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Oxymyoglobin

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Haemoglobin

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'''Haemoglobin''' (also '''hemoglobin''', or abbreviated '''Hb''') is a [[Proteins|protein]] which is used in red [[Blood|blood]] cells to store and transport [[Oxygen|oxygen]]. It is found in many multi-cellular [[Organism|organisms]] such as mammals where simple diffusion would be unable to supply adequate oxygen to tissue and cells.

Haemoglobin is made up of four [[Polypeptide|polypeptide]] subunits, two alpha (α) subunits and two beta (β) subunits. Each of the four subunits contains a [[Heme|heme]] ( contains iron) molecule, where the [[Oxygen|oxygen]] itself is bound through a reversible reaction, meaning that a haemoglobin molecule can transport four oxygen molecules at a time.

The reversible nature of the binding of oxygen allows for both the uptake of [[Oxygen|oxygen]] in the [[Lung|lungs]] and its release in body tissues.

The heme molecules each contain a single central iron atom and are responsible for giving the red colour to haemoglobin, and thus to the blood as a whole. <ref>Alberts B, Bray D, Hopkin K, Johnson A, Lewis J, Raff M, Roberts K and Walter P (2010) Essential Cell Biology, 3rd Edition, New York: Garland Science</ref>

The four subunits of Hemoglobin are similar to [[Myoglobin|myoglobin]] <ref>Berg J., Tymoczko J and Stryer L. (2011) Biochemistry, 7th edition, England: W.H. Freeman and Company p 207</ref>. '''Myoglobin''' is a single polypeptide, existing in either the '''[[Deoxymyoglobin|deoxymyoglobin]]''' form (not bound to oxygen) or the '''oxymyoglobin''' form (bound to oxygen)<ref>Berg J., Tymoczko J and Stryer L. (2011) Biochemistry, 7th edition, England: W.H. Freeman and Company p204</ref>. Myoglobin contains [[Heme|heme]]<ref>Berg J., Tymoczko J and Stryer L. (2011) Biochemistry, 7th edition, England: W.H. Freeman and Company p207</ref>. '''Heme''' contains a central iron atom surrounded by '''[[Protoporphyrin|protoporphyrin]]''', which is the organic component<ref>Berg J., Tymoczko J and Stryer L. (2011) Biochemistry, 7th edition, England: W.H. Freeman and Company p207</ref>. When O2 binds to the iron atom (the iron must be in the Fe2+ state for O2 to bind), the iron atom actually moves from outside of the plane of the porphyrin to within the plane of the [[Porphyrin|porphyrin]]<ref>Berg J., Tymoczko J and Stryer L. (2011) Biochemistry, 7th edition, England: W.H. Freeman and Company p208</ref>.

The binding of O2 in hemoglobin is '''cooperative''', meaning that the binding of O2 in each of the one subunit is not independent of the binding at other subunits<ref>Berg J., Tymoczko J and Stryer L. (2011) Biochemistry, 7th edition, England: W.H. Freeman and Company p207</ref>, so as one oxygen binds to a heme group it causes conformational changes to the other heme groups making them more accesible to oxygen, thus leading to the successive binding of other oxygen atoms<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 5th edition, New York: WH Freeman</ref>. Even though myoglobin has a higher affinity for O2 than hemoglobin, hemoglobin is more effective and efficient at '''delievering oxygen to tissues'''. In lungs, 98% of hemoglobin is saturated, whereas in the tissues, only 32% of hemoglobin is saturated<ref>Berg J., Tymoczko J and Stryer L. (2011) Biochemistry, 7th edition, England: W.H. Freeman and Company p208</ref>. This means that in the tissues, 66% of hemoglobin subunits released their oxygen. In contrast, in lungs, 98% of myoglobin would be saturated, and 91% of myoglobin would be saturated in tissues<ref>Berg J., Tymoczko J and Stryer L. (2011) Biochemistry, 7th edition, England: W.H. Freeman and Company p208</ref>. Compared to myoglobin, hemoglobin has a much more '''complete.''' Hemoglobin has a T and R state. In the T ('''tense''') state, or '''deoxygenated''' state, the binding sites of hemoglobin are constrained. In the R ('''relax''') state, or '''oxygenated''' state, the binding sites are less constrained, making it easier for the hemoglobin subunits to bind to [[Oxygen|oxygen]] <ref>Berg J., Tymoczko J and Stryer L. (2011) Biochemistry, 7th edition, England: W.H. Freeman and Company p210</ref>. There are two models that attempt to explain the '''cooperativity of hemoglobin'''. The first model is the '''concerted''', or '''MWC''' model. This model proposes that whenever an O2 molecule binds to a subunit of hemoglobin, it shifts the equilibrium between the T and R states. According to this model, when none of the hemoglobin subunits are bound to oxygen, the T state of the protein is favored. As more and more sites are bound to oxygen, the reaction shifts to favor the R state. A transition from the T state to the R state will increase the binding affinity of the other sites for O2. The '''sequential model''', on the other hand, suggests that you don't have to have a conversion from the T state to the R state to increase the affinity of other binding sites. A mixture of both models explains what is observed about hemoglobin cooperativity better than either one of these models can achieve on its own. It is observed that when 3 out of 4 subunits of hemoglobin are bound to O2, the protein is almost always in the R state. Another observation is that when 1 out of 4 hemoglobin subunits are bound to O2, the protein is almost always in the T state<ref>Berg J., Tymoczko J and Stryer L. (2011) Biochemistry, 7th edition, England: W.H. Freeman and Company p211</ref>.

