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Rho dependent termination

2018-11-24T14:12:40Z

180289002: Cleared up reference formatting

The three main stages of [[Transcription|transcription]] are known as initiation, [[Elongation|elongation]] and termination, the latter of which can be assisted by a protein that associates with the RNA polymerase complex, in ''[[E. coli|Escherichia coli]]'' this known as a [[Rho|Rho (ρ) factor]]. '''Rho dependent termination''' is one of two types of termination in prokaryotic transcription, the other being [[Factor independent termination|intrinsic (or Rho-independent)]].

[[RNA Polymerase|RNA polymerase]] is able to terminate the transcription of some genes without assistance, for example at a series of several U residues following a hairpin; at other sites however it requires the participation of an additional factor. The method of termination observed in the presence of the Rho factor is similar to that found in intrinsic termination though the terminator sequences recognised by the protein are long and complex<ref>Hartl, D.L. and Ruvolo, M. (2012) Genetics: Analysis of Genes and Genomes. 8th edn. Burlington, MA: Jones &amp;amp;amp;amp; Bartlett Learning.</ref>.

The rho protein is an [[ATP|ATP]] dependent helicase composed of six identical subunits that binds to an exposed region of single stranded RNA following the [[Open reading frame|open reading frame]]. Each of the sub units has an ATP-hydrolysis domain and an RNA-binding domain allowing RNA to pass through the centre of the hexameric protein. Rho is initiated by sequences that are rich in [[Cytosine|cytosine]] but poor in [[Guanine|guanine]]. After binding to the newly formed RNA chain, ρ factor moves along the molecule in a 5’-3’ direction and encourages dissociation from the [[DNA|DNA]] template and RNA polymerase<ref>Foster, J. W. and Slonczewski, J. (2013) Microbiology: An Evolving Science. 3rd edn. New York: W.W. Norton &amp;amp;amp;amp; Co.</ref>. It disrupts the transcriptional complex by acting as an RNA-DNA [[Helicase|helicase]] when it reaches the [[Transcription Bubbles|transcriptional bubble.]] A [[Polypeptide|polypeptide]] loop of the ρ protein is formed when it reaches a termination signal, this stops the elongation stage from being carried out as it is inserted into the main channel of the RNA polymerase complex, separating the RNA/DNA hybrid.

The discovery of this process was prompted by the observation that RNA molecules when made [[In vivo|in vivo]] are shorter than those synthesised [[In vitro|in vitro]] by RNA polymerase alone. This lead to the isolation of Rho as the protein that caused the appropriate termination of the chain and further information about the termination factor has been gained through the addition of ρ to an incubation mixture at varying times after the initiation of RNA synthesis<ref>Berg, J.M., Tymoczko, J.L. and Stryer, L. (2011) Biochemistry. 7th edn. Basingstoke: Palgrave Macmillan.</ref>. 

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Vasodilation

2018-11-23T11:49:40Z

180289002: Corrected reference

Vasodilation occurs when the [[Smooth muscle|smooth muscles]] in our blood vessels relax and thus the inside of the [[Blood vessels|blood vessels]] becomes wider in diameter. And now with the increase in space within each vessel, there is less vascular resistance so there is much greater rate of blood flow<ref>Rakhimov, D. A. (2004-2013). NormalBreathing.com. Retrieved from http://www.normalbreathing.com/</ref>.

Also with the cardiac output remaining constant but a greater volume of space available, your [[Blood pressure|blood pressure]] decreases. 

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Chromosome X

2018-11-23T11:49:12Z

180289002: Corrected references

Chromosome X is one of the two [[Sex chromosomes|sex-determining chromosomes]] found in humans and many other animals, the other being the [[Y chromosome|Y chromosome]]. In a normal human female, there are two X chromosomes (these are known as [[Homogametic|homogametic]]), and in a normal male there is one X and one Y (these are [[Heterogametic|heterogametic]])<ref>Ross, MT et al. (2005). The DNA sequence of the human X chromosome. Nature, 434:325-337</ref>.

An X chromosome is much larger than a Y chromosome. As human males have only one X chromosome, the likelihood of inheriting an X chromosome linked disease in males is much greater than females. 

=== X Chromosome related illnesses ===

Many X chromosome related diseases result from an abnormal number of chromosomes due to [[Nondisjunction|nondisjunction]] during [[Meiosis|meiosis]]. Some examples of these include:

*[[Klinefelter syndrome|Klinefelter syndrome]] - this is caused by the presence of at least one extra X chromosome in a male [[Karyotype|karyotype]] giving a 47,XXY karyotype or less frequently 48,XXXY, 49,XXXXY and 48,XXYY karyotypes. The extra X chromosome interferes with the males sexual development and reduces levels of testosterone<ref>Who.int, (2014). WHO | Gender and Genetics. [online] Available at: http://www.who.int/genomics/gender/en/index1.html#KlinefelterSyndrome [Accessed 26 Nov. 2014].</ref>.
*[[Turner syndrome|Turner syndrome]] - this is caused by the presence of only one X chromosome giving a 45,X karyotype. This results in altered development, short stature and infertility<ref>Who.int, (2014). WHO | Gender and Genetics. [online] Available at: http://www.who.int/genomics/gender/en/index1.html#Turnersyndrome [Accessed 26 Nov. 2014].</ref>.
*[[Trisomy X|Trisomy X]] - this is caused by an extra copy of an X chromosome in female cells and gives a 47,XXX karyotype. It shows no obvious characteristics different to the rest of the female population except accelerated growth and speech and language impairment<ref>Who.int, (2014). WHO | Gender and Genetics. [online] Available at: http://www.who.int/genomics/gender/en/index1.html#XXXFemales [Accessed 26 Nov. 2014].</ref>.

