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

Fugu Rubripes

2012-10-22T14:56:30Z

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''Fugu Rubripes ''is more commonly known as the Pufferfish, it has the smallest known vertebrate [[Genome|genome]].  

Fugu Rubripes

2012-10-22T14:56:01Z

101488314: Created page with "''Fugu Rubripes ''is more commonly known as the Pufferfish, it has the smallest known vertebrate genome.  "

''Fugu Rubripes ''is more commonly known as the Pufferfish, it has the smallest known vertebrate genome.  

Transgenic

2012-10-22T14:52:14Z

101488314: Created page with "An organism which contains DNA from another species is Transgenic."

An organism which contains DNA from another species is Transgenic.

Anion

2012-10-22T14:47:44Z

101488314: Created page with "An anion is a ion with a negative charge."

An anion is a ion with a negative charge.

Protein

2012-10-19T15:26:08Z

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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 to form a [[Polypeptide|polypeptide]] chain. The [[Peptide bond|peptide bond]] is 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. 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. One important technique used to analyse proteins in [[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>. 

=== Primary Structure ===

The [[Primary structure|primary structure]] is the sequence of [[Amino acids|amino acids]] joined togther by peptide bond. There are 20 different [[Amino acids|amino acids]] found in nature. This is determined by the [[DNA|DNA]] sequence that encodes for that particular protein, called 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.

=== Tertiary Structure ===

[[Tertiary structure|Tertiary structure]] relates to the protein function.  If the [[Tertiary structure|tertiary structure]] is wrong 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. Finally, if there is more than one peptide chains linked together to form a protein then you get a [[Quarternary structure|quarternary structure]]. 

=== Quarternary Structure ===

One or more tertiary stuctures of protein build up a [[Quarternary structure|quarternary 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 a haem group. 

== 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 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, this forms 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).

 

== See also ==

*[http://bms.ncl.ac.uk/wiki/index.php/Amino_acids Amino acid] 

== References ==

<references />

Lac operon

2011-12-02T12:16:37Z

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Francois Jacob and Jacques Monad proposed a model for an [[Operon|operon]], which consisted of a [[Regulator gene|regulator gene]], an operator site consisting of a regulatory [[DNA|DNA]] sequence and one or more structural [[Gene|genes]].

The model displayed how stimuli from the environment can promote/inhibit genetic mechanisms which control metabolic events e.g. the presence/absence of [[Glucose|glucose]] and [[Lactose|lactose]] in the ''lac'' operon <ref>Cellular and Molecular Life Sciences, Matthews KS, Swint-Kruse L, Wilson CJ, Zhan H, The Lactose Repressor System: Paradigms for Regulation, Allosteric Behaviour and Protein Folding.January 2007; 64(1):3-16</ref>. The ''lac'' operon consists of an additional [[Promoter|promoter]], in front of the regulator [[Gene|gene]], the role of which is to ensure the [[RNA Polymerase|RNA Polymerase]] binds to the correct transcription initiator.

The repressor protein is a homotetramer and a product of the ''lac''I gene, and will bind tightly to the operator, under the correct conditions i.e. when [[Glucose|glucose]] is present and [[Lactose|lactose]] absent. When the repressor is bound to the operon, the [[RNA polymerase|RNA polymerase]] is unable to unwind the [[DNA|DNA]] in order to expose the bases and hence is unable to transcribe the structural genes as there is no template for the [[RNA synthesis|RNA synthesis]] to occur. The group of structural genes act as a single transcription unit, coding for a single [[MRNA|mRNA]] [[Molecule|molecule]] termed a [[Polycistronic|polycistronic transcript]] i.e. coding for multiple proteins and transcription is dependent upon the correct environmental conditions as described below: In the presence of lactose, the lac operon is induced by allolactose, which binds to the lac repressor and a conformational change occurs, which results in a decreased affinity of the ''lac'' repressor for the ''lac'' operator and transcription of the structural genes occurs. In the absence of glucose, cAMP accumulates (glucose metabolites prevent this build up when glucose is present), and [[CAMP|cAMP]] is able to bind to a cAMP binding site on the ''lac'' operon activating the operon and promoting transcription <ref>Berg Jeremy.M, Tymoczko John.L, Stryer Lubert, 2007, Biochemistry, Sixth Edition, W.H.Freeman, New York, Pages 897-900</ref>.

