The School of Biomedical Sciences Wiki - User contributions [en]

Fat

2016-10-17T14:04:47Z

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Fatty acids are a source of energy for many living organisms. There are 3 main types of fat:

#[[Saturated Fats|Saturated Fats]]
#[[Unsaturated Fats|Unsaturated Fats]]
#[[Trans Fats|Trans Fats]]

Saturated fats are mainly found in animal products and are solid at room temperature. They are saturated due to containing no [[Double carbon-carbon bonds|double carbon-carbon bonds]] in its structure. A high intake of saturated fats can lead to health problems such a coronary [[Heart disease|heart disease]]. Unsaturated fats come in many forms such as polyunsaturated fats (many/multiple double carbon-carbon bonds) and monounsaturated fats (one double carbon-carbon bond present). Unlike saturated fats these are commonly found in [[Plants|plant]] sources for example seeds and nuts. These fats are in liquid form at room temperature. There seems to be a correlation between a decrease in [[Cholesterol|cholesterol]] levels and unsaturated fats, which shows they play a major health benefit and could possibly play a role in decreasing the risk of heart disease<ref>hhtp://sportsmedicine.about.com/od/sportsnutrition/a/Fat.htm, 29/11/2013, 12/10/2007, Elizabeth Quinn.</ref>.

Fatty acids also play a major sturcural role in organisms. [[Fatty acids|Fatty acids]] are a component of [[Cell_membrane|cell membranes ]]and are organised into bilayers. The fatty acids are made up of two [[Hydrophobic|hydrophobic]] fatty acid tails which face inwards in the [[Lipid_bilayer|bilayer]], and then a hydrophilic head, which consists of a polar group, a phosphate molecule and [[Glycerol|glycerol]]. Due to fatty acids having hydrophobic tails and a hydrophilic head they are referred to as being [[Amphiphilic|amphiphilic]].<ref>Bruce Alberts et al, 2008, Molecular Biology of The Cell, Fifth Edition, New York, Garland Science.</ref>

=== References ===

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Eukaryotic Cell

2016-10-16T17:03:42Z

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A eukaryotic cell is a cell that has its [[DNA]] in a distinct [[Compartmentalisation|compartment ]]from the [[Cytoplasm|cytoplasm]] of the cell due to a membrane; [[DNA|DNA]] is inside a [[Nucleus|nucleus]]. They also have a [[Cytoskeleton|cytoskeleton]] that holds the cell's shape, gives it mechanical strength and helps to move things around the cell. Eukaryotic cells have membrane bound [[Organelles|organelles]] such as the [[Endoplasmic reticulum|endoplasmic reticulum]], [[Golgi apparatus|Golgi apparatus]] and [[Mitochondria|mitochondria]]. Eukaryotic cells are typically much larger than [[Mitochondria|prokaryotic cells]]. Animal cells are an example of eukaryotic cells<ref>Alberts, Johnson, Lewis, Raff, Roberts and Walter. (2008) Molecular Biology of the Cell. 5th edition, New York: Garland Science (pp26-27)</ref>.   

=== Different Structures ===

The two main types of eukaryotic cell are the animal cell and plant cell, between which there are a few differences. 

Animal cells have a [[Plasma membrane|plasma cell membrane]] inside of this are all the [[Organelles|organelles]] and [[Cytosol|cytosol]]. There is the [[Nucleus|nucleus]] which contains the [[Genome|genome]] enclosed in the [[Nuclear envelope|nuclear envelope]]. This is surrounded by the [[Endoplasmic_Reticulum|endoplasmic reticulum]] which can have [[Ribosomes|ribosomes]] attached. Surrounding this are the organelles as follows: the [[Golgi Apparatus|Golgi Apparatus]], free [[Ribosomes|Ribosomes]], [[Lysosome|Lysosomes]], [[Peroxisomes|Peroxisomes]], [[Centrosome|Centrosome]] and [[Mitochondria|Mitochondria]]. Other structures within the cell include [[Vesicles|Vesicles]], [[Actin filaments|Actin Filaments]], [[Microtubules|Microtubules]] and [[Intermediate filaments|Intermediate Filaments]]<ref>Watson J D, Gilman M, Witkowski J and Zoller M (1992) Recombinant DNA, 2nd Edition, New York: W H Freeman and Company (Chapter 6)fckLRBerg J M, Tymoczko J L and Stryer L (2007) Biochemistry, 6th edition, New York: W H Freeman and Company (P140-142)</ref>.

