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    Now is the time where i need to sum up everything i have learned.

    Amino acids:

    there are 20 naturally occurring amino acids. Amino acids react with each other to form polypeptides which is monomer units of amino acids. The polypeptide backbone is -C-C-N- this gives rise to different structures of polypeptides. A polypeptide chain is a linear polymer of amino acids.

    Primary structure: A sequence of amino acid residues

    Secondary structure: this is the folding of the backbone of the polypeptide chain which is stabilized by hydrogen bonding. The two known structures are:

    a-helix ----> the polypeptide chain is coiled up into a spiral, like a narrow tube forming 3.6 residues per turn. The R groups of amino acid residues project outwards from the spiral. Each peptide group is involved in two hydrogen bonds. The C=O hydrogen bonds to the N-H of the peptide group four units ahead of the primary structure

    B-pleated sheet -----> polypeptide is not coiled but lengths of the chain lie fully stretched side by side, forming a sheet. The R groups of the amino acid residues point above and below the plane of the sheet while the C=O and N-H groups of the peptide groups in adjacent sections point towards each other

    Tertiary structure-----> this is where the R groups of the amino acid residues take part in particular interactions to form the third hierarchy in protein folding (quick question, a protein is formed by two or more polypeptide units isn't it? a quaternary structure)

    The possible interactions are:

    (1) - ionic attractions between charged R groups
    (2) - non-polar side chains by Van der Waals' forces
    (3) disulphide bonding between cysteine residues
    (3) hydrogen bonding between polar R groups

    The last structure being the quaternary structure which consists of two or more polypeptide units. The type of forces that hold them together is the same as in the tertiary structure.

    An example of this is Haemoglobin - oxygen carrier. Haemoglobin consists of four protein chains. Each of these four protein chains is also bound to a non-protein haem group(what does this mean?) that contains iron(II) ions. This is the complex ion and binds reversibly with the oxygen to form oxyhaemoglobin.

    Hb + 4O2 -----> HbO8

    The ligands are the haem group.......

    That's pretty much all there is on amino acids and proteins for me. The questions i have given in brackets, if people could answer them that would be great and anything else i have missed out.

    Thanks in advance and i will be adding more shortly.
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    Now for enzymes. Enzymes are biological catalysts that speed up an reaction without being used itself in the reaction. They provide alternate pathways. They are also very specific in their reactions...... They contain active sites which bind to a substrate molecule(the target molecule) by recognition of the shape which is similar to the enzyme (just so i am clear the enzyme binds to the substrate yes?)

    The conversion of substrates into products at an active site is carried out by specific R groups (this suggest it only works on amino acids cause they have R groups?) these R groups interact chemically with the R groups of the substrate molecule and catalysis takes place.

    Factors affecting enzyme activity.......
    (1) temperature - high temperature causes denaturation
    (2)pH - change the pH you're changing how the R groups interact and therefore the shape of the structure of the protein.

    Then you have inhibition of enzyme activity. An inhibitor is a chemical other than the substrate, whose presence affects enzyme function. There are two types of inhibitors

    (1) competitive inhibitor - is an enzyme that has a similar shape and chemical characteristics to the substrate molecule. They bind to the active site but cannot take part in the catalysed reaction. There is a competition between the inhibitor and the substrate molecule and the only way the substrate will bind is if you increase the concentration of it.

    (2) non-competitive inhibitor - The inhibitor binds to the enzyme but not at the active site, therefore changing the shape of the active site so that substrate cannot bind. Catalysis cannot also take place. Adding more concentration will have no effect on this cause this type of inhibitor effect is that there a fewer functional enzymes available.

    Enzymes are used commercially and industrially. It is used as a biological washing powder to remove stains. Enzymes are also immobilised. This technique is used to prolong the use of the enzyme in industrial processes. This is done by attaching it to a solid surface so it can't react with water readily. The advantages to this are that:

    (1) it can be stored and used for longer periods
    (2) enzyme can be removed from a reaction mixture by filtration or centrifuging(what is this exactly?)
    (3) stability of enzyme to thermal denaturation can be increased, enabling the enzyme to be used for longer periods(how is that done?)
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    Nearly done now. Now onto carbohydrates, a lot of information here i need to remember so let's see. The simplest sugar is glucose which is a monosaccharide with the general formula (CH2O)n. This provides instant-access energy in anaerobic exercises that release lactic acid. Also used in photosynthesis.

    C6H12O6 + 6O2 -----> 6CO2 + 6H2O(anything else i missed out please include)

    Disaccharides are dimers of monosaccharides and act as structural units for polysaccharides. Some important disaccharides i need to know about if i can name them is:

    (1) maltose- alpha glucose forms an 1a-4 glycosidic link(this is the formation of an oxygen bridge by removal of water)
    (2) cellobiose - beta glucose which forms an 1B-4 glycosidic link

    Structures of polysaccharides. These are polymers of monosaccharides or disaccharides. The three important disaccharides are
    (1) starch - exists in two forms, amylose and amylopectin.
    (2) glycogen
    (3) cellulose

    starch - amylose is an unbranched(what does this mean exactly?) molecule. Amylose forms a helix due to the orientation of the 1a-4 glycosidic links. Internal(intramolecular) Hydrogen bonding stabilises the helical structure which involves the hydroxyl groups on carbon-2 and carbon-3 in each ring.