[[Image:Hemoglobin ribbon 4subunits.jpg|left|250x199px|Hemoglobin ribbon 4subunits.jpg]]'''Haemoglobin''' (also spelled Hemoglobin and abbreviated Hb or Hgb) is a respiratory pigment, which transports oxygen essential for cellular [[Metabolism|metabolism]]. 

In its quarternary structure is a [[Globular protein|globular protein]], its chains are closely coiled together to form a compact, almost spherical molecule. A single molecule consists of 4 subunits: two α-polypeptide chains (each identical and containing 141 [[Amino acid|amino acids]]) and two β-polypeptide chains (each identical and containing 146 amino acids). The location of the genes for both types of polypeptide chains differs: α-chain gene is located on chromosome 16, the β-chain gene is located on chromosome 11. <ref>Klug William S., Essentials of genetics, 8th edition, 2013, Boston: Pearson, p.376-377</ref>

Each [[Polypeptide|polypeptide]] is associated with [[Haem group|haem]], which is the prosthetatic group that mediates reversible binding of [[Oxygen|oxygen]] by haemoglobin. It contains a ferrous (Fe2+) ion. Each Fe2+ ion can combine with a single oxygen molecule (O2), making a total of four oxygen molecules that can be carried to the tissues and return carbon dioxide (CO2) from the tissue to the lungs.<ref>[Anon]. 2002. Hemoglobin synthesis [Online]. [Accessed 21.11.2014] Available from: http://sickle.bwh.harvard.edu/hbsynthesis.html</ref> 

The cell that produces haemoglobin is called an [[Erythrocyte|erythrocte]] (also known as RBC, red blood cell). Each red cell contains about 280 million molecules of haemoglobin.<ref>Sears, Duane W. 1999. Overview of Hemoglobin's Structure/Function Relationships. [Online]. [Accessed 20.11.2014]fckLRAvailable from: http://mcdb-webarchive.mcdb.ucsb.edu/sears/biochemistry/tw-hbn/hba-overview.htm#Top</ref>

Haemoglobin (also spelled hemoglobin) is [[Iron|iron]] containing compund that binds to [[Oxygen|oxygen]] gas. It is found in the [[Red blood cells|red blood cells]] of vertebrates. It transports oxygen from the respiratory organ, the [[Lungs|lungs]], to the different cells of body. It is a [[Protein|protein]] that contains a quaternary structure made up of 4 sub-units. They consist of 2 alpha sub units and 2 beta subunits. Each subunit conatins a heme group which contains and iron [[Atom|atom]]. Each iron atom binds to 1 oxygen molecule. Thus 1 haemogobin molecule transports 8 atoms of oxygen. When absorbtion of oxygen occurs haemoglobin becomes [[Oxyheamoglobin|oxyhaemoglobin]] and it forms the reddish colour of the red blood cells. Upon arrival at a cell it deposits its oxygen thus allowing oxidization of glucose to take place via [[Respiration|respiration]]. This releases energy in form of [[ATP|ATP]]. The waste product, [[Carbon dioxide|carbon dioxide]] is transported by haemoglobin to the lungs for expiration <ref>Berg, J. Stryer, L. Tymoczko J. (2012) Biochemistry, 7th Edition : W.H. Freeman and Company. Chapter 7, Page 203-207</ref>.

Haemoglobin also acts as a buffer that helps maintain the physiological pH. It has a histidine group that can uptake H+ ions when the pH decreases and dissociate to release H+ ions when pH increases<ref>2. Abelow B. Understanding acid-base. Baltimore: Williams and Wilkins; 1998.</ref>. When it works together with the lungs, it is able to control the uptake of carbon dioxide which controls the [[Buffer|bicarbonate buffer system]] thus being able to sustain the physiological pH. 

