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Virus

2013-10-24T14:24:28Z

120070877:

A virus is a non-living [[Obligate|obligate]] [[Intracellular|intracellular]] [[Parasite|parasite]]. They can only replicate inside of a living [[Cell|cell]] as they lack the necessary [[Enzymes|enzymes]] and molecular building blocks to be self sufficient. Viruses can be classified by structure (icosahedral, enveloped, complex etc), [[Genome|genome]] ([[Retroviruses|retroviruses]] have an [[RNA|RNA]] genome) or by the route through transcription (Baltimore classification).

They have a large [[Glycoprotein|protein]] coat, called a capsid, which is formed from many repeating protein subunits which join non-covalently to produce a large icosahedron sphere. Inside this sphere is where the virus' free [[Nucleic acid|nucleic acids]] are kept. The structure of this sphere is such that is protects the [[Nucleic acid|nucleic acid]] but also allows the [[Nucleic acid|nucleic acid]] to exit so it can go on to infect other cells<ref>Alberts, B. Johnson, A. Lewis, J. Raff, M. Roberts, K. Walter, P. (2008) Molecular Biology Of The Cell. Fifth Edition, New York:Garland Science(148-149)</ref>.

=== References ===

=== <references /> ===

Virus

2013-10-24T14:22:31Z

120070877:

A virus is a non-living [[Obligate|obligate]] [[Intracellular|intracellular]] [[Parasite|parasite]]. They can only replicate inside of a living [[Cell|cell]] as they lack the necessary [[Enzymes|enzymes]] and molecular building blocks to be self sufficient. Viruses can be classified by structure (icosahedral, enveloped, complex etc), [[Genome|genome]] ([[Retroviruses|retroviruses]] have an [[RNA|RNA]] genome) or by the route through transcription (Baltimore classification).

They have a large [[Glycoprotein|protein]] coat, called a capsid, which is formed from many repeating protein subunits which join non-covalently to produce a large icosahedron sphere. Inside this sphere is where the virus' free [[Nucleic_acid|nucleic acid]]s are kept. The structure of this sphere is such that is protects the [[Nucleic_acid|nucleic acid]] but also allows the [[Nucleic_acid|nucleic acid]] to exit so it can go on to infect other cells<ref>Alberts, B. Johnson, A. Lewis, J. Raff, M. Roberts, K. Walter, P. (2008) Molecular Biology Of The Cell. Fifth Edition, New York:Garland Science(148-149)</ref>.

Amino acids

2012-11-24T23:12:35Z

120070877:

<references />Amino acids are the building blocks of proteins. There are 20 naturally occurring amino acids. Amino acids exist in proteins as L-optical [[Isomer|isomers]], however they can extist as D-isomers in isolated examples, e.g. some bacterial cell walls contain D-isomers.

Amino acids can also be characterized as [[Polar amino acids|polar]] or [[Non-polar amino acids|non-polar]], these dictate the amino acid function. There are 10 non-polar amino acids, these are found in [[Protein|protein]] core. There are also 10 polar amino acids, these have [[Enzyme|enzymatic]] roles, they can be used to bind [[DNA|DNA]], metals and other naturally occuring ligands. There are essential amino acids and non-essential amino acids. Essential amino acids are the ones that the body cannot synthesise on its own. The essential amino acids in humans are histidine, leucine, isoleucine, lysine, methionine, valine, phenylalanine, tyrosine and tryptophan.<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg650.</ref> These amino acids have to be supplied to the body via digested proteins that are then absorbed in the intestine and transported in the blood to where they are needed<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg650.</ref>. The digestion of cellular proteins is also an important source for amino acids. Non-essential amino acids can be synthesised from compounds already existing in the body.

Amino acids have been abbreviated into a 3 letter code as well as a 1 letter code. For example, [[Glycine|glycine]] has the 3 letter code 'Gly' and is assigned the letter 'G' (see single letter amino acid codes).

'''List of the 20 Amino acids, single letter code, three letter code, their charges, and side chain [[Polarity|polarity]]:'''

{| style="width: 357px; height: 460px" border="1" cellspacing="1" cellpadding="1" width="357"
|-
| '''Amino acid'''
| '''single letter code'''
| '''three letter code'''
| '''charge'''
| '''polarity'''
|-
| [[Alanine|alanine]]
| A
| ala
| neutral
| nonpolar
|-
| [[Arginine|arginine]]
| R
| arg
| +ve
| polar
|-
| [[Asparagine|asparagine]]
| N
| asn
| neutral
| polar
|-
| [[Aspartate|aspartate]]
| D
| asp
| -ve
| polar
|-
| [[Cysteine|cysteine]]
| C
| cys
| neutral
| polar
|-
| [[Glycine|glycine]]
| G
| gly
| neutral
| nonpolar
|-
| [[Glutamine|glutamine]]
| Q
| gln
| neutral
| polar
|-
| [[Glutamate|glutamate]]
| E
| glu
| -ve
| polar
|-
| [[Histidine|histidine]]
| H
| his
| +ve
| polar
|-
| [[Isoleucine|isoleucine]]
| I
| ile
| neutral
| nonpolar
|-
| [[Leucine|leucine]]
| L
| leu
| neutral
| nonpolar
|-
| [[Lysine|lysine]]
| K
| lys
| +ve
| polar
|-
| [[Methionine|methionine]]
| M
| met
| neutral
| nonpolar
|-
| [[Phenylalanine|phenylalanine]]
| F
| phe
| neutral
| nonpolar
|-
| [[Proline|proline]]
| P
| pro
| neutral
| nonpolar
|-
| [[Serine|serine]]
| S
| ser
| neutral
| polar
|-
| [[Threonine|threonine]]
| T
| thr
| neutral
| polar
|-
| [[Tryptophan|tryptophan]]
| W
| trp
| neutral
| nonpolar
|-
| [[Tyrosine|tyrosine]]
| Y
| tyr
| neutral
| polar
|-
| [[Valine|valine]]
| V
| val
| neutral
| nonpolar
|}

