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Oxygen

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Oxygen is the 8th Element of the [[Periodic Table]]. At the atmospheric pressure and temperature of the Earth it is in the form of a colourless, odourless dimeric gas, O2, and makes up around 21% of the atmosphere. Atomically, oxygen contains 8 [[Protons|protons]], 8 [[Neutrons|neutrons]] and 8 [[Electrons|electrons]] when not in the form of an [[Isotope]]. It has a [[Melting point|melting point]] of 54.36 K and a [[Boiling Point|boiling point]] of 90.20 K. 

Oxygen plays an important role in the biological process of [[Respiration]] where it is used as a [[Substrate|substrate]] in combination with [[Glucose]] to produce [[Carbon dioxide|Carbon Dioxide]] and [[Water]] <ref>Essential Cell Biology, Bruce et al. 3rd ed 2009, New York p488-9</ref>. It is also produced in the process of photosynthesis, where carbon dioxide and water are involved in the presence of light energy to form oxygen and glucose.

=== References ===

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Nucleotide

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Nucleotides are the fundamental building blocks of [[DNA|DNA]] and [[RNA|RNA]].  They are similar to the structure of [[Nucleoside|nucleosides but]] differ in the fact that they have one or more [[Phosphate group|phosphate group]](s) added. 

A compound consisting of a [[Nitrogenous base|nitrogenous base]], a [[Phosphate group|phosphate group]] and a sugar. Nucleotides are bonded together by [[Phosphate-sugar linkage|phosphate-sugar linkages]] to form [[DNA|DNA]] or [[RNA polymerase II|RNA]].

== Structure ==

The contituents of nucleotides are a nitrogenous base, a 5-carbon sugar and one or more [[Phosphate|phosphate]] group(s), the types of which vary between [[DNA|DNA]] and [[RNA|RNA]]. In DNA the base can be either one of the [[Purines|purines]], [[Adenine|adenine]] (A) or [[Guanine|guanine]] (G), or one of the [[Pyrimidines|pyramidines]], [[Thymine|thymine]] (T) or [[Cytosine|cytosine]] (C). This is similar in RNA with the exception of one base; thymine is replaced with [[Uracil|uracil]].The base of each nucleotide is joined to C1' of the sugar by a beta-glycosidic linkage from either N-9 of a purine or N-1 of a pyrimidine<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman p109</ref>. 

The presence of thymine in [[DNA|DNA]] rather than uracil is used to maintain the active repair system which corrects deamination of [[Cytosine|cytosine]]. The [[Deamination|deamination]] of [[Cytosine|cytosine]] to form [[Uracil|uracil]] (which occurs spontaneously in [[DNA|DNA]]) is potentially mutagenic as [[Uracil|uracil]] is complementary to [[Adenine|adenine]]. This means that during replication one of the daughter strands would contain a U-A [[Base pair|base pair instead]] of the original C-G base pair. [[Uracil|Uracil]] is recognised as foreign to [[DNA|DNA]] by a repair system in order to prevent this mutation from occurring. The repair enzyme, [[Uracil DNA glycosylase|uracil DNA glycosylase]], [[Hydrolize|hydrolyzes]] the [[Glycosidic bond|glycosidic bond]] between [[Uracil|uracil]] and [[Deoxyribose|deoxyribose]] but does not attack thymine-containing nucleotides. Once [[Uracil|uracil]] is removed by the [[Enzyme|enzyme]], [[Cytosine|cytosine]] is reinserted to repair the mutation. The methyl group on [[Thymine|thymine]] enables the[[Enzyme|enzyme to]] distinguish between [[Thymine|thymine]] and [[Deaminated cytosine|deaminated cytosine]]. If [[Uracil|uracil]] was used in [[DNA|DNA]] rather than [[Thymine|thymine]], the [[Uracil|uracil]] which was correctly placed would not be distinguishable from the potentially mutagenic [[Uracil|uracil]] formed from deamination of [[Cytosine|cytosine]]. Thus, all [[Uracil|uracil]] would be removed regardless of whether it was mutagenic or not and the fidelity of the genetic code would be decreased<ref>Berg Jeremy M., Tymoczko John L., Stryer Lubert., (2007) Biochemistry, Sixth Edition, New York, W.H. Freeman and Company. P809</ref>.

