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Retinitis Pigmentosa

2016-10-18T16:28:24Z

150252119:

Retinitis Pigmentosa is an inherited eye disease leading to death of the [[Rod photoreceptors|rod photoreceptors]] and subsequent death of the the cones due to [[Oxidative damage|oxidative damage]], resulting in blindeness. Several mutations, particularly in the gene coding for [[Rhodopsin|rhodopsin]], have been found to cause Retinitis Pigmentosa.  It can be inherited as an [[Autosomal dominant|autosomal dominant]], autosomal recessive, or X-linked recessive disorder.<ref>http://www.ncbi.nlm.nih.gov/protein/4506527</ref>.

Retinitis Pigmentosa is usually diagnosed at a young age as a teen or a young adult.<ref>http://www.webmd.com/eye-health/retinitis-types-symptoms-treatment</ref>.

It has recently been concluded that [[N-acetylcysteine|N-acetylcysteine]] might help prevents cone death in the retina <ref>Lee SY, Usui S, Zafar AB, Oveson BC, Jo YJ, Lu L, Masoudi S, Campochiaro PA., Nov 10, 2010, fckLRN-acetylcysteine promotes long term survival of cones in a model of retinitis pigmentosa, retrieved from: http://www.ncbi.nlm.nih.gov/pubmed/21069814</ref>.

The result of mutations in the rhodopsin gene, affects between 16% to 35% of the Western population who suffer will from adRP (autosomal dominant Retinitis Pigmentosa)<ref>Beryozkin A, Levy G, Blumenfeld A, Meyer S, Namburi P, Morad Y, Gradstein L, Swaroop A, Banin E, Sharon D. (2016) Genetic Analysis of the Rhodopsin Gene Identifies a Mosaic Dominant Retinitis Pigmentosa Mutation in a Healthy Individual. Israel, Abstract, page 1</ref>.

Symptoms

*Night Blindness
*Tunnel Vision
*Aversion to glare
*Blurred Vision 
*Loss of central vision (in more serious case)

=== Treatment ===

Although no effective treatments to cure the disease have been discovered, a number of studies have inferred that treating a patient with [[Antioxidants|antioxidants]] such as sizeable doses of Retinyl palmitate ([[Vitamin A palmitate|vitamin A palmitate]]) will slow down the progress of the disease. There are compllications to this treatment, retinyl palmitate can cause serious damage to a patients [[Liver|liver]], so treatment benefits have to be weighed against the risks. 

=== References ===

<references />

Retinitis Pigmentosa

2016-10-18T16:25:39Z

150252119:

Retinitis Pigmentosa is an inherited eye disease leading to death of the [[Rod photoreceptors|rod photoreceptors]] and subsequent death of the the cones due to [[Oxidative damage|oxidative damage]], resulting in blindeness. Several mutations, particularly in the gene coding for [[Rhodopsin|rhodopsin]], have been found to cause Retinitis Pigmentosa.  It can be inherited as an [[Autosomal dominant|autosomal dominant]], autosomal recessive, or X-linked recessive disorder.<ref>http://www.ncbi.nlm.nih.gov/protein/4506527</ref>.

Retinitis Pigmentosa is usually diagnosed at a young age as a teen or a young adult.<ref>http://www.webmd.com/eye-health/retinitis-types-symptoms-treatment</ref>.

It has recently been concluded that [[N-acetylcysteine|N-acetylcysteine]] might help prevents cone death in the retina <ref>Lee SY, Usui S, Zafar AB, Oveson BC, Jo YJ, Lu L, Masoudi S, Campochiaro PA., Nov 10, 2010, fckLRN-acetylcysteine promotes long term survival of cones in a model of retinitis pigmentosa, retrieved from: http://www.ncbi.nlm.nih.gov/pubmed/21069814</ref>.

The result of mutations in the rhodopsin gene, affects between 16% to 35% of the Western population who suffer will from adRP (autosomal dominant Retinitis Pigmentosa)<references />.

Symptoms

*Night Blindness
*Tunnel Vision
*Aversion to glare
*Blurred Vision 
*Loss of central vision (in more serious case)

=== Treatment ===

Although no effective treatments to cure the disease have been discovered, a number of studies have inferred that treating a patient with [[Antioxidants|antioxidants]] such as sizeable doses of Retinyl palmitate ([[Vitamin A palmitate|vitamin A palmitate]]) will slow down the progress of the disease. There are compllications to this treatment, retinyl palmitate can cause serious damage to a patients [[Liver|liver]], so treatment benefits have to be weighed against the risks. 