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Dominant

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A term given to an [[Allele|allele]] that will always be expressed in the [[Phenotype|phenotype]] of an [[Organism|organism]]. The opposite of a [[Dominant allele|dominant allele]] is known as a [[Recessive|recessive]] allele <ref>Molecular Biology of The Cell. 5th Edition, Alberts 2008 Glossary:11</ref>. 

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Mutation

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A '''mutation''' is a change in a [[Gene|gene]] (or genetic material) that is heritable and results in a [[Mutant|mutant]] (as opposed to the [[Wild - type]]) <ref>Hartl DL, Jones EW (2009). "Genetics; analysis of genes and genomes". Jones and Bartlett Publishers. 7th Edition. 26-27.</ref>. A mutation produces mutant [[MRNA|mRNA]], which is translated into a mutant [[Protein|protein]]. As such, they can be exhibited as a mutation in the [[Organism|organism]] as long as the mutation is not a silent mutation. Mutations can alter the protein produced, affect the function of the gene, or have no effect at all as in silent mutation. Studies show that around 70% of mutations<ref>Sawyer SA, Parsch J, Zhang Z, Hartl DL (2007). "Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila". Proc. Natl. Acad. Sci. U.S.A, 6504–10.</ref> will have damaging effects to the organism, with the others being either beneficial or silent. While a mutation is typically damaging, some can have positive effects on the organism and aid in [[Evolution]].

Mutation is the change in [[DNA|DNA]] sequence of a cell due to errors in [[DNA|DNA]] replication or during [[Meiosis|meiosis]]. It can also be caused by environmental agents called [[Mutagens|mutagens]] though induced mutation. Mutagens are physical or chemical agents that lead to changes in genetic material of an organism. There are various types of mutations:

[[Point mutation|Point mutation]] is the addition or deletion of a single base pair within the [[DNA|DNA]]. It usually occurs through base substitution and even though it only causes a minute change in [[DNA|DNA]] it can still have important consequences. [[Silent mutation|Silent mutation]] is the change in [[Nucleotide|nucleotide]] sequence of an [[Amino acid|amino acid]] in a [[Polypeptide|polypeptide]]. Even though an [[Nucleotide|nucleotide]] sequence is changed it does not alter the [[Amino acid|amino acid]] of the [[Polypeptide|polypeptide]], this is because silent mutation only occurs in the third base of codons as genetic code is degenerate. As silent mutations does not affect the function of the protein it is considered as a neutral mutation.

[[Missense mutation|Missense mutation]] occurs through base substitution which changes a single [[Amino acid|amino acid]] in the [[Polypeptide|polypeptide]]. [[Missense mutation|Missense mutation]] can also be considered as a neutral mutation as it may not alter the function of the protein. They are not always neutral mutation and can also have a large effect on the function of the protein.

[[Nonsense mutation|Nonsense mutation]] is another mutation which can have a dramatic effect on the [[Polypeptide|polypeptides]] sequence. It affects the [[Codon|codons]] of the [[Polypeptide|polypeptide]], changing a normal codon to a [[Stop codon|stop codon]]. This causes early termination of translation resulting in a truncated [[Polypeptide|polypeptide]], which is less likely to function properly.

[[Frameshift mutation|Frameshift mutation]] can also have a dramatic effect on the [[Polypeptide|polypeptide]] sequence even causing inhibition of [[Protein|protein]] function. It involves addition or deletion of [[Nucleotides|nucleotides]] which are not in multiples of three. As [[Codon|codons]] come in multiples of three, frameshift causes a completely different amino acid sequence to be read downstream from point of mutation <ref>Robert J. Brooker, Eric P. Widmaier, Linda E. Graham, Peter D. Stilling. (2008) Biology, McGraw-Hill International Edition, New York: McGraw-Hill. Chapter 14, Page 278-283.</ref>. 

= Causes =

Mutations can be either spontaneous or induced. They often occur at hotspots, where they are more likely to happen. The rate at which this and other mutations happen vary by [[Species|species]], and can have both damaging and beneficial effects.