The base present in [[ATP|ATP]] is [[Adenine|adenine]] and in [[GTP|GTP]] it is [[Guanine|guanine]]. The sugar present in nucelotides is either [[Deoxyribose|deoxyribose]] in [[DNA|DNA]] or [[Ribose|ribose]] in [[RNA|RNA]]; the [[Sugar|sugar]] present in both [[ATP|ATP]] and [[GTP|GTP]] is the same as the sugar present in [[RNA|RNA]], [[Ribose|ribose]]. These are almost identical in structure except for one difference; in [[Deoxyribose|deoxyribose]] the 2' carbon has two [[Hydrogen|hydrogen]] [[Atom|atoms]] attached, in [[RNA|RNA]] one of the [[Hydrogen|hydrogen]] [[Atom|atoms]] on the 2' carbon is replaced with a hydroxyl (OH) group<ref>Hart D.L and Jones E.W (2009) Genetics: Analysis of Genes and Genomes, 7th Edition, Jones and Bartlett's Publishers, p.41</ref>. The final constituent which is present in the same form in both [[DNA|DNA]] and [[RNA|RNA]] is a [[Phosphate|phosphate]] group. In [[ATP|ATP]] and [[GTP|GTP]] there is not just one phosphate group present but three phosphate groups, hence the name triphosphate. In all nucleotides, the base is attached to the relevant sugar, [[Deoxyribose|deoxyribose]] or [[Ribose|ribose]], on the 1' carbon and the phosphate group is attached to the 5' carbon of the relevant sugar. The multiple phosphate groups present in [[ATP|ATP]] and [[GTP|GTP]] are attached to one another. This altogether attachment is the final structure of a nucleotide. [[ATP|ATP]] and [[GTP|GTP]] are not always naturally found as triphosphates; they also exist as dipohosphates ([[ADP|ADP]] and [[GDP|GDP]]) and monophosphates ([[AMP|AMP]] and [[GMP|GMP]]) where either two (a pyrophosphate) or only one phosphate groups are attached respectively. 

Polynucleotide chains can be formed which are simply repeating units of nucleotides which are joined by bonds called [[Phosphodiester bond|phosphodiester bonds]]. [[Phosphodiester bond|Phosphodiester bonds]] form between a phosphate groups and two 5-carbon sugars each from a different nucleotide. The phosphate group, which is already attached to one sugar at the 5' carbon forms a bond with an OH group on the 3' carbon of another sugar<ref>Hartl D.L and Jones E.W (2009) Genetics: Analysis of Genes and Genomes, 7th Edition, Jones and Bartlett's Publishers, p.41</ref>. These [[Polynucleotide Chain|polynucleotide chains]] make up the [[DNA|DNA]] and [[RNA|RNA]] phosphate-sugar backbone. 

=== References ===

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Phosphate

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Phosphates are molecules with the chemical formula PO4-. The presence of a negative charge causes phosphates to act as a [[Nucleophile|nucleophile]]; it seeks a positive charge, therefore it is always found bound to other [[Atom|atoms]] or [[Molecule|molecules]]. In organic systems, the phosphate molecule is the form that bodily [[Phosphorus|phosphorus]] is used mainly in the form of nucleic acids [[DNA|DNA]] and [[RNA|RNA]] and the [[Nucleotide|nucleotides]] that form them.

=== DNA and RNA ===

In [[DNA|DNA]] and [[RNA|RNA]] phosphates are used to build the phosphate-sugar backbone, which fixes the [[Nucleotide|nucleotide]] bases in place. This is achieved by the formation of a [[Phosphodiester bond|phosphodiester bond]], in which the phosphate molecule reacts with a [[Hydroxylation|hydroxyl]] group on the [[Ribose|ribose]] sugar forming a bond and releasing water as a byproduct. Without the phosphate attached, the molecule consisting of just the base and the ribose sugar or deoxyribose sugar is called a nucleoside as opposed to a nucleotide<ref>Hartl D. L and Ruvolo M. (2012) Genetics, Analysis of Genes and Genomes, Eighth Edition, Burlington, Jones and Bartlett Learning</ref>.