== What is the Lac operon? ==

The lac operon is a good example of how genes are regulated. The lac operon was studied in ''E. coli ''<ref>Hartl, D. L. and Jones, E. W., 2009. Genetics: Analysis of genes and genomes. 7th edition. Sudbury: Jones and Bartlett Publishers pg 383</ref>. It contains 3 [[Gene|genes]] that are needed to produce proteins that are required to break down lactose when it is present in the cell. These 3 [[Gene|genes]] are Lac Z, Lac Y and Lac A. Each code for B- galactosidase, Permease and Transacetylase respectively <ref>http://users.rcn.com (2011) "The operon" – 30th March 2010 – Available from: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/L/LacOperon.html [Accessed 3rd January 2011]</ref>.

Further up the genetic code from these three genes, upstream, lies the promoter sequence. [[RNA polymerase|RNA polymerase]] needs a region in which it can join the genetic code, the promoter sequence, before it can start transcribing. RNA polymerase is required in transcription of the Lac operon <ref>Hartl, D. L. and Jones, E. W., 2009. Genetics: Analysis of genes and genomes. 7th edition. Sudbury: Jones and Bartlett Publishers pg 386</ref>. [[Image:Lac operon - basic.JPG]] 

== When does the Lac operon function? ==

The Lac operon does not function all the time and so has to be regulated. When lactose is present in the cell and glucose is absent, then the Lac operon is active and the 3 genes are transcribed to break down this lactose in the cell. 

== Negative gene regulation ==

The conditions inside the cell are changing all the time. So what happens when glucose is present and lactose levels are low? The Lac operon is no longer required to make the proteins to break down lactose and so its function is switched off. This is done by the use of a repressor protein <ref>Hartl, D. L. and Jones, E. W., 2009. Genetics: Analysis of genes and genomes. 7th edition. Sudbury: Jones and Bartlett Publishers pg 384</ref>. Upstream of the promoter sequence there is another gene. This is the Lac I gene. The Lac I gene is transcribed to make the repressor protein which binds to the operator sequence. The repressor protein is a tetramer and binds two operators on the template strand by looping the strand.

[[Image:Lac operon - with lac I and operator seq.JPG|690x391px|Lac operon - with lac I and operator seq.JPG]] [[Image:Lac operon - with lac I and operator seq nd repressor.JPG|690x391px|Lac operon - with lac I and operator seq nd repressor.JPG]]

Once the repressor protein is bound, it stops the [[RNA polymerase|RNA polymerase]] enzyme from transcribing the genes. Effectively, it acts as a block <ref>Sadava (2011) “ The Lac Operon” – 2008 – Available from: http://www.sumanasinc.com/webcontent/animations/content/lacoperon.html [Accessed 3rd January 2011]</ref>.

When the conditions in the cell change, the glucose levels deplete and the lactose levels rise, the repressor has to be removed in order to transcribe the required genes. This is done by an inducer molecule. This [[Molecule|molecule]] comes from lactose and is Allolactose. This binds to the [[Repressor protein|repressor protein]] and causes it to change, a conformational change. Once it has bound, the repressor can no longer bind to the operator sequence as it did before, its affinity has changed, and so is removed. [[RNA polymerase|RNA polymerase]] can work as it is not blocked and the Lac Z, Lac Y and Lac A genes are transcribed <ref>BioCoach Activity (2011) "The lac inducer: Allolactose" – Available from: http://www.phschool.com/science/biology_place/biocoach/lacoperon/inducer.html [Accessed 3rd January 2011]</ref>.