There are also many [[X-linked|X linked]] diseases which can be inherited from parents. If only the mother is affected by the disease (either [[Genotype|genotypcially]] or [[Phenotype|phenotypically]]), a son is more likely to have the disease. This is because they only have one X chromosome so the affected gene will be expressed. A daughter will have a 50% chance of inheriting the disease. If only the father has the disease, 100% of daughters will be carriers as they inherit an X chromosome from each parent. A son will not inherit the disease as they inherit their X chromosomes maternally<ref>http://genome.wellcome.ac.uk/doc_WTD020851.html</ref>.

=== X chromosome Inactivation ===

[[X chromosome Inactivation|X chromosome inactivation]] is the process by which all but one X chromosomes are defunctionalized in a cell and become [[Barr Body|barr bodies]]<ref>Ahn, J. and Lee, J. (2008) X chromosome: X inactivation. Nature Education, 1(1):24</ref>. 

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Plasma membrane

2018-11-23T11:47:17Z

180289002: Corrected reference

A plasma membrane encapsulates each and every [[Cell|cell]], and is also known as the cell membrane. It acts as a selective barrier which is necessary to allow different concentrations of substances to be maintained between the cell and it's environment. [[Eukaryotic cells|Eukaryotic cells]] have internal membranes which surround [[Organelles|organelles]], allowing different constituent concentrations within the [[Cell|cell]]<ref>Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walkter P., (2008) Molecular Biology Of The Cell, 5th edition, Newy York: Garland Science</ref>. 

The plasma membrane is a [[Lipid bilayer|lipid bilayer]] embedded with [[Proteins|proteins]] and [[Cholesterol|cholesterol]] which is 5nm thick. Lipid bilayers are composed of [[Phospholipid|phospholipids]], the most common being [[Phosphatidylcholine|phosphatidylcholine]]. The head part of which is made up of a [[Phosphate|phosphate]] and a [[Hydrophilic|hydrophilic]] [[Choline|choline]], the tail component of the phospholipid is comprised of two fatty acid chains, long hydrocarbon structures with a chemically active [[Carboxylic acid (COOH)|COOH]]. Since the head is [[Hydrophilic]] and the tails are [[Hydrophobic|hydrophobic]], the phospholipid is said to be [[Amphipathic|amphipathic]]. The structure of the bilayer is such that the tails are shielded from contact with [[Water|water]], creating a selectively-permeable barrier which will be impermeable to most hydrophilic molecules.  

The plasma membrane has many functions and is a fundamental part of the cell. It communicates with the environment and other cells by means of a [[Glycocalyx|glycocalyx]], a system of protein-linked and lipid-linked [[Carbohydrate|carbohydrates]]. It allows passage of selective molecules in and out of the cell via [[Carrier proteins|carrier]] or [[Channel proteins|channel proteins]] embedded within the membrane, and it regulates cell growth, shape, movement and division. 

The membrane is associated with proteins, both integral and peripheral which act as either:

*transporters
*linkers
*[[Receptor|receptors]]  
*[[Enzyme|enzymes]] 

The [[Lipid|lipids]] within the [[Lipid bilayer|bilayer]] can freely move, they can diffuse laterally along the membrane (across the same layer), or rotate along their axis, but move occasionally between layers (transverse diffusion). Therefore, plasma membranes are highly assymetric, as protein and lipid composition on intracelullar and extracellular faces of membranes varies<ref>Voet D., Voet J. (2011): Biochemistry, 4th Edition, Hoboken: John Wiley and Sons, Inc. p410</ref>.

Lipids are said to be fluid within the system.This fluidity is dependent on:

*the length of the [[Phospholipid|phospholipid]] tail
*whether the tail is saturated or not
*the presence of [[Cholesterol|cholesterol]]. 

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Morpholinos

2018-11-23T11:46:44Z

180289002: Corrected spellings

Morpholinos are small [[Oligomer|oligomers]] that are roughly 25 base pairs long, and they are used to block [[Gene expression|gene expression]]. They are similar to [[DNA|DNA]] and [[RNA|RNA]] in structure and function, but possess a different backbone which is non-ionic.

This [[Non-ionic|non-ionic]] back bone also means that morpholinos are less likely to interact non selectively with cellular [[Protein|proteins]], and due to their back bone being different of that of a [[Nucleic acid|nucleic acid]], it means that [[Enzyme|enzymes]] that interact with [[Nucleotide|nucleotides]] ([[Nuclease|nucleases]]) do not break it down and they are not degraded by [[Cell|cells]].