=== Metabolism ===

The nucleotides most notably [[ATP|ATP]] and [[GTP|GTP]] are all triphosphate molecules which are highly efficient at releasing energy. This is because of the three phosphate molecules bound closely together on the [[ATP|ATP]] or [[GTP|GTP]] molecule, the negative charges on each phosphate exhibit repulsive forces between each other, so they can be [[Hydrolysis|hydrolysed]] in order to overcome these repulsive forces, and energy is released from phosphoanhydride bond hydrolysis.

ATP _> ADP + Pi (Pi is an inorganic phosphate)

GTP _> GDP + Pi

These high energy phosphoanhydride bonds, on average, have a ΔG of -30.5 kJ/mol<ref>ATP/ADP [Internet]. Chemistry LibreTexts. 2018 [cited 6 December 2018]. Available from: https://chem.libretexts.org/Textbook_Maps/Biological_Chemistry/Metabolism/ATP%2F%2FADP</ref>. Thus, the energy released from these bonds will be used for a cellular interaction such as a conformation shape change in a [[Protein|protein]] in skeletal muscle [[Contraction|contraction]]<ref>Biochemistry, sixth edition, Berg, Tymoczko and Stryer</ref>.

It is possible to recycle the [[ADP|ADP]] and inorganic phosphate using the [[Respiration|respiration]], where [[Glucose|glucose]] sugars are broken down to produce energy to reform the phosphodiester bond between ADP and Pi, recycling the molecules and forming ATP to be used again as an intermediate for energy release. 

=== References ===

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Nucleoside

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A nucleoside is a unit made up of a [[Pentose|pentose]] [[Sugar|sugar]] (ribose or deoxyribose) and a nitrogenous [[Base|base]] (purine or pyrimidine), which are attatched by a ß N-[[Glycosidic bond|glycosidic linkage]] (the base is above the plane of the sugar). The sugar will be either [[Ribose|ribose]] (for [[RNA|RNA]] nucleosides) or [[Deoxyribose|deoxyribose]] (for [[DNA|DNA]] nucleosides). If the base is a [[Purine|purine]], then it is attached to C-1' by N-9, and if the base is a [[Pyrimidine|pyrimidine]] then it is attached to C-1' by N-1.

There are four nucleoside units in [[RNA|RNA]] - [[Adenosine|adenosine]], [[Guanosine|guanosine]], [[Cytidine|cytidine]] and [[Uridine|uridine]]. The four nucleoside units in [[DNA|DNA]] are called [[Deoxyadenosine|deoxyadenosine]], [[Deoxyguanosine|deoxyguanosine]], [[Deoxycytidine|deoxycytidine]] and [[Thymidine|thymidine]]. A nucleoside can have a [[Phosphate|phosphate]] group attached to the C-5' through a [[Condensation reaction|condensation reaction]], producing a [[Nucleotide|nucleotide]], a [[Monomer|monomer]] of [[Nucleic acid|nucleic acid]]<ref>Berg et al, Biochemistry, 6th Edition, New York: W.H. Freeman and Company, 2007</ref><ref>Berg JM, Tymoczko JL and Stryer L, 2012, Biochemistry 7th edition, NY, W. H Freeman and Company, page 115</ref>.

=== References ===

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Lipid

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A lipid is a "water-insoluble biomolecule that is highly soluble in organic solvents" by definition <ref>Berg, JM. (2006) "Biochemistry" 6th Ed. p329, New York, W.H. Freeman and company</ref>. Their molecules tend to stay together to from droplets and bilayers <ref>Wood, E., Smith, C. A., and Pickering , W. R. (1997 ). Life Chemistry and Molecular Biology .</ref>. The lipid's we come across most often are those which play the most important role in forming the [[Lipid bilayer|lipid bilayer]] membranes around cells, these are [[Phospholipid|phospholipids]].  They (like all lipids) contain a [[Hydrophobic|hydrophobic]], long hydrocarbon chain 'tail', they also contain a hydrophilic 'head'. In phospholipids the main component of this 'head' is a phosphate, it is also formed from an alcohol and a platform bonded to the phosphate creating the [[Hydrophilic|hydrophilic]] part of the lipid. Lipids are [[Amphiphatic|amphiphatic]], they have both a hydrophilic and a hydrophobic part.

