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Oxygen

2018-12-09T22:52:59Z

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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 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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Uracil

2018-12-09T22:40:33Z

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[[Image:0192801015 uracil 1.jpg|thumb]]

Uracil (U) is a [[Pyrimidine|pyrimidine]] base. It is one of the four bases found in [[RNA|RNA]] where it replaces [[Thymine|Thymine]] (T) which is found in [[DNA|DNA]]. The structure of uracil differs from thymine in that thymine contains an extra [[Methyl group|methyl group]] on the 5-C [[Carbon|carbon]] at[[Carbon]]om whereas [[DsRNA|uracil just]] has a [[Hydrogen|hydrogen]] atom. It has a chemical formula of C4H4N2O2. However, the base-pairing is unaffected by the lack of this [[Methyl group|methyl group]], therefore the U-A base pairs are very similar to T-A base pairs <ref>Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. page 303</ref> e.g. there are 2 [[Hydrogen bonds|hydrogen bonds]] formed between the bases <ref>Berg, J.M. Tymoczko, J.L. Stryer, L. (2007). Biochemistry. 6th ed. New York: W.H. Freeman and Company. p109.</ref>.

=== References ===

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Thymine

2018-12-09T22:38:03Z

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Thymine is one of the four bases which make up [[DNA|DNA]] molecules. It uses two [[Hydrogen|hydrogen]] bonds to form a complementary base pair with [[Adenine|Adenine]] (A). It has the chemical formula C5H6N2O2. Thyamine is not present in RNA, instead it is replaced by the base [[Uracil|Uracil]]. Thymine is a [[Pyrimidine|pyrimidine]]; a [[Pyrimidine|pyrimidine is]] a heterocyclic [[Aromatic compound|aromatic compound]].  

Thymine combined with [[Deoxyribose|deoxyribose]] creates the [[Nucleoside|nucleoside]] [[Deoxythymidine|deoxythymidine]], which is synonymous with the term thymidine. Thymidine can be phosphorylated with one, two, or three [[Phosphoric acid|phosphoric acid]] groups, creating, respectively, TMP, TDP, or TTP (thymidine mono-, di-, or triphosphate)<ref>https://en.wikipedia.org/wiki/Thymine</ref>. 

=== References  ===

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Adenine

2018-12-09T22:35:48Z

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Adenine is one of the four nitrogen-containing base pairs found in [[DNA|DNA]], the others being [[Cytosine|Cytosine]] (C), [[Guanine|Guanine]] (G) and [[Thymine|Thymine]] (T). It is one of the purine bases along with guanine. Both cytosine and thymine are pyrimidines. It has the chemical formla C5H5N5. Adenine has a [[Molecular weight|molecular weight]] of ~135 g/mol. In [[DNA|DNA]] it provides stability to the [[Double helix|double helix by]] forming two [[Hydrogen bonds|hydrogen bonds]] with [[Thymine|thymine]], which is adenine's complementary base pair. However in [[RNA|RNA]] it forms [[Hydrogen bonds|hydrogen bonds]] with [[Uracil|uracil]] instead of [[Thymine|thymine]]. [[Purines|Purines]] are 6-membered rings attatched to a 5-membered ring with nitrogens at positions 1, 3, 7 and 9, making them a heterocyclic aromatic compound.

Adenine plays an important role in cellular organisms in the form of [[ATP|ATP]], an energy-rich molecule used during proccesses such as [[Respiration|respiration]] and other chemical reactions within the cell<ref>http://www.chem.duke.edu/~jds/cruise_chem/Exobiology/adenine.html</ref>.

=== References ===

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DNA

2018-12-09T22:33:06Z

180400010: Added links

[[Image:BASE PAIRINGS.png|left|DNA Helix]]

DNA ([[Deoxyribonucleic_acid|deoxyribonucleic acid]]) is the genetic information found in the [[Nucleus|nuclei]] of most [[Organism|organisms]]. It is arranged into structures called [[Chromosome|chromosomes]]. The structure of DNA was first identified as having a [[Double helix|'double-helix' structure]] by [[Watson|Watson]] and [[Crick|Crick]] in 1953. DNA is composed of 4 [[Base|bases]]: the [[Purine|purines]], [[Adenine|adenine]] (A) and [[Guanine|guanine]] (G) and [[Pyrimidine|pyrimidines]] ,[[Thymine|thymine]] (T) and [[Cytosine|cytosine]] (C)<ref>HARTL AND JONES,2009:41, GENETICS : ANALYSIS OF GENES AND GENOMES SEVENTH EDITION.</ref>. These form complementary base pairs of A-T and G-C. DNA also contains a [[Phosphate|phosphate]] group connected to a [[Deoxyribose sugar|deoxyribose sugar]]. The phosphate group is attached to the sugar through a [[Phosphodiester bond|phosphodiester bond]]. Humans have 99.5% similarities with other humans in their DNA.