Plant cells are different in that they have a [[Cellulose|Cellulose]] [[Cell wall|Cell Wall]] as well as a [[Cell membrane|Cell Membrane]] and large [[Vacuole|Vacuoles]]. Other differences include [[Chloroplasts|Choroplasts]] instead of [[Mitochondria|Mitochondria]], Plastids for storage, and not having [[Peroxisomes|Peroxisomes]] <ref>Pearson NCS (2014), Plant Cell, Available at http://biology.tutorvista. com/animal-and-plant-cells/plant-cell.html (Last Accessed 27/11/2014)</ref>. 

=== References ===

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Bioinformatics

2015-12-01T23:07:55Z

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=== '''Why Bionformatics?''' ===

Bioinformatics is essentially the collection, collation, storage and retrieval of biological data. These data ranges from [[DNA|DNA]], [[Protein|Protein]], Biochemical information etc. Bioinformatics can also be defined as the use of biomedical tools - software or programs to analyse, data which are stored, or retrieved from the [[Genomics|genomic]], [[Proteomics|proteomics]] or biochemical databases. These tools make it possible to do [[Sequence alignment|sequence alignment]], [[Homology search|homology search]], identification of [[Protein|protein]] function, structure, and its role in a normal cell or in pathology.

=== So is it all about data, information, [[Proteins|proteins]], or [[DNA|DNA]]? ===

Well, the answer is no, bioinformatics is beyond these definitions given above. Bioinformatics is the way forward for researchers, students, and even doctors. Today, bioinformatics tools are integrated into many branches of science and, in the near future, even the general public may be able to use them to analyse their own [[DNA|DNA]] sequence.

=== So, why bother to study bioinformatics as a student? ===

All what have been said so far is, "it is essential for..." In my own subjective view it is more useful not only for final year project, but also to reinforce study or lecture materials. Whatever the area of profession for a student, these tools are still important in doing a background study of unknown proteins, disease, etc. It can also aid in making research more rapid than working in a laboratory. In the near future, will it be possible perhaps, to even do laboratory work without needing the laboratory itself?  

=== How do you access them? ===

Bioinformatics tools can be accessed via computer or phone. this means that, everybody can use bioinformatics tools. Some important software or web access is [[NCBI|NCBI]], [[ProSite|ProSite]], [[Pfam|Pfam]] etc. 

A small intro to[[Pubmed|PubMed]] as a Bioinformatics Tool:

PubMed is a site affiliated with NCBI site, which if you don't use currently you will probably use in the future. It is often used to search:

*research papers
*information regarding proteins and genes (including their respective sequences)

However because of the great amounts of information within this site it is important to know how navigate through it.

Ethidium Bromide

2015-12-01T23:04:53Z

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Ethidium Bromide is commonly used during [[Gel electrophoresis|gel electrophoresis]] in molecular biology labs. The Ethidium Bromide intercalates itself between [[Base pair|base pairs]] allowing the [[DNA|DNA]] banding pattern to be visualised when illuminated with a [[Ultra Violet|UV]] light source. As might be expected, the addition of ethidium bromide will affect the mobility and rigidity of the DNA molecule through the [[Agarose gel|agarose gel]] <ref>http://www.ncbi.nlm.nih.gov/pubmed/8957173</ref>. 

=== References ===

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Ethidium Bromide

2015-12-01T23:04:03Z

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Ethidium Bromide is commonly used during [[Gel electrophoresis|gel electrophoresis]] in molecular biology labs. The Ethidium Bromide intercalates itself between[[Base_pair|base pairs]] allowing the [[DNA|DNA]] banding pattern to be visualised when illuminated with a [[Ultra Violet|UV]] light source. As might be expected, the addition of ethidium bromide will affect the mobility and rigidity of the DNA molecule through the [[Agarose gel|agarose gel]] <ref>http://www.ncbi.nlm.nih.gov/pubmed/8957173</ref>. 