=== Fatty Acids and Triacylglycerols (Triglycerides)  ===

A good place to start thinking about lipids is the fatty acids. A fatty acid has the chemical formula CH3(CH2)''n''CO2-, where ''n ''can be anything from 1 to 20 or more<ref>Wood, E., Smith, C. A., and Pickering , W. R. (1997 ). Life Chemistry and Molecular Biology .</ref>.  Triglyceride molecules are composed of a [[Glycerol|glycerol]] (glycerol backbone) and three fatty acids. The glycerol backbone is always constant but fatty acids that are attached to the backbone may differ<ref>http://www.differencebetween.com/difference-between-triglycerides-and-phospholipids/</ref>.

Long fatty acid chains arrange themselves into a spherical globule called a ''[[Micelle|micelle]] ''form which are achieved by the hydrophobic chains associating together while their hydrophilic heads face outwards, interacting with the water; such structures can act as various detergents or soaps<ref>Wood, E., Smith, C. A., and Pickering , W. R. (1997 ). Life Chemistry and Molecular Biology .</ref>.

Triacylglycerols are referred to as 'natural fats' and their molecules tend to cluster together to form droplets and keep away from water<ref>Wood, E., Smith, C. A., and Pickering , W. R. (1997 ). Life Chemistry and Molecular Biology .</ref>. The fact that they isolate themselves as hydrophobic droplets makes storage easy, for example storage of energy in cells which can be released when required via enzyme action. Triclyglycerols also can act as thermal and mechanical insulators and in aquatic animals, can supply buoyancy<ref>Wood, E., Smith, C. A., and Pickering , W. R. (1997 ). Life Chemistry and Molecular Biology .</ref>.

=== Phospholipids ===

[[Phospholipids|Phospholipids]] are a group of compounds that are similar to triaclyglycerols except that one of the fatty acid chains is instead replaces by a [[Phosphate group|phosphate group]]; several other varying small molecules may be attached to the phosphate giving a group of different structures<ref>Wood, E., Smith, C. A.,and Pickering , W. R. (1997 ). Life Chemistry and Molecular Biology .</ref>. The phospholipids position themselves in a bilayer; the hydrophobic groups in contact with each other on the inside of the bilayer and the hydrophilic groups on the outsides of the bilayer. The role of phospholipid bilayer is to allow the conditions inside the cell to be different to those outside and to control the movement of substances into and out of the cell. It is the phospholipids in the membrane that control the movement of the substances into and out of the cell. As only lipid-soluble molecules to pass through them therefore entering and leaving the cell and water-soluble molecules cannot pass throught therefore are prevented from entering and leaving the cell<ref>AQA As level biology text book, page 52</ref>. 

=== '''Cholestrol ''' ===

Cholestrol is another group of lipid which contain different and unique structure. It consist of short hydrocarbon chain with 4 linked hydrocarbon rings and a hydroxyl group. It shares the same properties as phospholipids which is amphipathic (contain both hydrophobic and hydrophilic regions)<ref>Albert et al. (2008) 'Molecular Biology of The Cell' -- Fifth Edition. New York, Garland Science.</ref>. 

=== References ===

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Protein

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A protein is a biological [[Polymer|polymer]] which is made up of structures called [[Amino acid|amino acids]]. The [[Amino acids|amino acids]] are joined together with a [[Peptide bond|peptide bond]] to form a [[Polypeptide|polypeptide]] chain. The [[Peptide bond|peptide bond]] is formed by joining the ɑ-[[Carboxyl group|carboxyl group]] of an [[Amino acid|amino acid to]] the ɑ-amino group of another [[Amino acid|amino acid]]<ref name="null">Berg et al., (2006) Biochemistry, 6th edition, New York. Pg 34</ref>. A protein can be made up of a single polypeptide chain or multiple [[Polypeptides|polypeptides]] linked together. There are three types of proteins: [[Fibrous|fibrous]], [[Globular protein|globular]] and [[Membrane protein|membrane proteins]]. Examples of proteins include [[Enzyme|enzymes]], [[Receptor|receptors]] and [[Hormone|hormones.]] They are found in every form of life from [[Virus|viruses]] to [[Bacteria|bacteria]]; [[Yeast|yeasts]] to [[Humans|humans]]. One important technique used to analyse proteins is [[SDS polyacrylamide-gel electrophoresis|SDS polyacrylamide-gel electrophoresis]] ([[SDS polyacrylamide-gel electrophoresis|SDS-PAGE]]). Proteins can make up to 50% of the weight of a cell, and up to 25% of a human's dry bodyweight.