'''Spontaneous''' mutations occur on a molecular level and include;

*[[Tautomerism]] - A [[Hydrogen atom|hydrogen atom]] or [[Bond|bond]] is repositioned to bring about incorrect [[Base pairings|base pairings]] <ref>Roman M. Balabin (2009). "Tautomeric equilibrium and hydrogen shifts in tetrazole and triazoles: Focal-point analysis and ab initio limit". J. Chem. Phys. 131</ref>.
*[[Deamination]] - Removal of an [[Amine|amine]] group. 
*[[Depurination]] - A [[Purine|purine]] base (A or G) is lost <ref>Lindahl, T. (22 April 1993). "Instability and decay of the primary structure of DNA". Nature 362 (6422): 709–715</ref>.
*[[Slipped strand mispairing]] - Template strand joined in the wrong spot <ref>Levinson G, Gutman, G. A. (1987). "Slipped-Strand Mispairing: A Major Mechanism for DNA Sequence Evolution". Mol. Biol. Evol. 4 (3): 203–221</ref>.

'''Induced''' mutations on a molecular level include;

*[[Hydroxylamine]] - NH2OH <ref>Inoue S, Kawanishi S, Yamamoto K (1993). "Site-specific DNA damage and 8-hydroxydeoxyguanosine formation by hydroxylamine and 4-hydroxyaminoquinoline 1-oxide." Carcinogenesis. Jul;14(7):1397-401.</ref>
*[[Base analogs]] - substitute for a regular base <ref>Griffiths AJ, Wessler SR, Lewontin RC, Gelbart WM, Suzuki DT, Miller JH. Introduction to Genetic Analysis, 8th ed. New York:W.H.Freeman and Co, 2005.</ref>.
*[[Alkylating agents]] - mutates all types of [[DNA|DNA]].
*[[Oxidative damage]] - involved in many diseases <ref>Sies, H. (1985). "Oxidative stress: introductory remarks". In H. Sies, (Ed.). Oxidative Stress. London: Academic Press. pp. 1–7.</ref>.
*[[Nitrous acid]] - [[Amine]] groups to [[Diazo]] groups.
*[[Radiation]] - both [[Ultraviolet]] and [[Ionising]].
*[[Viral]] infections - such as herpes simplex <ref>Pilon L, Langelier Y, Royal A (1 August 1986). "Herpes simplex virus type 2 mutagenesis: characterization of mutants induced at the hprt locus of nonpermissive XC cells". Mol. Cell. Biol. 6 (8): 2977–83</ref>.

= Types =

'''Point mutations''' exchange one [[Nucleotide]] for another. Transitions see a [[Purine|purine]] changed for a [[Purine|purine]], or a [[Pyrimidine|pyrimidine]] for a pyrimidine, while transversion sees a [[Purine|purine]] for a [[Pyrimidine|pyrimidine]] or vice versa. The former is the most common.

*'''Silent''' mutations code for the same [[Amino acid|amino acid]] due to the [[Degenerate code|degenerate code]], so the same [[Protein|protein]] is produced.
*'''Missense''' mutations code for a different amino acid, so a different protein will be produced.
*'''Nonsense''' mutations code for a [[Stop codon|stop codon]] and result in a [[Truncated protein|truncated protein]] (ended early).

'''Insertion mutations''' occur when a nucleotide is added into the sequence. This will cause a [[Frame shift|frame shift]] as all following bases will be read in the wrong frame (different three read). It is more harmful the earlier it is.

'''Deletion mutations''' occur when a nucleotide is removed from the sequence. This also causes a frame shift as all following bases are moved back one. It is also more harmful the earlier it is found.

= Effects =

Mutations can be classed as loss of function or gain of function. Depending on the protein affected by the mutated sequence, it may result in a complete loss of function in that gene or allow it to gain a new or abnormal function. Loss of function mutations normally exhibit a [[Recessive|recessive]] [[Phenotype|phenotype]], and gain of function usually exhibit a [[Dominant|dominant]] [[Phenotype|phenotype]]. Furthermore, all mutations can be either harmful or beneficial, depending on whether they increase the fitness of the organism and make it more suited for survival. This is because mutations drive [[Natural selection|natural selection]]], and thus also for [[Evolution|evolution]] to occur. 

'''Harmful mutations''' is where the [[Fitness]] of the organism is decreased and so its [[Survival]] becomes less likely. Resultant [[Genetic disorders|genetic disorders]] can be hereditary if present in [[Germ cells|germ cells]], and while this is useful for natural selection in beneficial mutations, it is not useful in harmful mutations. Most mutations associated with genetic disorders are classed as harmful.