=== References ===

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Abc transporters

2015-12-01T23:03:13Z

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ABC transporters 'are the largest family of [[Membrane|membrane]] transporters'. ABC transporters are integral proteins, using energy from the [[Hydrolysis|hydrolysis]] of [[ATP|ATP]] to pump molecules across the memebrane. These transporters are used to transport small [[Molecules|molecules]] across the cell membrane. Each ABC traporter contains two [[ATP-binding domain|ATP-binding domains]] called cassettes. As ATP binds to the casettes they under go dimerization. Each cassette protrudes into [[Cytosol|cytosol]]. There are two halves of each transporter, of which they can either be made of a single [[Peptide|peptide]] or by one or more polypeptides, which form a similiar structure. When ATP isn't present the binding site is expressed on either the [[Intracellular|intracellular]] or [[Extracellular|extracellular]] space. As the ATP binds it causes a conformational change in the ABC transporter, which exposes the substrate binding site on the opposite face. As a molecule of [[ATP|ATP]] is hydrolysed, this is followed by the dissociation of [[ADP|ADP]]. The ATP hydrolysis returns the transporter to its original form <ref>P. M. Jones A. M. George . (2004). The ABC transporter structure and mechanism: perspectives on recent research. Cellular and Molecular Life Sciences CMLS . Volume 61, p682-699.</ref><ref>B Alberts, A Johnson, J Lewis, Martin Raff, K Raff, K Roberts, P Walter, J Wilson, T Hunt (2008). Molecular Biology of The Cell 5th Edition. New York: Garland Science. p660-p665.</ref>.

=== References ===

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Bronchioles

2015-12-01T22:59:20Z

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Bronchioles are a feature of the respiratory system and branch from the [[Bronchi|Bronchi]], they are the smallest of the airways.  [[Alveoli|Alveoli]] are found at the end of the bronchioles. 

=== Structure ===

Larger bronchioles have ciliated cells lining the [[Lumen|lumen]]. However, in smaller bronchioles the [[Epithelium]] is not lined with ciliated cells. <ref>University of Leeds Faculty of Biological Sciences, 2003. The Histology Guide: Bronchioles. Available at: http://www.histology.leeds.ac.uk/respiratory/conducting.php (Last accessed: 22.10.2015)</ref> 

=== Infection ===

The bronchioles are subject to many infections and diseases including Bronchiolitis obliterans-organizing pneumonia (BOOP) <ref>Pardo J, Panizo A, Sola I, Queipo F, Martinez-Peñuela A, Carias R.. (2013). Prognostic value of clinical, morphologic, and immunohistochemical factors in patients with bronchiolitis obliterans-organizing pneumonia.. Human pathology. 44 (5), 718-24</ref>. 

=== References ===

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Enzyme Inhibitors

2015-12-01T22:55:00Z

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[[Enzyme|Enzyme]] Inhibitors are substances that reduce the rate of enzyme activity in an enzyme [[Catalysed reaction|catalysed reaction]] <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg227.</ref>. These substances may be in the form of [[Molecule|molecules]] or ions that mimic the actual [[Substrate|substrates]] in order to bind to the [[Active_site|active site]] of the enzyme to form an enzyme-inhibitor (EI) complex. Enzyme inhibitors are of two types:

#[[Irreversible_inhibitors|Irreversible Inhibitors]]
#[[Reversible_inhibitor|Reversible Inhibitors]]

=== Irreversible Inhibitors ===

These substances bind permanently to an [[Amino_acid|amino acid]] side chain (commonly [[Serine|Serine]] or [[Cysteine|Cysteine]]) at or near the [[Enzyme active site|active site]] of an enzyme to form an EI complex. The binding permanently inactivates the enzyme by changing the shape of it so substrates can no longer bind. This interraction usually occurs via a strong [[Covalent bond|covalent bond]] between the enzyme and the inhibitor. It may also occur via a strong non-[[Covalent|covalent]] linkage. In irreversible inhibition, the separation of the inhibitor from the active site is usually very slow because of the strong covalent linkage that exist between the inhibitor and the enzyme. Irreversible inhibitors are used in pharmaceuticals for the synthesis of drugs. An example is the inhibition of [[Acetylcholinesterase|acetylcholinesterase]] by sarin gas which reacts with the [[Hydroxyl group|hydroxyl group]] of [[Serine|serine]] residue in the enzyme to form an [[Ester|ester]]. This prevents the breakdown of [[Acetylcholine|acetylcholines]] by [[Acetylcholinesterase|acetylcholinesterase]].