== Structure ==

A protein has several 'layers' of structure<ref>Elliott.W.H, Elliott.D.C (1997) Biochemistry and Molecular Biology. New York, United States: Oxford University Press.pp.47-49.ISBN 0199271992</ref>. The function of the protein is determined by its structure. Therefore each layer is dependent on the next<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman.</ref>.

=== Primary Structure ===

The [[Primary structure|primary structure]] is the specific sequence of [[Amino acids|amino acids]] joined together by [[Peptide bonds|peptide bonds in]] a [[Polypeptide|polypeptide]] chain. There are 20 different [[Amino acids|amino acids]] found in nature. The sequence of amino acids is determined by the [[DNA|DNA]] sequence that encodes for that particular protein. This is known as the [[Gene|gene]].

[[Image:Primary structure.jpg|Primary structure of a protein.]]

Example of primary structure of a protein<ref>Libretexts. Protein Structure. 2017 [cited 09/12/18]; Available from: https://bio.libretexts.org/LibreTexts/University_of_California_Davis/BIS_2A%3A_Introductory_Biology_(Britt)/Readings/Protein_structure</ref>.

=== Secondary Structure ===

[[Secondary structure|Secondary structure]] is the first level of protein folding. The two main folding structures of a protein are the [[Alpha-helix|alpha-helix]] or the [[Beta-sheet|beta-sheet]] depending on the sequence of [[Amino acids|amino acids]]. [[Alpha-helix|Alpha-helix]] can exists as right-handed or left-handed while [[Beta-sheet|beta-sheet]] can exists as anti-parallel or parallel. This, in turn, allows the protein to have a [[Hydrophobic|hydrophobic]] core and a [[Hydrophilic|hydrophilic]] surface. The secondary structure is stabilised by [[Hydrogen bonds|hydrogen bonds]] between the C=O and H-N groups<ref>Clark, J (2004) The Structure of Proteins. [Internet], Available from: http://www.chemguide.co.uk/organicprops/aminoacids/proteinstruct.html;[Accessed 20 October 2015].</ref>. for the peptide backbone.

[[Image:Secondary.jpg|500px|Secondary.jpg]]

Example of secondary structure of protein<ref>Libretexts. Protein Structure. 2017 [cited 09/12/18]; Available from: https://bio.libretexts.org/LibreTexts/University_of_California_Davis/BIS_2A%3A_Introductory_Biology_(Britt)/Readings/Protein_structure</ref>.

=== Tertiary Structure ===

[[Tertiary structure|Tertiary structure]] relates to the protein function. If the [[Tertiary structure|tertiary structure]] is altered, then the protein is unlikely to function properly. [[Tertiary structure|Tertiary structure]] is held together by either [[Hydrogen bonds|hydrogen bonds]] or [[Disulphide bridges|disulphide bridges]] depending on the [[Amino acids|amio acids]] present. Disulphide bridges are formed between multiple units of the amino acid [[Cysteine|Cysteine]]<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman.</ref>.

[[Image:Tertiary.jpg|700px|Tertiary.jpg]]

Example of tertiary structure<ref>Libretexts. Protein Structure. 2017 [cited 09/12/18]; Available from: https://bio.libretexts.org/LibreTexts/University_of_California_Davis/BIS_2A%3A_Introductory_Biology_(Britt)/Readings/Protein_structure</ref>.

=== Quaternary Structure ===

One or more tertiary structure of proteins linked together build up a [[Quaternary structure|quaternary structure]]. The quaternary structure can also refer to proteins with an inorganic prosthetic group attached, an example being [[Haemoglobin|haemoglobin]]: a tetramer consisting of four myoglobin subunits and an iron-containing [[Haem group|haem group]]. Two of the subunits are alpha, and two are beta<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman.</ref>.

== Functions of Proteins ==

Proteins make up 50% of each cell and have both structural and functional importance. Proteins transport a multitude of different particles from macromolecules to electrons. [[Enzymes|Enzymes]] are globular proteins that act as biological [[Catalysts|catalysts]], and collagen is a fibrous protein which provides strength and structural support in many tissues. Proteins in the form of hormones transmit information between specific cells.