They use [[Watson-Crick base pairing|Watson-Crick base pairing]] and bind to complementary [[Nucleic acids|nucleic acids]]. The morpholinos can be used in variety of techniques such as translation blocking, they do this by binding to [[Complementary base pairs|complementary base pairs]] on [[RNA|RNA]] and so stoping protein synthesis at the blocked sites. They can also be used for splice modification whereby they can change to [[MRNA|mRNA]] product by interfering with the splicing of the [[Pre-mRNA|pre-mRNA]] (this usually happens by deletion of an [[Exon|exon]]). The morpholinos also prevent [[MicroRNA|microRNA]] from reaching its mature and active form by blocking the [[Dorsha cleavage site|Dorsha]] or [[Dicer cleavage site|Dicer cleavage sites]] <ref>http://network.nature.com/groups/morpholinos/forum/topics/500</ref><ref>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC138935/</ref>.

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Phenotype

2018-11-23T11:45:47Z

180289002: Corrected reference

A phenotype is an observable trait in an [[Organism|organism]]. It is the manifestation or expression of the genetic constitution or [[Genotype|genotype]].

Phenotypes are also affected by [[Enviromental factor|environmental factors]]. For example, an individual having the necessary [[Alleles|allele]](s) for height (genetic factor) does not necessarily mean that they will be tall, as height is also influenced by proper diet and exercise (environmental factor). This suggests that a genotype will not always result in the same phenotype i.e. there are several phenotypes for one genotype.

Another side to the example given above is that an individual without the alleles for height can still be tall given the proper combination of environmental factors. This means that one phenotype is not coded for by one genotype. Other complex phenotypes e.g. body weight, skin colour, behaviour, susceptibility to disease, etc. are also coded for by several [[Genotype|genotypes]]; they are said to be [[Polygenic|polygenic]]<ref>Hartl D.L, Jones E.W. (2009) Genetics Analysis of Genes and Genomes, Seventh Edition, Massachusetts: Jones and Bartlett Publishers, Inc.</ref>.

The phenotype is an observable or identifiable trait that is coded for by the [[Genotype|genotype]]. This could be biochemical or physical. Phenotypes are not completely defined by the genotype. Other factors such as the environment can affect the observable traits. An example of this would be "two people with a genetic risk of lung cancer; if one smokes and the other does not, the smoker is much more likely to develop the disease<ref>Hartl, D (2012). Genetics, Analysis of Genes and Genomes. 8th ed. USA: Jones and Bartlett Learning. p63.</ref>". Examples of phenotypes could be: hair colour, eye colour, skin colour. Environmental factors can affect phenotypes, for example, skin colour can vary greatly with different levels of exposure to UV light from the sun causing darkening of the melanin. Phenotype is also dependent on the type of allele that is expressed: whether it is [[Dominant|dominant]] or [[Recessive|recessive]]. Also the phenotype can be a blend of phenotypes which is known as [[Incomplete dominance|incomplete dominance]] or both phenotypes expressed which is known as [[Co-dominance|co-dominant]].  

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Succinate

2018-11-23T11:45:19Z

180289002: Corrected reference

Succinate is a four carbon compound and is involved in the [[Citric acid cycle|citric acid cycle]] which takes place in the [[Mitochondria|mitochondria]] as part of [[Aerobic respiration|aerobic respiration]]. Succinate is formed by [[Succinyl coenzyme A|succinyl coenzyme A]], [[Water|water]], [[GDP|GDP]] and an inorganic phosphate group with the help of the [[Enzyme|enzyme]] [[Succinyl coenzyme A synthetase|succinyl coenzyme A synthetase]]. Succinate goes on to produce [[Fumarate|fumarate]] using [[Succinate dehydrogenase|succinate dehydrogenase]] where [[FAD|FAD]] assists and accepts hydrogens to become [[FADH2|FADH2]]<ref>Alberts et al. Molecular biology of the cell. (5th ed).</ref>.

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Bacteroidetes

2018-11-16T11:39:11Z

180289002: Corrected reference format

Bacteroidetes are found in several different niches such as the soil, salt water and fresh [[Water|water]]<ref>Front Microbiol. 2011 May 30;2:93 Thomas F1, Hehemann JH, Rebuffet E, Czjzek M, Michel G.</ref>. They are also very important members of the [[Microbiota|microbiota]] of many species and are particularly prevalent in the [[Intestine|gastrointestinal]] tract. Bacteroidetes are necessary for the degradation of large [[Polymer|polymers]] such as protein and [[Carbohydrates|carbohydrates]] in the gut and these species are thought to evolve due to pressure from the host's change in diet<ref>PLoS Biol. 2011 Dec;9(12):e1001221 Martens EC1, Lowe EC, Chiang H, Pudlo NA, Wu M, McNulty NP, Abbott DW, Henrissat B, Gilbert HJ, Bolam DN, Gordon JI.</ref>. 

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