=== References ===

<references />

Retinitis Pigmentosa

2016-10-18T16:24:51Z

150252119:

Retinitis Pigmentosa is an inherited eye disease leading to death of the [[Rod photoreceptors|rod photoreceptors]] and subsequent death of the the cones due to [[Oxidative damage|oxidative damage]], resulting in blindeness. Several mutations, particularly in the gene coding for [[Rhodopsin|rhodopsin]], have been found to cause Retinitis Pigmentosa.  It can be inherited as an [[Autosomal dominant|autosomal dominant]], autosomal recessive, or X-linked recessive disorder.<ref>http://www.ncbi.nlm.nih.gov/protein/4506527</ref>.

Retinitis Pigmentosa is usually diagnosed at a young age as a teen or a young adult.<ref>http://www.webmd.com/eye-health/retinitis-types-symptoms-treatment</ref>.

It has recently been concluded that [[N-acetylcysteine|N-acetylcysteine]] might help prevents cone death in the retina <ref>Lee SY, Usui S, Zafar AB, Oveson BC, Jo YJ, Lu L, Masoudi S, Campochiaro PA., Nov 10, 2010, fckLRN-acetylcysteine promotes long term survival of cones in a model of retinitis pigmentosa, retrieved from: http://www.ncbi.nlm.nih.gov/pubmed/21069814</ref>.

=== The result of mutations in the rhodopsin gene, affects between 16% to 35% of the Western population who suffer will from adRP (autosomal dominant Retinitis Pigmentosa)<references />. ===

Symptoms

*Night Blindness
*Tunnel Vision
*Aversion to glare
*Blurred Vision 
*Loss of central vision (in more serious case)

=== Treatment ===

Although no effective treatments to cure the disease have been discovered, a number of studies have inferred that treating a patient with [[Antioxidants|antioxidants]] such as sizeable doses of Retinyl palmitate ([[Vitamin A palmitate|vitamin A palmitate]]) will slow down the progress of the disease. There are compllications to this treatment, retinyl palmitate can cause serious damage to a patients [[Liver|liver]], so treatment benefits have to be weighed against the risks. 

=== References ===

<references />

Proline

2015-12-04T12:27:38Z

150252119:

Proline is an [[Imino acid|imino acid]]. It has a molecular weight of 115.13 and its molecular formula is C5H9NO2. It is also classified as a [[Hydrophobic|hydrophobic]] amino acid. 

Proline has an [[Aliphatic|aliphatic]] side chain, which is bonded to the nitrogen atom and the [[Alpha-carbon|alpha-carbon]] [[Atom|atom]]. It influences [[Protein|protein]] architecture, because it's structure makes it more conformationally restricted than other [[Amino acids|amino acids]] <ref>Biochemistry 6th ed. 2006, J.Berg ''et al.''</ref>.

Four codons translate for Proline, they are: CCU CCC CCA and CCG.

[[Image:Proline.png]]

=== References ===

<references />

Translation

2015-12-04T12:22:49Z

150252119:

Translation in an important, and complex feature of the process of [[Protein synthesis|protein synthesis]]. Genetic information codes for [[Proteins|proteins]] via protein syntheis, this is an essential process as proteins are responsible for the vast majority of cell function and structure. Protein synthesis involves [[MRNA|mRNA]] and [[TRNA|tRNA]] along with other [[Proteins|proteins]] and has three main steps:

#[[DNA replication|DNA replication]]
#[[Transcription|Transcription]]
#[[Translation|Translation]]

Translation is the most complex, it consists of the [[Nucleotide|nucleotide]] sequence of [[MRNA|mRNA]] being translated into the [[Amino acid|amino acid]] secquence of the specific protein. The direction that translation is carried out is very significant; it occurs in the same direction as transcription (5'-3') this results in proteins being produced more efficiently as translation can occur during transcription <ref>Berg et al., 2007:869</ref>.