=== Structure of DNA ===

DNA ([[Deoxyribonucleic acid|deoxyribonucleic acid]]) is a chain of [[Monomers|monomers]] (repeating units) called "[[Nucleotides|nucleotides]]". A [[Nucleotide|nucleotide]] consists of: a [[Deoxyribose|2` deoxyribose sugar]] (A five-carbon [[Pentose sugar|pentose similar]] to that of [[Ribose|ribose]] [[Sugar|sugar found]] in [[RNA|RNA]]. Its chemical formula is C5H10O4), a [[Phosphate group|phosphate group]] (which forms a [[Phosphodiester bond|phosphodiester bond]]: connecting 2 [[Deoxyribose|deoxyribose sugars]] together) and a [[Nitrogenous base|nitrogenous base]] (one from [[Adenine|A]] (Adenine), [[Cytosine|C]] ( Cytosine), [[Guanine|G ( Guanine) or]] [[Thymine|T]] (Thymine), which forms a side chain branching from the 1' carbon of the 2` [[Deoxyribose sugar|deoxyribose sugar]]).

The [[Deoxyribose sugar|deoxyribose sugar]]/[[Phosphate group|phosphate group]] region is regarded as the [[Sugar-phosphate backbone|'backbone']] of DNA strands due to its structural purpose and the sequence of [[DNA bases|bases carries]] the [[Genetics|gentic information]]. In order to produce a double-stranded DNA structure, interactions occur between [[Complementary base pairs|complementary bases.]] The [[Complementary base pairs|complementary base pairs]] in DNA interact with one another via [[Hydrogen bonds|hydrogen bonds]]: A-T interactions consist of 2 intermolecular [[Hydrogen bonds|hydrogen bonds]], whereas G-C interactions consist of 3 intermolecular [[Hydrogen bonds|hydrogen bonds]]. In between these bases are hydrophobic interactions known as [[Van der Waals forces|van der Waal forces]]<ref>Lawrie Ryan and Roger Norris, Cambridge International AS and A Level, Second Edition, Cambridge United Kingdom, Latimer Trend 2014</ref>. These interactions form bridges between two DNA chains, thus creating a double-stranded 'ladder' shaped structure. Each strand acts as a template for the other one in [[Dna replication|DNA replication]]. DNA is copied into [[MRNA|mRNA]] (messenger RNA) which carries the information from the original DNA template strand to be involved in [[Protein synthesis|protein synthesis]]. The process of DNA being copied into [[MRNA|mRNA]] is termed [[Transcription|transcription]]. The transcribed [[mrna|mRNA]] is then translated to a [[Polypeptide|polypeptide in]] a process called [[Translation|translation]] by [[TRNA|tRNA]].

In the DNA [[Double helix|double helix]] the strands of the [[Sugar phosphate backbone|backbone]] are closer together on one side of the [[Helix|helix]] than they are on the other. This leads to the formation of major and minor grooves<ref name="null">Boston University (N.d.) 'Major and Minor Grooves', Available at: https://tandem.bu.edu/knex/knex.pdf</ref>. The [[Major groove|major groove]] is much wider than the [[Minor groove|minor groove]] and this means that specific [[DNA-protein interactions|DNA-protein interactions]] can take place on the major groove due to the backbone not being in the way. The specific [[Nucleotides|nucleotides]] that face into the major groove are the N7 and C6 groups of [[Purines|purines]] and the C4 and C5 groups of [[Pyrimidines|pyrimidines]], which accept hydrogen ions from the [[Amino acids|amino acids]] in the [[Proteins|protein]] to form [[Hydrogen bonds|hydrogen bonds]]<ref>Delmar Larsen (N.d.), 'B-Form, A-Form, Z-Form of DNA', Available at: http://biowiki.ucdavis.edu/Genetics/Unit_I%3A_Genes,_Nucleic_Acids,_Genomes_and_Chromosomes/Chapter_2._Structures_of_nucleic_acids/B-Form,_A-Form,_Z-Form_of_DNA, Accessed: 25th November 2014</ref>.