=== Reversible Inhibitors ===

These substances bind to the active of an enzyme to form an EI complex. These bonds are not as strong as that of irreversible inhibitors and this causes a separation of the EI complex. Reversible inhibitors are of three types:

*Reversible-competitive Inhibitor
*Reversible-Non-competitive Inhibitor
*Reversible-Uncompetitive Inhibitor[[|]]

=== Reversible-competitive Inhibitor ===

In this type of inhibition, the formation of the EI complex prevents the binding of a substrate. The inhibitor compete with the substrate for the [[Enzyme active site|active site]] because they have similar shapes and this therefore lowers the rate of enzyme catalysed reaction by reducing the number of active sites available to bind other substrate molecules. This can be overcome by increasing the substrate concentration until the inhibitor dissociates from the enzyme active site. They are mostly used as therapeutic agents, e.g. if our body has an inflammatory response to a certain [[Stimulus|stimuli]], then Ibroprofen can be used as it is a [[Competitive_inhibitors|competitive inhibitor]] of the enzymes involved in the signaling pathways of the inflammatory response. Competitive inhibitors cause [[Km|Km]] to increase and [[Vmax|Vmax]] to remain the same <ref name="same">Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg227.</ref>.

=== Reversible-Non-competitive Inhibitor ===

These molecules bind away from the active site of an enzyme and modifies the shape of the active site. This does not effect the affinity of which the substrate is bound (i.e. Km remains unaltered). It can also bind to an already existing [[Enzyme-substrate_complex|enzyme-substrate (ES) complex]]. This type of inhibition cannot be overcome by increasing the substrate concentration like reversible-competitive inhibition. Non-competitive inhibitor reduces the number of substrate molecules that can be converted to products by one enzyme molecule in 1 second i.e the [[Turnover number|turnover number]] (Kcat). Non-competitive inhibitors have no effect on Km but Vmax is lowered <ref name="same">Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg227.</ref>.

=== Reversible-Uncompetitive-Inhibitor ===

These substances binds only to an already existing enzyme-substrate complex. Once bound to the enzyme-substrate complex the enzyme-substrate-inhibitor complex, ESI complex, will take a very long time to produce any product. They attach to the ES complex away from the active site. Uncompetitive inhibition essentially decreases the concentration of functional enzymes. Like Non-competitive inhibition, uncompetitive inhibition cannot be overcome by increasing the substrate concentration. As the concentration of substrate increases, this increases the rate of inhibition. Uncompetitive inhibitors decrease both KM and Vmax. <ref name="same">Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg227.</ref><ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg227.</ref>.

=== References ===

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Gamete

2015-12-01T22:45:53Z

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Gamete is a reproductive (germ) cell that contains only one set of [[Chromosome|chromosomes]] - [[Haploid|haploid]]. Produced by a [[Cell_division|cell division]] process called [[Meiosis|meiosis]] <ref name="null">Daniel L. Hartl, Elizabeth W. Jones (2009) 'Genetics. Analysis of genes and genomes', Jones and Bartlett publishers, Inc., Sudbury, Massachusetts, USA, 7th edition: 83</ref>. 

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Mendel's Second Law

2015-12-01T22:43:49Z

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Mendel's 2nd law is that during [[Gamete|gamete]] formation the segregation of each [[Gene|gene]] pair is independent of other pairs. Mendel's 2nd law is often referred to as the[[Principle_of_Independent_Assortment|principle of independent assortment]]. Both of Mendel's laws are about segregation, which is the seperation of [[Allele|allele]] pairs. The law states that the seperation of one pair of alleles isn't related to the sepearation of other pairs of alleles. This law is very important in [[Mendelian genetics|Mendelian genetics]]. The only time there is an exception to this rule is when [[Gene linkage|linkage]] is involved <ref>Hartl D.L. and Ruvolo M. (2011) Genetics: Analysis of genes and genomes, page 91, 8th Edition, Published by Jones &amp;amp;amp;amp; Bartlett Learning</ref>, 

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