'''Beneficial mutations''' is where the [[Fitness|fitness]] of the organism is increased and so its [[Survival|survival]] becomes more likely. Environmental changes mean that organisms with specific mutations are better adapted to survive, and so are more likely to reproduce and pass on this mutation to their offspring. This drives evolution as eventually these mutations could give rise to a new [[Species]]. Both types of mutations can be seen in [[Sickle Cell]] disease. The sickle-shape of the [[Red blood cells|red blood cells]] is harmful to those who carry both [[Recessive alleles]] and therefore suffer from the disorder. However, having just one of the alleles and thus being a [[Carrier|carrier]] still causes some sickle cell symptoms, but also gives the benefit of [[Malaria]] resistance. This is because malaria infection is stopped when a blood cell sickles <ref>Aidoo M, Kariuki S, Kolczak MS, Kuile FOT, Lal AA, McElroy PD, Nahlen BL, Terlouw DJ, Udhayakumar V (2002). "Protective effects of the sickle cell gene against malaria morbidity and mortality." The Lancet. 359; 1311-1312.</ref>. In Africa, there is a [[Selection pressure|selection pressure]] against malaria, so carriers of the sickle cell allele are more likely to reproduce and pass on this resistance. 

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Kinetichore

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The Kinetochore is a multilayer [[Protein|protein]] structure that forms at the [[Centromere|centromere]] region of each [[Sister chromatids|sister chromatid]].  The plus end of the [[Microtubules|microtubules forming]] [[Mitotic spindle|mitotic spindles]] from the [[Centrosomes|centrosomes]] bind to the kinetochore at specialised sites and form a bridge between the [[Chromatids|chromatids]] and the mitotic[[Mitotic spindle| spindles]] in such a way that allows continual [[Polymerisation|polymerisation]] and [[Depolymerisation|depolymerisation]] of the [[Microtubules|microtubule]]. This is key to the movement of chromatids during [[Anaphase|anaphase]].<ref>Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2008) Molecular Biology of the Cell, 5th Edition, New York, Garland Science</ref> During [[Anaphase|anaphase]] of [[Mitosis|mitosis]] the [[Mitotic spindles|mitotic spindles]] contract to pull apart the[[Sister chromatids|sister chromatids]]. The kinetochore is essential for this movement as it binds to a [[Microtubule motor protein|microtubule motor protein]] that moves the [[Sister chromatids|sister chromatid to]] the minus end of the [[Mitotic spindles|mitotic spindle]] at the poles of the cell.  Free kinetochores with no [[Microtubules|microtubules]] bound act as a check point for [[Mitosis|mitosis]], halting the process until all [[Chromatids|chromatids]] are bound, ensuring correct separation of [[Chromatids|chromatids]] and preventing [[Aneuploidy|aneuploidy]].<ref>Cleveland, Mao, Sullivan (2003) "Centromeres and Kinetochores: From Epigenetics to Mitotic Checkpoint Signaling" Cell Volume 112, Issue 4, pp407–421</ref>

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Metaphase

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Metaphase is the 3rd Phase in the process of [[Mitosis|Mitosis]] and [[Meiosis|Meiosis]], proceeding [[Interphase|Interphase]] and [[Prophase|Prophase]] but preceding [[Anaphase|Anaphase]] and [[Telophase|Telophase]]. In Metaphase the Mitotic [[Spindles|spindles]] made from bundles of [[Microtubules|microtubules]] attach to the [[Centromere|centromere]] by binding to the [[Protein|protein]] known as the [[Kinetichore|kinetochore]]. The [[Chromosomes|chromosomes]] line up along the centre line of the [[Nucleus|nucleus]] known as the metaphase plate. At this time the chromosomes are in the middle of the cell equidistant from the poles of the nucleus. Being aligned on the [[Metaphase plate|metaphase plate]] the chromosomes are easiest to count and examine due to reaching their maximum contraction. With all the chromosomes aligned on the Metaphase plate, Anaphase can subsequently occur <ref>Essential Genetics. A Genomics Perspective, Hartl and Jones</ref>. 

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Patau Syndrome

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Patau Syndrome is a [[Trisomy|trisomy]] of [[Chromosome 13|chromosome 13]] due to a [[Nondisjuction|nondisjunction]] during [[Meiosis|meiosis]]. Patau Syndrome can also result from a [[Translocation|Robertsonian translocation]], a section of chromosome 13 attaches to another [[Chromosome|chromosome]]. This results in [[Cell|cell]] containing 2 intact copies of chromosome 13 and an extra partial copy. Patau Syndrome has a prevalence of around 1 in every 10,000 live births<ref>"http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0002625/", Trisomy 13, PubMed Health, 04-08-2011. Retrieved 17-10-2012.</ref> .