Due to the [[Double helix|double helical]] structure of DNA, the [[Nitrogenous base|nitrogenous bases]] are found on the inside of the structure, forming a [[Hydrophobic|hydrophobic]] interior. The negative charge from the [[Phosphate group|phosphate groups]] gives the [[Sugar phosphate backbone|sugar-phosphate backbone]] of DNA a negative charge, which repels [[Nucleophile|nucleophiles]], including [[Water|water]]. This makes DNA less vulnerable to nucleophilic attack, thus DNA is considered to be a very stable molecule. DNA is much more stable then [[RNA|RNA]] since [[RNA|RNA]] is only single-stranded - the [[Nitrogenous base|nitrogenous bases]] are left exposed to attack by [[Nucleophile|nucleophiles]] on one side.

In 1953, despite many other theories, [[James watson|James Watson]] and [[Francis Crick|Francis Crick]] discovered the true structure of a double stranded DNA molecule to be a 'Double Helix'. This was solved as a result of 'stick-and-ball' models they created, along with utilising the work of fellow scientists [[Rosalind Franklin|Rosalind Franklin]] and [[Maurice Wilkins|Maurice Wilkins]] on [[X-ray crystallography|X-ray crystallography]]<ref>http://nobelprize.org/educational/medicine/dna_double_helix/readmore.html</ref>. The [[X-ray diffraction|X-ray diffraction]] photographs obtained from [[DNA|DNA]] fibres, displayed a unique X-shape, which illustrates a helical stucture, although they indicated a repeating structure of 3.4 Å apart per turn of the helix, each base is rotated 36 degrees from the next one. The diameter of the helix is 23.7 Å. They found that the sugar-phosphate backbone was on the outside and the bases are positioned on the inside of the helix<ref>http://www.chm.bris.ac.uk/motm/dna/dna.htm</ref><ref>J.Berg, J.Tymoczko, L.Stryer;, 113-115, 2012 Freeman; Biochemistry</ref>.

The above information described the B-form of DNA. DNA is also found in A- and Z-forms<ref>Berg, J.M., Tymoczko, J.L. and Stryer, L. (2011) Biochemistry. Seventh Edition. Basingstoke: Basingstoke : Palgrave Macmillan. p20</ref>. When the DNA becomes dehydrated, the A-form can be observed<ref>Ferrier, D.R. (2014) Biochemistry. Baltimore, Md. ; London: Baltimore, Md. ; London : Lippincott Williams and Wilkins. p398</ref>. It is also right-handed, but there are 11 bases per turn and the helix is broader. The diameter is 25.5 Å. Another difference is that the tilt of the base pairs increases by 18o, to 19o from perpendicular to the helix axis.

The Z-form differs far more as it is a left-handed double helix. This form is rarely seen without the help of high salt concentrations<ref>Bae, S., Kim, D., Kim, K.K., Kim, Y.-g., Hohng, S. and Kim, Y.-G. (2011) 'Intrinsic Z- DNA is stabilized by the conformational selection mechanism of Z- DNA-binding proteins', Journal of the American Chemical Society, 133(4), p. 668.</ref>. The bonds are zigzagged as the bonds are alternating anti and syn (whereas A- and B-forms are anti only). The Z-form is narrower, having a diameter of only 18.4 Å, but there is a 3.8 Å rise per base pair. It is thought that transitions between the B and Z forms of DNA may be involved in the regulation of gene regulation.

B-DNA is most commonly seen in all life forms<ref>Malacinski, G. Essentials of molecular biology.4th Ed. New Delhi: Narosa. 2003.</ref>, however, A-helical and Z-helical structures co-exsist in cells; i.e. it is very common to observe a molecule of B-DNA and Z-DNA , in a predominantly B-DNA confirmation.

The DNA of the Indian muntjac which is an Asiatic deer has the longest length (approximately 3 billion nucleotides) among all the known DNA molecules of other organisms<ref name="null">Berg, J.M, Biochemistry, 7th ed, 2012:117</ref>.