[[Image:Lac operon - allolactose.JPG]]

== Positive Gene regulation ==

Sometimes promoters are not strong enough to initiate transcription on their own and so require another molecule or complex to help. In the Lac operon, this is done by the CRP – [[CAMP|cAMP]] complex. When glucose levels in the cell are low, the levels of cAMP build up <ref>Mulligan, M. E. (2002) “The lac operon: positive regulation” – Available from: http://www.mun.ca/biochem/courses/3107/Topics/Lac_positive_control.html [Accessed 3rd January 2011]</ref>. This then combines with CRP and forms a complex. The complex can then join to the promoter sequence as well as the [[RNA polymerase|RNA polymerase]] and acts as a positive activator and encourages transcription <ref>Hartl, D. L. and Jones, E. W., 2009. Genetics: Analysis of genes and genomes. 7th edition. Sudbury: Jones and Bartlett Publishers pg 389</ref>. When the levels of [[Glucose|glucose]] increase again, the amount of [[CAMP|cAMP]] synthesised is reduced and so the complex levels decrease. This therefore inhibits the Lac operon from working. 

== References ==

<references />

Consensus sequence

2011-12-02T12:12:18Z

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Is the ideal promoter, its never actually found in DNA. It is a sequence of bases downstream of the start site, in E-coli it is found at -35 and -10 . It was determined experimentally by comparison of known [[Promoter]] sequences and selecting the most common bases at each position. Therefore, the closer to the consensus sequence the stronger the [[Promoter]] will be.[[]]

Amino acid acceptor stem

2011-12-02T11:43:40Z

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Is the part on a [[TRNA|tRNA]] molecule where the [[Amino_acid|Amino Acid ]]will bind.

Amino acid acceptor stem

2011-12-02T11:42:35Z

101488314: Created page with "Is the part on a tRNA molecule where the Amino Acid will bind."

Is the part on a tRNA molecule where the Amino Acid will bind.

Transcription

2011-12-02T11:39:13Z

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Transcription is the process by which single [[MRNA|mRNA]] is coded from double stranded [[DNA|DNA]]. This process is highly regulated and controlled to ensure the right amount of a specific [[Gene|gene]] is coded for at a specific time. It is said to be the first initial step in the process of gene expression in living organisms.

== mRNA ==

[[Proteins|Proteins]] are synthesised in the [[Cytosol|cytosol]], however, [[DNA|DNA]] does not leave the [[Nucleus|nucleus]], therefore a copy of the [[Gene|gene]] coding for the desired [[Protein|protein]] is sent as a messenger to the [[Cytosol|cytosol]] from the [[Nucleus|nucleus]]. This is called messenger RNA '[[MRNA|mRNA]]', which is a single stranded molecule that is a complementary copy of the [[DNA|DNA]] strand it was synthesised from. [[RNA|RNA]] is made from ribose nucleotides<ref>HGS Biology A-Level notes, Dr Millar, 2006</ref> that are free in the nucleus ([[RATP|rATP]], [[RGTP|rGTP]], [[RCTP|rCTP]] and [[RUTP|rUTP]]). Pre mRNA is first transcribed which contains non coding Introns these introns are spliced out to leave mRNA that contains only the coding exons.

== Double stranded DNA ==

[[DNA|DNA]] is double stranded as apposed to [[MRNA|mRNA]] which is single stranded, therefore only one strand of [[DNA|DNA]] is copied. The copied strand is called the 'template strand', the other strand is called the 'non-template strand'. [[MRNA|mRNA]] is synthesised by the enzyme '[[RNA polymerase|RNA polymerase]]', however, in order for the [[RNA|RNA]] to synthesise [[MRNA|mRNA]] it must bind to a single strand of [[DNA|DNA]]. The [[DNA|DNA]] must be unwound and unzipped, which is done via an enzyme called '[[DNA helicase|DNA helicase]]',<ref>HGS Biology A-level notes, Dr Millar, 2006</ref> which unwinds and unzipps the double stranded [[DNA|DNA]] at the loci of the [[Gene|gene]] to be transcribed, causing an area of single stranded [[DNA|DNA]] to be accessible to the [[RNA polymerase|RNA polymerase]].