=== Signs and Symptoms of Trisomy 13 ===

Infants ususally have a normal birth weight, a tiny head and a titlted forehead. <ref>http://www.aboutkidshealth.ca/EN/HEALTHAZ/CONDITIONSANDDISEASES/GENETICDISORDERS/Pages/trisomy-13-patau-syndrome.aspx</ref>

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Action potential

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An action potential is a message in the form of an electrical impulse caused by a rapid change in a cell's [[Membrane|membrane]] potential. 

When a stimulus reaches the threshold at the [[Axon hillock|axon hillock]], an action potential begins.

An action potential relies on many [[Protein|protein]] channels.  In a neurone, the [[Potassium leak channel|Potassium leak channel]] and [[Sodium pump|Sodium-Potassium pump]] maintain the resting potential. The [[Sodium voltage-gated ion channels|voltage gated sodium channel]] and the [[Voltage gated potassium channels|voltage gated potassium channel]] are involved in the progression of an action potential along the membrane.

The action potential progression can be separated into a several steps; 

#Voltage channels are closed and the Potassium leak channel and the sodium pump maintain the resting membrane potential of -70 mV. The Sodium/Potassium Pump (ATPase) is responsible for maintaining the membrane potential at -70mv, the protein actively pumps three sodium ions out of the cell and pumps two potassium ions into the cell.
#The [[Neurone|neurone]] becomes stimulated. The [[Voltage gated sodium channels|voltage gated sodium channels]] begin to open and the membrane potential begins to slowly depolarises and sodium enters the cell down its concentration gradient. All the voltage gated Sodium channels open when the membrane potential reaches around -55 mV and there's a large influx of Sodium, causing a sharp rise in voltage. As the potential nears +30mV, the rate of depolarisation slows down as the voltage gated Sodium channels become saturated and inactivate, preventing further sodium ions from entering the cell.
#[[Voltage gated potassium channels|Voltage gated potassium channels]] open, and [[Potassium|potassium]] leaves the cell down its concentration gradient. The depolarisation of the cell stops and repolarisation can occur through these voltage gated Potssium channnels.
#Voltage gated sodium channels are completely deactivated and potassium floods out through the [[Voltage gated potassium channels|voltage gated potassium channels]],
#Voltage gated potassium channels are slow to close, and therefore [[Hyperpolarisation|hyperpolarisation]] occurs. This is where the membrane potential drops below the resting potential of -70 mV as potassium continues to leave.
#Once the [[Voltage gated potassium channels|voltage gated potassium channels]] close, the resting state can be re-established through the Potassium leak channel and Sodium pump. 

The action potential travels along the neurone's [[Axon|axon]] via current loops in order to reach the [[Axon terminal|axon terminal]].

An action potential is a transient, electrical signal, which is caused by a rapid change in [[Resting membrane potential|resting membrane potential ]](-70 mV). This occurs when the [[Threshold potential|threshold potential]] (-55 mV) is reached, this causes a rapid opening in the voltage gated sodium channels leading to a influx of sodium into the cell.  The [[Threshold potential|threshold potential]] also causes a slow opening of voltage gated potassium channels leading to the eflux of potassium out of the cell. This causes the cell to [[Depolarisation|depolarise]], meaning the inside of the cell is now positive compared to the outside.

The action potenial starts in the axon hilock as there is a high density of voltage gated sodium channels here, it is also where [[Graded potentials|graded potentials]] need to reach the threshold potential to cause a action potential. If the do not reach the [[Supratheshold|supratheshold level]], then an Action Potenitial is not triggered and the graded potenital is known as [[Subthreshold|subthreshold]]. Above threshold, increase in the strength of a stimulus will not increase the size of the corresponding action potential. The strength of a stimulus, or the size of a graded potential, is indicated by frequency of action potentials travelling along a neurone.

The action potential travels via current loops. In myelinated axons its jumps from [[Node of ranvier|node of ranvier]] to node of ranvier, this is known as [[Saltatory conduction|saltatory conduction]].

The higher the density of the [[Myelin Sheath|myelin sheaths]] and higher the membrane resistance of the myelinated axon, the faster the axon potential can travel.

The point at which the membrane of an axon is depolarised causes a local circuit to be set up between the depolarised region and the region either side of it. This causes the resting at regions either side to become depolarised also. In this way the action potential sweeps along the axon.

The [[Refractory Period|refractory period]] prevents the action potential from travelling backwards. There are two types of refractory periods, the absolute refractory period and the relative refractory period. The absolute refractory period is when the membrane cannot generate another action potential no matter how large the stimulus is, this is because the voltage- gated sodium ion channels are inactivited. The relative refactory period is when the membrane can produce another action potential if the stimulus is larger than normal, this is because the voltage-gated soduim ion channels have recoveredand the voltage-gated potassium ion channels are still open. The relative refractory period is the period of hyperpolarisation after an action potential <ref>The McGill Physiology Virtual Lab, Refractory Period. Available at: http://www.medicine.mcgill.ca/physio/vlab/cap/refract.htm (Last accessed 9.11.13)</ref>.