DNA is negatively charged due to the negativley charged [[Inorganic phosphate|phosphate ions in]] the [[Sugar-phosphate backbone|sugar-phosphate backbone]]. Hence it can be used for [[Gel electrophoresis|gel electrophoresis]] to identify different lengths of DNA. The negative charge of the backbone, along with the [[OH group|OH-groups on]] the [[Deoxyribose sugar|deoxyribose sugar]], means that the backbone is [[Hydrophillic|Hydrophillic]] as [[Water|water can]] form [[Hydrogen bonds|hydrogen bonds with]] it. The centre of the DNA molecule is [[Hydrophobic|hydrophobic]] due to the lack of charge in [[DNA bases|DNA bases]]. The [[Hydrophillic|hydrophillic outer]] and [[Hydrophobic|hydrophobic inner]] of the DNA molecule means that it is soluble in water<ref>Ruvolo M, Hartl, DL (2012) Genetics : analysis of genes and genomes, 8th ed, Burlington, MA : Jones and Bartlett Learning</ref>.

=== Replication ===

The double stranded nature of DNA is important to the "[[Semi-conservative replication|semi-conservative replication]]" method of DNA replication. In this process, the e[[Enzyme|nzyme]] DNA [[DNA helicase|helicase]] unwinds the double helix by breaking the [[Hydrogen bonds|hydrogen bonds]] between the complementary bases on each strand revealing the 2 seperate strands. On these strands are the revealed bases, which attract complementary bases on free [[Nucleotide|nucleotides]]. The free [[Nucleotide|nucleotides]] are joined together by an [[Enzyme|enzyme]] [[DNA polymerase|DNA polymerase]]. Deoxyribonucleotide triphosphate ([[DNTP|dNTPs]]) are added onto the 3' hydroxyl group on the growing strand through the 5' triphosphate group on the incoming dNTP in a esterification reaction<ref>Berg JM, Tymoczko JL, Gatto GJ jr, Stryer L. Biochemistry. 8th ed. New York: W.H. Freeman and Company. 2015. P107-111</ref>. The joining of nucleotides forms a new strand of DNA which is identical to the other double strand of DNA, as it uses one of the original strands as a template for replication. Each daughter double strand of DNA is made up of a parent strand and a newly sythesised strand.

Even though both strands in the parental DNA molecule are copied to form identical products, the two strands are copied in a slightly different manner from each other. This is due to the fact that DNA is always synthesised in a 5' to 3' direction. The 3' to 5' strand, known as the leading strand, is copied continuously by [[DNA Polymerase|DNA polymerase]]. The other strand is called the lagging strand, as it is replicated more slowly. To replicate the [[Lagging strand|lagging strand]], RNA [[Primers|primers]] are placed on several points along the lagging strand by an enzyme called [[DNA Primase|primase]]. The gaps on the lagging strand between the RNA primers are replicated by DNA polymerase, and the short fragments of replicated DNA are known as [[Okazaki fragments|Okazaki fragments]]. However, in order to complete the replication of the lagging strand, RNA primers must be replaced by DNA sequences. Another DNA polymerase removes the RNA primers and synthesises DNA fragments to replace them. The [[Okizaki fragment|Okazaki fragments]] and the RNA primer replacements are still not joined, so [[DNA ligase|DNA ligase]] comes in an ligates all the fragments of DNA together<ref>Hartl, D. L. and Ruvolo, M., 2012. Genetics: Analysis of Genes and Genomes. 8th ed. Burlington: Jones and; Bartlett Learning. Pages 205-210</ref>.

The theory of [[Semi-conservative replication|semi-conservative replication]] was proven to be correct by the Messelson-Stahl experiment. In this experiment, [[Escherichia coli|''E.coli'']] were grown in a medium containing 15-N for a number of generations. The bacteria were then transferred to a medium containing 14-N. After one replication cycle DNA was extracted from the bacteria and [[Centrifugation|centrifuged]]. The centrifugation separated the DNA by density, producing one band wita h density between that of 15-N DNA and 14-N DNA. This showed that one strand came from the parent (15-N) and one strand was newly synthesised from free nucleotides (14-N)<ref>Berg J.M, Tymoczko J.L, Stryer L, Biochemistry, 7th ed. 2012:123, New York: W.H Freeman and Company</ref>.