The [[MRNA|mRNA]] and [[TRNA|tRNA]] play very important specific roles during translation; firstly [[MRNA|mRNA]] acts as a template for the production of the [[Polypeptide|polypeptide]] chain from the [[Genetic code|genetic code]]. The genetic code have three important features:

#[[Triplet code|Triplet code]] 
#Non-overlapping
#[[Degenerate code|Degenerate]]

The genetic code is degenerate because it has 64 codons but only 20 amino acids, therefore most amino acids are coded for by more than one codon. 61 of these codons are used for amino acids and 3 are used as stop codons which will end translation. Only 1 codon is used for the amino acid Methionine and this is the start codon (AUG).

The [[TRNA|tRNA]] acts as an adaptor molecule to decode the [[MRNA|mRNA]] into the protein, it interacts with the [[MRNA|mRNA]] through its anticodon.The [[TRNA|tRNA]] is also responsible for [[Proof-reading|proof-reading]] the [[Amino acids|amino acid]] chain, this ensures that mistakes are very rare (less than 1 per 10000). This is done by many [[TRNA|tRNA]] having an editing site as well as an activation site. These change or reject [[Amino acids|amino acids]] if they are larger or smaller than they should be. 

There are 3 main steps in Prokaryotic translation; Initiation, Elongation and Termination. 

=== Initiation: ===

This involves the initiation factors IF1, IF2, IF3; [[GTP|GTP]] is required for energy. 

IF1 and IF3 bind to the free 30S subunit, releasing it from the 50S subunit. IF2 forms a complex with GTP and binds to the 30S subunit, which attaches to an [[MRNA|mRNA]] molecule. mRNA has a ribosome binding site (RBS), which is adjacent to the stat codon AUG. The start codon is approximately 7-10 nucleotides away from the RBS. It is important to note that the 30S subunit is complementary to the ribosome binding site, so [[Watson-crick base pairing|base pairing]] can occur with the 16S rRNA. A charged initiator tRNA (fMet-tRNAfmet), then binds to this start codon. IF3 is released, allowing a 50S subunit to bind to the 30S complex to form the 70S initiation complex which has a P (peptidyl) and A (acceptor) site . During this formation, IF1 is released and both IF2 and [[GTP|GTP]] are [[Hydrolysis|hydrolysed]]. GTP--> GDP + Pi.

=== Elongation: ===

Elongation requires the elongation factors<ref>Stryer, Biochemistry, Seventh edition, 2007: 936</ref> EF-Tu, EF-Ts and EF-G as well as GTP to supply the energy. Elongation describes the process of aminoacyl tRNA molecules binding to the codon. A [[Peptide bond|peptide bond]] is formed between the amino acid of the tRNA in the P site and the amino acid in the tRNA molecule that has just arrived at the A site; the formation of this peptide bond is catalysed by the 23S subunit. The amino acid in the P site is released from its tRNA molecule and the ribosome moves along so as to transfer the tRNA currently in the A site into the P site. This step is known as transloaction. The uncharged tRNA i.e. tRNA without an amino acid, moves into the E (empty) site. <ref>http://rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/translate.htm</ref> 

#EF-Tu: It will bind to aminoacyl-tRNA in GTP form and then release the aminoacyl-tRNA to the ribosome  when GTP is hydrolysed into GDP.
#EF-T: It induces dissociation of GDP in EF-Tu and restore EF-Tu to GTP form enable it to bind to another aminoacyl-tRNA.
#EF-G: It enhances translocation by displacing peptidyl-transferase in A-site to P-site of ribosome. 

=== '''Elongation factors are involved in proof reading to improve accuracy of translation:''' ===

Amongst other proof reading mechanisms in translation, elongation factors are involved mainly in [[Proof-reading|proof reading]] of amino acid sequences, in the newly forming [[Polypeptide|polypeptide chain]]. This takes part in 2 ways:

1. While leading the aminoacyl- tRNA towards the [[Ribosome|ribosome]], the[[GTP|GTP bound]] elongation factor EF-Tu checks whether the match between the [[TRNA|tRNA]] and the amino acid is correct. The exact details of how this is accomplished isn't clear, however 1 hypothesis suggests that correct matches between the tRNA and an amino acid has a narrow affinity for EF-Tu. This allows the EF-Tu to selectively choose the correctly matched tRNAs before bringing them to the ribosome. 2. EF-Tu monitors the intial match between the codon and the anti-codon. When the aminoacyl-tRNA arrives in the A site of the ribosome, the GTP bound EF-Tu allows formation of [[Hydrogen bond|hydrogen bonding]] between the [[MRNA|mRNA]] and the tRNA, but bends the aminoacyl-tRNA into a conformation which prevents the interaction between the amino acid and the growing polypeptide chain. This prevents peptide bond from forming. Only when the correct[[Codon|codon]]-anti codon match is made, the ribosome triggers hydrolysis of GTP on the EF-Tu which releases the tRNA, and dissociate from the ribosome. This allows the tRNA in the A site to donate its amino acid, thus peptide bond forms between the newly recruited amino acid and the growing polypeptide chann

=== Termination: ===

A [[Stop codon|stop codon]] attaches to the A site and the newly synthesised [[Polypeptide|polypeptide chain]] occupies the P site. Proetins called release factors binds to the stop codon, initiating the release of the polypeptide chain which is transferred to the cytoplasm<ref>http://staff.jccc.net/pdecell/proteinsynthesis/translation/steps.html</ref> . Several release factors are involved as they recognise different amino acid sequences. These are RF1, RF2 and RF3. RF1 recognises UAA or UAG. RF2 recognises UAA or UGA. RF3 mediates interation between the ribosome and RF1 or RF2. <ref>Jeremy M. Berg; Biochemistry; 7th edition;</ref>RRF (ribosome release/ rec-cycling factor), EF-G and GTP hydrolysis promotes the dissociation of the ribosome from mRNA so the [[MRNA|mRNA]] can be released<ref>Bruce Alberts. Molecular Biology Of The Cell. 5th ed. New York: Garland Science. Page 377</ref>. 

=== References ===

<references />

Agarose gel electrophoresis

2015-12-04T11:50:24Z

150252119:

Agarose gel [[Gel_Electrophoresis|electrophoresis]] is used for separating of large DNA fragments. Fragments are generally classed as large if they are between 100bp and 25kbp. <ref>Voytas D, Agarose gel electrophoresis, Current protocols in molecular biology - edited by Frederick M. Ausubel, May 2001</ref>These larger fragments require gels with larger pores, which is why agarose is used rather than standard [[SDS polyacrylamide-gel electrophoresis|acrylamide]] gels. Agarose is derived from seaweed <ref>Smith DR, Agarose gel electrophoresis, Methods in Molecular Biology, 1993, 18: pp443-8</ref>and is made of repeated agarobiose (a disaccharide made up of D-galactose and 3,6-anhydro-L-galactopyranose.) The concentration of the agarose affects how easily the DNA can pass through it, and therefore the degree of migration. Distance travelled is also affected by the size of the molecule. Smaller molecules travel further as they experience less resistance than longer DNA fragments.

DNA has a fixed negative charge density, and so doesn't require treatment with [[SDS|SDS]] - sodium dodecyl sulphate. This is because DNA is already charge-independent, and its highly coiled [[Double helix|double helix]] makes it shape-independent too. <ref>Lee PY, Costumbrado J, Hsu CY and Kim YH, Agarose gel electrophoresis for the separation of DNA fragments, Journal of visualised experiments, April 2012, 20;62:3923</ref>DNA samples tend to be treated before electrophoresis; the two most common processes being cutting it into smaller fragments using [[Restriction enzymes|rectriction enzymes]], and selection and amplification using the [[Polymerase Chain Reaction (PCR)|polymerase chain reaction]]. The DNA sample is mixed with a dye Ethidium bromide (EtBr) prior to it being inserted into the wells, to make it easier to see the bands of DNA. When this is exposed to UV light, it fluoresces.

The gel is used to prevent convection currents from dispersing the molecules - this causes the molecules to move as a band. The gel's pore size also controls the migration speed of macromolecules, acting as a molecular sieve. As the phosphate groups in the [[Sugar phosphate backbone|backbone of DNA]] are negatively charged, so when the molecules are pipetted into wells near the cathode the DNA frgaments will migrate to the [[Anode|anode]] when a charge is applied. DNA fragments move at different rates through the agarose gel depending on how small and compact they are. Then the size of the fragment can be ascertained by comparing the sample to a marker lane, containing fragments of known molecular weight or size.

 

=== References: ===

<references />