    Amylopectin is a branched chain polymer(again what does that mean?) The polymer molecules are very large. This also contains a 1a-4 glycosidic link and branches are linked to the main chain by 1a-6 glycosidic links.

    Cellulose is a linear polymer, unbranched polymer linked by 1B-4 glycosidic bonds. Parallel neighboring chains are able to interact with each other by cross-linked hydrogen bonding.

    Glycogen is an energy storage molecule in animals. Structure of glycogen is very similar to amylopectin but is more extensively branched. The unbranched sections are formed from glucose molecules linked by 1a-4 glycosidic link. At the branch points, 1a-6 glycosidic bonds are found. Glycogen forms a far more compact structure.

    For all three of these structures, it is closely related to their function.

    Also, Carbohydrate solubility ----> monosaccharides and disccharides are more soluble in water than polysaccharides due to more scope of hydrogen bonding cause of the available hydroxyl groups whereas in polysaccharides they are mainly used up in intramolecular hydrogen bonding. But amylose is more soluble in water than amylopectin because it is unbranched but both are not really that soluble but because it is unbranched it has more scope for hydrogen bonding. Glycogen is even more extensively branched and therefore is only sparingly soluble in water.
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    (Original post by boromir9111)

    An example of this is Haemoglobin - oxygen carrier. Haemoglobin consists of four protein chains. Each of these four protein chains is also bound to a non-protein haem group (what does this mean?) that contains iron(II) ions. This is the complex ion and binds reversibly with the oxygen to form oxyhaemoglobin.

    Hb + 4O2 -----> HbO8

    The ligands are the haem group.......
    The ligands are nitrogen atoms in a porphyrin structure that consists of four heterocyclic ring systems linked together. This is the non-protein unit referred to.

    If you look at the structure of haemoglobin you will seee that the iron atom is bonded (liganded) to four nitrogen atoms which in turn form part of the aforementioned heterocyclic rings (rings containing both carbon and another atom)

    This leaves an axial sites that can ligand to oxygen for transport around the body (or carbon monoxide or any other reasonable ligand)
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    Now onto lipids and membranes. Lipids play essential roles in cell structure and metabolism. Lipids are largely insoluble in water, but soluble in non-polar solvents. Lipid molecules are not polymers but their non-polar nature means they tend to group together when placed in water (self-assembly known as, forms micelles). Biologically important lipids include

    (1) triglycerides---- major storage form of energy needed to drive reactions in plants and animals.
    Triglycerides are formed by an esterification reaction between 3 fatty acid molecules and a molecule of propane-1,2,3-triol(glycerol). This consists of of "polar head" region which is the ester linkage and propane-1,2,3-triol. It also has a non-polar "tail" which is the three long fatty acid chains. Triglycerides are hydrolysed which is the process known as saponification (soap making) with hot aqueous sodium hydroxide to form the alcohol and a sodium salt of fatty acid (soap). Triglycerides are not soluble in water because the nature of the hydrocarbon chains overwhelms any polarity a triglyceride might have due to the oxygen in the ester links. However the long hydrocarbon chains do interact with non-polar solvent through van der Waals' forces. Triglycerides are also soluble in polar organic solvents, such as halogenoalkanes.

    (2) phosphoglycerides - major lipid component of cell membranes is phosphoglycerides. Phosophoglycerides contain a charged phosphate group instead of a 3rd fatty acid molecule on carbon-3 and is known as the the polar "head".

    now onto self-assembly - triglycerides form micelles which are spherical structures formed when enough triglycerides are present in water where the polar "head" is facing the water and the non-polar "tail" is facing into the air.

    Bimolecular layers are only formed by phosphoglycerides because this more complicated than the micelles formed from the triglycerides due to the "bulk of the three hydrocarbon chains in a triglyceride molecule"(what does that mean exactly?) Bimolecular layers can take different forms (what are these forms and i don't really understand still what a bimolecular layer is and how it is different to a micelle?)

    Now onto lipids and energy. Triglycerides(fats) release more energy than carbohydrates(glycogen) because carbohydrates are essentially (CHOH)n units where the oxygen is partially oxidised so it releases less energy (CO2 and H2O i believe) whereas triglycerides are essentially (CH2)n units which are long chain hydrocarbons and release more energy per mole. I think that's that on this section but if there is more please do include.
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    (Original post by charco)
    The ligands are nitrogen atoms in a porphyrin structure that consists of four heterocyclic ring systems linked together. This is the non-protein unit referred to.