=== References ===

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Neurotransmitter

2018-12-09T21:39:05Z

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Neurotransmitters are signalling [[Molecule|molecules]] released by [[Exocytosis|exocytosis]] from vesicles in the pre-synaptic cell causing [[Depolarisation|depolarisation]], they diffuse across the [[Synaptic cleft|synaptic cleft]] in response to an [[Action potential|action potential]]. The neurotransmitter causes an electrical change in the post-synaptic cell.

The signals can be excitatory (open [[Cation channels|cation channels]] (e.g. [[Sodium|Na]][[Sodium|+]])) or inhibitory (open Cl- or [[Potassium Channel|K]][[Potassium Channel|+]][[Potassium Channel|channels]]). Excitatory signals bring the cell closer to threshold where as inhibitory signals cause the cell to move away from threshold value. When the cell reaches threshold an [[Action potential|action potential]] is fired<ref>Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science</ref>.

Transmission of a signal between two neurones can be improved if the neurotransmitter is repeatedly released from the presynaptic membrane, this is called [[Long term potentiation|long term potentiation]] (LTP). An example of this is the release of the neurotransmitter [[Glutamate|glutamate]]. The postsynaptic membrane holds two ligand-gated ion channels ([[Iontrophic receptor|iontrophic receptors]]): the [[AMPA receptor|AMPA receptor]] and the [[NMDA receptor|NMDA receptor]]. When [[Glutamate|glutamate]] diffuses across the synaptic cleft and binds to the [[AMPA receptor|AMPA receptor]], the ion channel opens and allows the entry of sodium ions (Na+) into the [[Postsynaptic cell|postsynaptic cell]]. Entry of sodium ions causes the voltage to become less negative. This initiates an EPSP ([[Excitatory post-synaptic potential|excitatory post-synaptic potential]]) which in turn can trigger an action potential if the voltage reaches or exceeds the [[Threshold_potential|threshold]] (-55 mV). In contrast, [[Glutamate|glutamate]] initially has no effect on the [[NMDA receptor|NMDA receptor]] as a [[Magnesium|magnesium]] ion (Mg2+) attached to the receptor inhibits it from opening. But as [[Glutamate|glutamate]] is repeatedly released, further depolarisation of the postsynaptic membrane triggers the release of the [[Magnesium|magnesium]] ion from the receptor. This allows the entry of [[Calcium|calcium]] ions (Ca2+) which then activates other [[Molecules|molecules]] in the [[Secondary messenger|secondary messenger]] pathway<ref>Alberts B, Johnson A, Lewis J, Raff M, Walter P (2008) Molecular Biology Of The Cell, Garland Science Taylor and Francis Group, New York pg 691-692</ref>.

=== Different types of Neurotransmitters: ===

==== G-protein linked receptors (Metabotropic neurotransmitters): ====

*[[Histamine|Histamines]]
*[[Epinephrine|Epinepherine]]
*[[ATP|ATP]]
*[[Acetylcholine|Acetylcholine]]

==== Other Neurotransmitters (that don't require receptors): ====

*[[Nitric oxide|Nitric oxide]]
*[[Testosterone|Testosterone]]

=== References ===

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Neurotransmitter

2018-12-09T21:37:15Z

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Neurotransmitters are signalling [[Molecule|molecules]] released by [[Exocytosis|exocytosis]] from vesicles in the pre-synaptic cell causing [[Depolarisation|depolarisation]], they diffuse across the [[Synaptic_cleft|synaptic cleft]] in response to an [[Action potential|action potential]]. The neurotransmitter causes an electrical change in the post-synaptic cell.

The signals can be excitatory (open [[Cation channels|cation channels]] (e.g. [[Sodium|Na]][[Sodium|+]])) or inhibitory (open Cl- or [[Potassium Channel|K]][[Potassium Channel|+]][[Potassium Channel|channels]]). Excitatory signals bring the cell closer to threshold where as inhibitory signals cause the cell to move away from threshold value. When the cell reaches threshold an [[Action potential|action potential]] is fired<ref>Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science</ref>.