Action potentials in neurons are also known as "nerve impulses" or "spikes" <ref>Silverthorn, D. (2012). Human physiology. 5th ed. San francisco Claifornia: Pearson Education, p.261.</ref>.

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Substrate

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This is the term referred to a [[Molecule|molecule]] which an [[Enzyme|enzyme]] interacts on to form an [[Enzyme-sustrate complex|enzyme-substrate complex]], through a [[Lock and key mechanism|lock and key mechanism]] or [[Induced fit mechanism|induced fit mechanism]]. This then causes a change in the structure of the enzyme by binding or cleaving parts. The substrate is then released from the enzyme as a [[Product|product]] <ref>Alberts, Molecular biology of a cell, fifth edition</ref>.

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Primary structure

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The primary structure is the first structure of a [[Protein|protein]] made. It is the underlying basis of how the [[Proteins|protein]] folds up and what conformational shape it takes. It is made of a linear string of [[Amino acid|amino acids]] ([[Polypeptide|polypeptide]] chain) which have been coded for by [[Codon|codons]] by [[DNA|DNA]] base sequences in the translation process. Each [[Amino acid|amino acid]] is individually different and the different chemistries of the side chains allow the [[Polypeptide|polypeptide chain]] to fold up in a unique way allowing a specific function for that [[Protein|protein]] <ref>Molecular Biology of the Cell, 5th edition, Bruce Alberts et al, p127, p131.</ref>.

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Cell

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Cells are a fundamental component of all biological existence, often referred to as the 'building blocks' of life. Some [[Organism|organisms]], such as [[Bacteria|bacteria]], are unicellular; [[Cells|cells]] exist as independent units of life. Other higher organisms are [[Multicellular|multicellular]], comprised of many cells. Within these multicellular organisms, groups of specialised cells collaborate to perform specific functions (these collaborations are referred to as tissues).

All cells adhere to specific fundamental principals, irrespective of their [[Eukaryotic|eukaryotic]] or [[Prokaryotes|prokaryotic]] classification. All cells must: have a [[Plasma membrane|plasma membrane]], to separate the [[Intracellular space|intracellular space]] from the [[Extracellular space|extracellular space]]; contain heritable genetic material, to ensure the propagation of the [[Species|species]]; contain [[Intracellular compartment|intracellular compartments]], to regionalise specific functions; regulate their [[Osmotic gradient|osmotic gradient]] via the transportation of chemical species ([[Ions|ions]], [[Compound|compounds]], [[Sugars|sugars]]) across their [[Membrane|membrane]].

Cells are comprised of inner compartments, known as [[Organelles|organelles]] that control the cells processes, these include the [[Nucleus|nucleus]], [[Mitochondria|mitochondria]], [[Endoplasmic reticulum|endoplasmic reticulum]], [[Golgi apparatus|Golgi apparatus]], [[Ribosomes|ribosomes]], [[Lysosome|lysosomes]] and [[Vacuole|vacuoles]], which are all adapted to their own specific function within the cell, organelles tend to exist solitary within the cell but some exist in large quantities for example mitochondria, which is an adapation of the cell for its function, many mitochondria for a large amount of energy.  Cells within different tissue create different proteins, but all cells contain the same genetic code throughout the entire body<ref>http://www.ehow.com/about_5079491_human-cells.html</ref>. Gene expression regulates cell differentiation and it is this that allows cells to become complex<ref>Nature Education 1(1):127 (2008)</ref> 

=== References ===

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Glucose

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Glucose is a [[Monosaccharide|monosaccharide]] with the chemical formula of C6H12O6. It is involved in many biological processes including [[Glycolysis|glycolysis]]. [[Glycolysis|Glycolysis]] involves the conversion of [[Glucose|glucose]], to [[Pyruvate|pyruvate]]. This process is fundamental to [[Respiration|respiration]]. Glucose can form a [[Glycosdic bond|glycosidic bond]] with another glucose to form a [[Disaccharide|disaccharide]] called [[Maltose|maltose]] through a condensation reaction. Glucose monomers can be joined by α-1,4- [[Glycosidic bond|glycosidic bond]] to form a polysaccharide molecule known as [[Starch|starch]]. 