== Promoter regions ==

[[RNA polymerase|RNA polymerase]] must recognise and bind to a region upstream of the gene being transcribed called the '[[Promoter|promoter region]]'. This region is a sequnce of bases that determines the strength of the binding of [[RNA polymerase|RNA polymerase]] to the [[DNA|DNA]] strand and therefore determining the efficiency of trancription of the gene it is accossiated with. If the promoter is a strong promoter, then [[RNA polymerase|RNA polymerase]] binds strongly to the [[DNA|DNA]] strand. If the promoter is a weak promoter, then the [[RNA polymerase|RNA polymerase]] can become hindered and can even unbind from the [[DNA|DNA]] strand. The [[Promoter|promoter region]] strength is determined by how promoter sequence compares to other promoters on separate [[Gene|genes]]. When different [[Promoter|promoters]] are compared, a sequence of bases can be determined that are most common in all the promoter sequences of that type, this is called a 'consensus sequence'. The closer the promoter sequence is to the consensus sequence, the stronger the promoter and the stronger the binding of the [[RNA polymerase|RNA polymerase]].

== Sigma factors ==

[[RNA polymerase|RNA polymerase]] cannot bind to the promoter region unless a sigma factor is present. Sigma factors ensure that the [[RNA polymerase|RNA polymerase]] binds to the correct promoter region, this is another method in which transcription is regulated. The sigma factor binds to the RNA polymerase via specific binding sites on its structure and forms a ‘[[Holoenzyme|holoenzyme]]’.

In ''E. coli'' the holoenzyme recognises specific [[Consensus_sequence]] at -35 and -10 within the promotor region. At the -35 sequence the DNA remains double stranded, and a closed complex is formed, however at the -10 sequence (or Pribnow box) about 14 bases are melted, and the closed complex becomes a [[Transcription_Bubbles|Transcription_Bubble]] with exposed bases.

== Initiation ==

Once the sigma factor has bound to the [[RNA polymerase|RNA polymerase]], the [[RNA|RNA]] can bind to the [[Promoter|promoter region]] upstream of the gene on the single stranded [[DNA|DNA]]. The [[RNA|RNA]] is then free to transcribe the [[Gene|gene]]. Free ribose nucleotides bind to the [[DNA|DNA]] sequence via complementary base pairing. Instead of the base Thymine found in [[DNA|DNA]], the base [[Uracil|uracil]] is used in [[RNA|RNA]]. The [[RNA polymerase|RNA polymerase]] joins the [[Nucleotide|nucleotides]] together via strong [[Covalent|covalent]] [[Phosphodiester bond|phosphodiester bonds]], this forms the single strand of [[MRNA|mRNA]]. This process is called initiation.

== Elongation ==

When 10 nucleotides of [[MRNA|mRNA]] have been synthesised, the sigma factor is released from the [[RNA polymerase|RNA polymerase]]. The [[RNA polymerase|RNA polymerase]] continues to transcribe the [[Gene|gene]]. This is called elongation, where the [[RNA polymerase|RNA polymerase]] moves along the [[DNA|DNA]] strand and creates a single strand of [[MRNA|mRNA]] that is complimentary to the [[DNA|DNA]] sequence. Only 8 nucleotides of [[MRNA|mRNA]] remain attached to the [[DNA|DNA]] sequence at a time<ref>HGS Biology A-Level notes, Dr Millar, 2006</ref>. The [[MRNA|mRNA]] peels of the [[DNA|DNA]] sequence but still remains attached to the rest of the [[MRNA|mRNA]] molecule. Once the [[MRNA|mRNA]] has been synthesised from specific [[Nucleotide|nucleotides]], an enzyme recombines the two [[DNA|DNA]] strands and rewinds it into its helix structure. This occurs while the [[RNA polymerase|RNA polymerase]] is still transcribing during elongation.