Transmission of a signal between two neurones can be improved if the neurotransmitter is repeatedly released from the presynaptic membrane, this is called [[Long term potentiation|long term potentiation]] (LTP). An example of this is the release of the neurotransmitter [[Glutamate|glutamate]]. The postsynaptic membrane holds two ligand-gated ion channels ([[Iontrophic receptor|iontrophic receptors]]): the [[AMPA receptor|AMPA receptor]] and the [[NMDA receptor|NMDA receptor]]. When [[Glutamate|glutamate]] diffuses across the synaptic cleft and binds to the [[AMPA receptor|AMPA receptor]], the ion channel opens and allows the entry of sodium ions (Na+) into the [[Postsynaptic_cell|postsynaptic cell]]. Entry of sodium ions causes the voltage to become less negative. This initiates an EPSP ([[Excitatory post-synaptic potential|excitatory post-synaptic potential]]) which in turn can trigger an action potential if the voltage reaches or exceeds the threshold (-55 mV). In contrast, [[Glutamate|glutamate]] initially has no effect on the [[NMDA receptor|NMDA receptor]] as a [[Magnesium|magnesium]] ion (Mg2+) attached to the receptor inhibits it from opening. But as [[Glutamate|glutamate]] is repeatedly released, further depolarisation of the postsynaptic membrane triggers the release of the [[Magnesium|magnesium]] ion from the receptor. This allows the entry of [[Calcium|calcium]] ions (Ca2+) which then activates other [[Molecules|molecules]] in the [[Secondary messenger|secondary messenger]] pathway<ref>Alberts B, Johnson A, Lewis J, Raff M, Walter P (2008) Molecular Biology Of The Cell, Garland Science Taylor and Francis Group, New York pg 691-692</ref>.

=== Different types of Neurotransmitters: ===

==== G-protein linked receptors (Metabotropic neurotransmitters): ====

*[[Histamine|Histamines]]
*[[Epinephrine|Epinepherine]]
*[[ATP|ATP]]
*[[Acetylcholine|Acetylcholine]]

==== Other Neurotransmitters (that don't require receptors): ====

*[[Nitric oxide|Nitric oxide]]
*[[Testosterone|Testosterone]]

=== References ===

<references />

Ionic interactions

2018-12-09T21:30:55Z

180400010: Added links

[[Ionic|Ionic]] interactions are a type of bonding that occurs between two groups of oppositely [[charged|charged]] [[Ions|ions]] due to [[Electrostatic force|electrostatic forces of attraction]]<ref>ScienceDirect. Ionic Interaction. 2015 [cited 09/12/18]; Available from: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/ionic-interaction</ref>.

 

 

 

 

 

 

 

 

 

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Ionic interactions

2018-12-09T21:27:47Z

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Ionic interactions are a type of bonding that occurs between two groups of oppositely charged [[Ions|ions]] due to [[Electrostatic force|electrostatic forces of attraction]]<ref>ScienceDirect. Ionic Interaction. 2015 [cited 09/12/18]; Available from: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/ionic-interaction</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 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]]

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]]

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 ==

<references />

<references />

Protein

2018-12-09T21:22:51Z

180400010:

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 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]]

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]]

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 ==

<references />

<references />

Protein

2018-12-09T21:21:35Z

180400010: Added images of secondary and tertiary structures.

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 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]]

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]]

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 ==

<references />

<references />

File:Tertiary.jpg

2018-12-09T21:17:26Z

180400010: Tertiary structure of a protein.

Tertiary structure of a protein.

File:Secondary.jpg

2018-12-09T21:17:01Z

180400010: Secondary structure of a protein

Secondary structure of a protein

Protein

2018-12-09T21:15:22Z

180400010: Added an image of primary structure

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 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.

=== 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>.

=== 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 ==

<references />

<references />

Protein

2018-12-09T21:03:28Z

180400010: Added an image of primary structure

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 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>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.

=== 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>.

=== 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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File:Primary structure.jpg

2018-12-09T20:42:17Z

180400010: Primary structure of protein

Primary structure of protein

Ionic interactions

2018-12-09T20:32:06Z

180400010: Created page with "Ionic interactions are a type of bonding that occurs between two groups of oppositely charged ions due to electrostatic forces of attraction..."

Ionic interactions are a type of bonding that occurs between two groups of oppositely charged [[Ions|ions]] due to [[Electrostatic force|electrostatic forces of attraction]]<ref>https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/ionic-interaction</ref>.

 

 

 

 

 

 

 

 

 

= References =

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