA denatures the more guanine and cytosine base pairs are present. this variation in the number of hydrogen bonds a nucleic base can make in a watson crick base pair is also pertenant for the designing of primers for [[Polymerase Chain Reaction (PCR)|PCR]]. To ensure both primers anneal proportionally to their binding sites they must be designed such that they produce hydrogen bonds of similar affinity. The greater strength of hydrogen bonding between guanine and cytosine is also utilised during PCR primer design to ensure that primers is thoroughly bound to the target DNA at it's 3' end so that the polymerase can begin reading in the 3' to 5' direction. The inclusion of guanine or cytosine at the 3' end of a primer is known as a GC clamp. 

Protein

*An alpha-helix contains hydrogen bonds that is form between the carbonyl oxygen on residue N to the amide nitrogen on residue N + 4. between the N-H of one peptide bongs and the C=O of another peptide bond which is found 4 [[Peptide bond|peptide bonds]] away on the same chain.
*Also the individual, antiparallel strands of the beta-pleated-sheet have hydrogen bonds which connect the peptide bonds of different strands <ref>Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. p137</ref>. 

=== References: ===

<references />

Secondary structure

2014-11-27T22:09:57Z

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Amino acids

2014-11-27T22:04:58Z

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Amino acids are the building blocks of [[Proteins|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. When two amino acids join they for 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 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]]:'''

{| cellspacing="1" cellpadding="1" border="1" width="357" style="width: 357px; height: 460px"
|-
| '''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. 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 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. The formation of a dipeptide from two amino acids is accompanied by the loss of a water molecule.  

=== 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 <ref>Berg J, Tymoczko J, Stryer L (2007) Biochemistry sixth edition, New York: W. H. Freeman and Company (page 34)</ref>.

=== References ===

<references />