In open chain [[Glucose|glucose]] Carbon 1 (the [[Carbonyl group|carbonyl]] carbon) is not [[Chiral centre|chirally]] active. However in the ring structure it becomes assymetric, allowing it to form two ring structures: [[Α-D-glucopyranose|α-D-glucopyranose]] and [[Β-D-glucopyranose|β-D-glucopyranose]]. <ref>Berg J., Tymoczko J and Stryer L. (2012) Biochemistry, 7th edition, New York: WH Freeman. pg 333</ref> 

[[Image:D-glucose.jpg|D-glucose forming alpha and beta rings.]]

Taken from: [http://www.ncbi.nlm.nih.gov/books/NBK22547/ http://www.ncbi.nlm.nih.gov/books/NBK22547/]<ref>http://www.ncbi.nlm.nih.gov/books/NBK22547/</ref> 

The main family of transporters are known as the GLUT family with 5 known variants all with different properties and found in different tissues.

*[[GLUT1|GLUT1]]
*[[GLUT2|GLUT2]]
*[[GLUT3|GLUT3]]
*[[Glut 4|GLUT4]]
*[[GLUT5|GLUT5]]

=== References: ===

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Respiration

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Respiration is the essential [[Metabolic|metabolic]] process whereby energy is created in the form of [[ATP|ATP]].  There are two types of respiration, [[Aerobic|aerobic]] respiration and [[Anaerobic|anaerobic]] respiration.  In [[Aerobic respiration|aerobic respiration]], there is a reaction between [[Oxygen|oxygen]] and [[Glucose|glucose]], resulting in the generation of 38 [[ATP|ATP]], with [[Carbon dioxide|carbon dioxide]] and [[Water|water]] being produced as waste products.  There are a number of steps in this process, which involve a series of complex reactions.  [[Anaerobic respiration|Anaerobic respiration]] is the process whereby [[ATP|ATP]] is generated in the absence of [[Oxygen|oxygen]].  [[Glucose|Glucose]] is broken down into 2[[ATP|ATP]] and [[Lactic acid|lactic acid]] as a waste product. Aerobic respiration goes through complex stages (phases) in the next order:

#[[Glycolysis|Glycolysis]]: Where one [[Glucose|glucose]] molecule (6-Carbon molecule), is transformed to two [[Pyruvate|pyruvate]] molecules (3-Carbon molecules), and four [[ATP|ATP]] molecules.
#Link Reaction: One [[Pyruvate|pyruvate]] molecule is changed to one [[Acetyl-CoA|acetyl-CoA]] molecule (2-Carbon molecule) by releasing one carbon atom in the form of carbon dioxide.
#[[Krebs cycle|Krebs Cycle]]: Also called the [[Krebs cycle|TCA]] ([[Tricarboxylic acid|tricarboxylic acid]]) Cycle, occurs twice for one glucose molecule (because each glucose molecule is split into two pyruvates which produce one [[Acetyl-CoA|Acetyl-CoA]] each) producing: 2 ATP molecules, six [[NADH|NADH]] molecules, two [[FADH2|FADH2]] Molecules and four [[Carbon dioxide|CO2]] molecules 
#[[Electron transport chain|Electron transport chain]]: Where electrons pass from one carrier to the other, with [[Oxygen|O2]] as the las carrier, producing 32 [[ATP|ATP]] molecules, using [[ATP synthase|ATP_synthase]].

Protein

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A protein is a biological polymer which is made up of [[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, [[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 [https://teaching.ncl.ac.uk/bms/wiki/index.php/Homo_sapiens humans]. One important technique used to analyse proteins is [[SDS polyacrylamide-gel electrophoresis|SDS polyacrylamide-gel electrophoresis]] ([[SDS polyacrylamide-gel electrophoresis|SDS-PAGE]]).

== 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 basic sequence of [[Amino acids|amino acids]] joined together by peptide bonds in a 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 know as the [[Gene|gene]].  

=== 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]]. This, in turn, allows the protein to have a [[Hydrophobic|hydrophobic]] core and a [[Hydrophilic|hydrophilic]] surface. The secondary structure is stabilised by [https://teaching.ncl.ac.uk/bms/wiki/index.php/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 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 stuctures of protein linked together build up a [[Quaternary structure|quaternary structure]].  Quaternary structure can also refer to proteins with an inorganic prosthetic group attatched, an example being haemoglobin: a tetramer consisting of four myoglobin subunits and an iron-containing 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. [[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.

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 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, cell movement, migration of [[Chromosomes]] during [[Mitosis]] and the direction of 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 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>.

== See also ==

*[[Amino acid|Amino acid]] 

== References ==

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