== Termination ==

Once the [[Gene|gene]] has been synthesised, the [[RNA polymerase|RNA polymerase]] must stop transcribing or it would continue to transcribe uncontrollably. The sequence present at the end of a [[Gene|gene]] sequence that stops transcription is called the ‘terminator sequence’. There are two types of terminator. The first is called ‘Factor independent termination’. The sequence of bases at the end of the gene have a region rich and G+C bases with a sequence in-between, followed by 4 to 10 A+T bases. Once this area of the [[Gene|gene]] has been transcribed, the section of rich G+C on the [[MRNA|mRNA]] molecule bind together by complimentary base pairing. This forms a hairpin structure at the end of the [[MRNA|mRNA]] molecule. This hairpin structure has properties that cause the [[RNA polymerase|RNA polymerase]] to pause in transcribing the [[Gene|gene]]. Once paused, the [[RNA polymerase|RNA polymerase]] unbinds from the [[DNA|DNA]] molecule and releases the complete [[MRNA|mRNA]] molecule, thus terminating transcription. There is also a second method of termination. This is called Rho dependant termination. This involves a helicase enzyme called a Rho factor which unwinds the [[MRNA|mRNA]] from the [[DNA|DNA]] molecule faster than it does naturally. The Rho factor unwinds the [[MRNA|mRNA]] until it reaches the [[RNA polymerase|RNA polymerase]]. This causes the [[RNA polymerase|RNA polymerase]] to pause and stop transcribing proteins, causing the [[RNA polymerase|RNA polymerase]] to unbind from the [[DNA|DNA]] and the complete [[MRNA|mRNA]] molecule to be released.

The [[MRNA|mRNA]] molecule then exits the nucleus into the [[Cytosol|cytosol]] where it will be translated into proteins the cell requires in the second step in gene expression known as ‘translation’. 

== References ==

<references />

Consensus sequence

2011-12-02T11:37:18Z

101488314:

Is the ideal promoter, its never actually found in DNA. It is a sequence of bases downstream of the start site, in E-coli it is found at -35 and -10 . It was determined experimentally by comparison of known [[Promoter]] sequences from numerous species and selecting the most common bases at each position. Therefore, the closer to the consensus sequence the stronger the [[Promoter]] will be.[[]]

Consensus sequence

2011-12-02T10:43:16Z

101488314: Created page with "Is the ideal promoter, its never actually found in DNA. It is a sequence of bases found at -35 and -10 downstream of the start site. It was determined experimental..."

Is the ideal promoter, its never actually found in DNA. It is a sequence of bases found at -35 and -10 downstream of the start site. It was determined experimentally by comparison of known [[Promoter]] sequences from numerous species and selecting the most common bases at each position. Therefore, the closer to the consensus sequence the stronger the [[Promoter]] will be.[[]]

Terminator sequence

2011-12-02T10:37:11Z

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Is a [[Nucleotide]] sequence in [[DNA]] which ends [[Transcription]]

Terminator sequence

2011-12-02T10:36:43Z

101488314: Created page with "IsNucleotide a  sequence on DNA which ends Transcription"

Is[[Nucleotide]] a  sequence on [[DNA]] which ends [[Transcription]]

Factor independent termination

2011-12-02T10:34:37Z

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RNA [[Polymerase|polymerase]] stops transcribing [[DNA|DNA]] into [[RNA|RNA]] at [[Terminator sequence|terminator sequences]], factor independent termation one of the two types of termination. Factor independent terminators have a series of 4 to 10 consecutive [[Adenine|A]]-[[Thymine|T]] base pairs and a [[Guanine|G]] and [[Cytosine|C]] rich region with a [[Palindromic sequence|palindromic sequence]] that immediately preceeding the series of A-T base pairs. This palindromic region forms a stem loop leaving the RNA and DNA connected only by the few A - U and T - A base pairs, these are the weaker [[Watson-Crick_pairs]] as they only have 2 [[Hydrogen_bonds]] connecting them, this reduced affinity favours dissociation of the RNA and DNA [[template strand]].  

RNA world

2011-12-01T12:57:55Z

101488314: Created page with "All modern organisms have DNA as a store of genetic information, RNA as a message and Proteins as their major cellular catalyst. This is very complicated model and when we t..."

All modern organisms have DNA as a store of genetic information, RNA as a message and Proteins as their major cellular catalyst. This is very complicated model and when we think of the origins of life we ask how did it all start? Where did DNA come from as Proteins are involved in its replication? But DNA codes for Proteins? What came first Polynucleotides or Polypeptides?

The RNA world is the believed hypothesis in modern genetics, that answers these questions. RNA led to Proteins which led to DNA.

 

===== '''Evidence supporting the RNA world''' =====

RNA can behave as both a store of genetic information and as a cellular catalyst.