Structural proteins include:

*the silk-[[Beta pleated sheet|beta pleated sheet]] which has Alanine and Glycine residues forming a rigid, stable structure. Spiders can make silk and in this type of silk the rigid sections alternate with stretchy ones to make the structure both strong and elastic.
*[[Keratin|A-Keratin]] which is present in hair, nails, and wool (among others). This structure is usually stretchy and flexible. However, when many disulphide bridges are present (for example, in hooves and nails) the structure remains rigid and loses flexibility.
*[[Collagen|Collagen]], consisting of a coil of three strands of glycine-proline-proline which is 100 strands long. This is the most abundant protein in mammals.

Enzymes work by binding substrate at their active sites, which is a specific region dependant on amino acid sequence forming an enzyme-substrate complex. This causes a conformational change in the shape of the enzyme which encourages catalysis by putting a strain on the bonds in the substrate (and/or by other means).

A group of protein structures called motor proteins are responsible for activities such as [[Muscle contraction|muscle contraction]], cell movement, migration of [[Chromosomes]] during [[Mitosis]] and the direction of [[Organelles|organelles]]. There are two different types of [[Microtubules|microtubule]] motor proteins known as [[Kinesin|kinesins]] and [[Dynein|dyneins]]. Kinesins facilitate the carrying of organelles toward the positive end of the [[Microtubule|microtubule]] and dyneins are important of the movement of [[Cilia|cilia]] or [[Flagella|flagella]] in organisms<ref>Alberts.B et al, (Fifth Edition); Molecular Biology of the Cell; Taylor and Francis Group, pp 1014-1015</ref>.

A protein molecule's physical interaction with other molecules determines its biological properties. In some cases, these interactions are very strong; in others, it is weak and short-lived. But the binding always shows great specificity, in the sense that each protein molecule can usually bind just one of a few molecules out of many thousands of different types it encounters<ref>Alberts.B et al, (Sixth Edition); Molecular Biology of the Cell; Taylor and Francis Group, page 134</ref>.

=== Synthesis of Proteins ===

Protein synthesis can be divided into two sections, transcription and translation. In transcription DNA is used to code for the protein, it starts at a [[Promotor gene|promotor gene]] at the 5' end one of the two DNA strands, here [[RNA polymerase|RNA polymerase]], which does not require primers, moves down the strand and forms a complementary sequences of [[Pre-mRNA|pre-mRNA]]. (Thymine [[DNA bases|base]] is replaced with Uracil) This pre-mRNA contains non-coding [[Introns|introns]] and coding [[Exons|exon]], due to this, the pre-mRNA is spliced to remove the introns leaving only the coding sequences of mRNA. This mRNA is used to code for the [[Protein sequence|protein sequence]].

In translation the [[MRNA|mRNA]] binds to a ribosome, this ribosome then moves down the mRNA from the 5' to 3' end. [[TRNA|tRNA has]] an anticodon sequence with three bases on it that are complementary to a [[Codon|codon]] on the mRNA, it also carries a specific amino acid. Here the RNA carries this [[Amino acid|amino acid]] to the [[Ribosome|ribosome]] and its complementary triplet code on the mRNA. [[Peptide bonds|Peptide bonds]] are formed between amino acids next to each other ( when their two triplet codes are next to each other)<ref>Lesk A.M. Introduction to Protein Science, architecture, function and genomics. 3rd ed. Oxford. Oxford University Press. 2015</ref>. This forms the [[Primary structure|primary structure]] of proteins which is the amino acid sequence.

== See also ==

*[[Amino acid|Amino acid]]

== References ==

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Carboxyl group

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A carboxyl group is a [[Molecule|molecule]] that consists of 1 [[Carbon|carbon]] [[Atom|atom]], 2 [[Oxygen|oxygen]] atoms and 1 [[Hydrogen|hydrogen]] atom in its unionised form. The [[Functional group|functional group]] can be viewed as -COOH. When ionised it loses the hydrogen atom therefore becoming negative in charge. More commonly carboxyl groups are seen as part of a larger molecule such as an [[Amino acids|amino acids]]. In [[Protein|proteins]] (due to the negative charge) the carboxyl group can form [[Peptide bonds|peptide bonds]] or in [[Enzyme|enzymes]] the negative charge of the [[Carboxyl_group|carboxyl group]] can be used to disrupt the bonds in a [[Substrate|substrate]] and drive a reaction.