=== '''Amino acid structure''' ===

All amino acids have a carboxyl terminus, and an amino terminus, but they differ in their residual groups. Amino acids are bonded together by a [[Covalent|covalent]] linkage called a [[Peptide bond|peptide bond]] <ref>Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. (Page 59)</ref>. Amino acids contain both a [[Carboxyl group|carboxyl group]] (COOH) and an [[Amino group|amino group]] (NH2). The core amino acid structure is: 

              NH2-----C(H)(R)----COOH

where R is the side chain tha differ in all amino acids.

Large amino acids form the rigid region of the polypeptide backbone while the small amino acids form the flexible regions of the [[Polypeptide|polypeptide]] allowing the protein to fold into it's three dimensional shape. The core of the polypeptide is made up of the [[Hydrophobic|hydrophobic]] amino acids like [[Phenyalanine|phenyalanine]], [[Tyrosine|tyrosine]], and [[Tryptophan|tryptophan]] <ref>J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) Biochemistry, 6th edition, New York: W.H.Freeman and company (page 27).</ref>.

Amino acids are referred to as chiral due to the alpha carbon being connected to four different groups. They can exist as one of two mirror images referred to as the L isomer and the D isomer with only the L form of the amino acid isomer present within proteins. <ref>Berg J. Tymoczko J. Stryer L., Biochemistry Sixth Edition (2007, WH Freeman, New York (page 27)</ref>

=== Amino acids in Translation ===

During the [[Translation|translation]] of [[MRNA|mRNA]] amino acids bind to the [[Ribosome|ribosome]] as it reads the mRNA and using the information given it produces a specific amino acid sequence producing a polypeptide chain.

=== References ===

<ref>Berg. J, Tymoczko J, Stryer L,: Biochemsitry 6th Edition (2007), WH Freeman, New York, P.27</ref>Berg.J, Tymoczko J, Stryer L,:Biochemistry Sixth Edition(2007), WH Freeman, New York p.27

Enzyme Inhibitors

2012-11-24T23:04:50Z

120070877:

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

#Irreversible Inhibitors
#Reversible Inhibitors

=== Irreversible Inhibitors ===

These substances binds permanently to the [[Enzyme active site|active site]] of an enzyme to form an EI complex.These 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 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.

=== Reversible Inhibitors ===

These substances bind to the active of an enzyme to form an EI complex. These bond is 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]] and 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 stimuli, then Ibroprofen can be used as it is a competitive inhibitor of the enzymes involved in the signaling pathways of the inflammatory response. Competitive Inhibitors cause KM to increase and 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 binds to the active site of an enzyme and does not prevent the binding of a substrate to the same enzyme molecule. It can also bind to an already existing 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. Uncompetitive inhibition essentially decreases the concentration of functional enzymes.Like Non-competitive inhibition,uncompetitive inhibition cannot be overcome by increasing the substrate concentration. 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>

=== References ===

<references />Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg227.

Enzyme Inhibitors

2012-11-24T22:57:14Z

120070877:

[[Enzyme|Enzyme]] Inhibitors are substances that reduce the rate of enzyme activity in an enzyme [[Catalysed reaction|catalysed reaction]].These substances may be in the form of [[Molecule|molecules]] or ions that mimic the actual substrates in order to bind to the active site of the enzyme to form an enzyme-inhibitor (EI) complex. Enzyme inhibitors are of two types <ref>Berg J.,Tymoczko J. and Stryer L.(2011) Biochemistry,7th edition,New York:W.H Freeman</ref>;

#Irreversible Inhibitors
#Reversible Inhibitors

=== Irreversible Inhibitors ===

These substances binds permanently to the [[Enzyme active site|active site]] of an enzyme to form an EI complex.These 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 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.

=== Reversible Inhibitors ===

These substances bind to the active of an enzyme to form an EI complex. These bond is 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]] and 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 stimuli, then Ibroprofen can be used as it is a competitive inhibitor of the enzymes involved in the signaling pathways of the inflammatory response. Competitive Inhibitors cause KM to increase and Vmax to remain the same.

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

These molecules binds to the active site of an enzyme and does not prevent the binding of a substrate to the same enzyme molecule. It can also bind to an already existing 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.

=== 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. Uncompetitive inhibition essentially decreases the concentration of functional enzymes.Like Non-competitive inhibition,uncompetitive inhibition cannot be overcome by increasing the substrate concentration. Uncompetitive inhibitors decrease both KM and Vmax.

=== References ===

<references /> Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: W.H. Freeman and Company, pg227.