Carbohydrates

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Carbohydrates are a major source of energy for life and are important structural [[Molecules|molecules]] in many [[Organism|organisms]]. They are molecules that are made of [[Oxygen|oxygen]], [[Carbon|carbon]], and [[Hydrogen|hydrogen]], with the [[Empirical formula|empirical formula]] for most carbohydrates being (CH2O)n. They may also contain [[Sulphur]] and/ or [[Nitrogen]]. All carbohydrates have at least one hydroxyl group (OH) and an aldehyde or ketone group. The two simplest carbohydrates that are present naturally are [[Dihydroxyacetone]] and [[Glyceraldehyde]]. Carbohydrates contribute to structure, [[Protein targeting]], [[Energy source]],[[Metabolism]] and [[Cell recognition]].

The simplest types of carbohydrates are [[Monosaccharides|monosaccharides]]. These are [[Aldehyde|aldehydes or]] [[Ketone|ketones]] with one or more hydroxyl groups. The smallest monosaccharide is composed of three carbon [[Atoms|atoms]]. These are called trioses. Other simple monosaccharides are tetroses (4 carbon), pentoses (5 carbon) - [e.g the well-known ribose sugar in DNA], hexoses (6 carbon), and heptoses (7 carbon).

Many common [[Sugars|sugars]] exist in cyclic forms. This occurs when the [[Aldehyde|aldehyde]] or [[Ketone|ketone]] group of the carbohydrate reacts with one of its own [[Hydroxyl group|hydroxyl]] group to form either a hemiacetal or hemiketal. A 6-membered (6 carbon) cyclic hemiacetal/hemiketal is called a [[Pyranose|pyranose]]. A 5-membered ring is called a [[Furanose|furanose]]<ref>Berg J., Tymoczko J and Stryer L. (2011) Biochemistry, 7th edition, New York: WH Freeman. pg 332</ref>.

The most frequently occurring of these is glucose and is important in energy [[Metabolism|metabolism]]. When [[Glucose|glucose]] is not immediately required it is synthesized into [[Glycogen|glycogen]]. This is known as the [[Glycogen Synthase Reaction|Glycogen Synthase Reaction]] and it involves glucose donating a [[Glucosyl residue|glucosyl residue]] to the non-reducing end of a glycogen branch<ref>Matthews C, Van holde K, Ahern K, (2000) BIOCHEMISTRY, third edition, San Francisco, Addison-Wesley publishing company</ref>.

[[Disaccharides|Disaccharides]] are carbohydrates made up of two [[Monosaccharides|monosaccharides]] which are joined by an [[O-glycosidic bond|O-glycosidic bond]]. Polymers of carbohydrates can be created by the further addition of monosaccharides, complex carbohydrates containing more than one molecule are called [[Oligosachharides|oligosachharides]]<ref>Jeremy M. Berg, John l. Tymoczko, Lubert Stryer with Gregory J gatto, Jr, (2012), Biochemistry, International 7th edition, W.H Freeman and company</ref> and polymers of carbohydrates with more than ten monomers are called polysaccharides.

There is a vast range of [[Isomer|isomeric]] forms in which carbohydrates can exist. Carbohydrates with the same chemical formula can differ as a result of the arrangement of bonding of the [[Atom|atoms]], these isomers are called [[Constitutional isomers|constitutional isomers]]. They can differ as a result of the spatial arrangement of the atoms, and are referred to as [[Stereoisomer|stereoisomers]]. The [[Stereoisomer|stereoisomer]] can exist in either D or L configuration, which is determined by the orientation of the [[Asymmetric carbon|asymmetric carbon]] that is farthest away from the [[Ketone|keto]] or [[Aldehyde|aldehyde]] group of the carbohydrate. [[Enantiomers|Enantiomers]] are stereoisomers that are mirror images of each other, whereas diastereoisomers are stereoisomers that are not mirror images of each other<ref>Berg J., Tymoczko J and Stryer L. (2011) Biochemistry, 7th edition, New York: WH Freeman. pg 331</ref>.

=== References ===

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