    If you look at the structure of haemoglobin you will seee that the iron atom is bonded (liganded) to four nitrogen atoms which in turn form part of the aforementioned heterocyclic rings (rings containing both carbon and another atom)

    This leaves an axial sites that can ligand to oxygen for transport around the body (or carbon monoxide or any other reasonable ligand)
    Ahhh i see, the complex ion(Fe2+) is bonded to the nitrogen atoms(non-haem group) and also to O2 and a protein chain(is that the haem group?)
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    Now onto nucleic acids and protein synthesis. The "central dogma of molecular biology" is:

    Replication--->transcription--->RNA---->translation----> protein synthesis.

    None of this can happen without the nucleotides which consist of:
    (1) - a sugar (for DNA this is deoxyribose)
    (2) - base pairs
    (3) - phosphate group

    DNA is a condensation polymer of sugar and phosphate groups that forms a sugar-phosphate backbone. The phosphate group is linked to carbon 3 and 5 (known as 3"prime" and 5 prime) of the sugar molecule. The base pair is attached to carbon 1 of the sugar. For DNA this is AT and CG these form complementary base pairs. A and G are purines, two ring planar structure whereas C and T are pyrimidines, single ring planar structure. CG have three hydrogen bonding and AT have two. There is also Van der Waals' forces which hold the two chains of DNA together which are in anti-parallel. Where as RNA has the base Uracil instead of thymine, has ribose for a sugar and is single stranded but can fold itself to form helical loops.

    Now onto the processes. Replication is the process where a new DNA molecule is formed by the enzyme DNA polymerase. During replication, hydrogen bonds are broken and van der Waals' forces between the base pairs in the double helix. Original strands act as templates for the synthesis of new strands. Each new strand contains a sequence of bases complementary to the bases of the original strand. Hydrogen bonds and van der Waals' forces are formed between the original and new strands, creating a helical stable structure. This is known as a semi-conservative replication because each daughter molecule consists of a new strand and one strand from the original DNA molecule.

    As i forgot to mention earlier, the amino acid sequence for a particular polypeptide chain is encoded in a specific stretch of DNA(a gene). This code in a gene is used to make copies of a particular polypeptide chain by the next process.

    Transcription - This is where a gene for a particular particular polypeptide chain is copied onto a molecule of mRNA by the enzyme RNA polymerase. Part of the double helix unravels and an RNA copy of the gene is synthesised using appropriate nucleotides(form complementary base pairs with the DNA molecule)

    Translation - mRNA cannot bind directly to the amino acid. tRNA molecules act as vehicles for these interactions. One end of tRNA molecule carries amino acid corresponding to the base triplet on the other end. Triplet of bases on mRNA code for each amino acid in the polypeptide chain. tRNA attaches to mRNA using base triplet which is complementary to base triplet on mRNA. Attachment is by hydrogen bonding between base pairs, such as CG and AU.
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    (Original post by boromir9111)
    Ahhh i see, the complex ion(Fe2+) is bonded to the nitrogen atoms(non-haem group) and also to O2 and a protein chain(is that the haem group?)
    Not quite.

    The 'haem group' is the four nitrogen ring non-protein structure (porphyrin) with the central iron ion.

    This haem group is located in a crevice in the globin protein structure, which also connects to the iron via a histidine group at one of the unoccupied nitrogen sites, leaving the other for oxygen.
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    http://www.ocr.org.uk/download/pp_09...ce_2815_02.pdf

    3 (a) and (b) i pretty unsure what they are doing there tbh. AT and CG are base pairs..... so for (b) the hydrogen bond number would be (2*1) + (3*1) = 5 because there are two hydrogen bonds in AT and 3 for GC but it's 15. Explain please.
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    wait you have TA and AT that would make 4 bonds there, CG and GC are 6 bonds there... still i only get 10!!!!!
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    anyone?

    edit - oh wait, is it like this...... AT, TA and AT again....... GC,CG,CG again therefore you get 6+9 = 15. Is that the way you do it? how about part (a)?

    edit again - for the sequence well have GATACG -----> now we know that what the complementary base pairs are and they are there so why change them?
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    no-one?
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    For A, you just need to translate each base into its constituant. I haven't done this for a while (I did it in AS biology, I so wish we had a biochemistry module though :emo:) I think it Goes, A-->T, T-->A, C-->G and G--> C

    I will double check this.

    Your anser to b) is correct, Its 15

    EDIT: Just looked at the mark scheme, you don't use the base change durng protein synthesis

    Now give it a try and I will check with the MS that it is correct.

    2nd Edit: Ok I'm getting mixed up a bit lol. The stuff in the 1st part of this post is correct, but in the 2nd part (part c) (DNA --> mRNA) A is paired with U
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    (Original post by charco)
    The ligands are nitrogen atoms in a porphyrin structure that consists of four heterocyclic ring systems linked together. This is the non-protein unit referred to.

    If you look at the structure of haemoglobin you will seee that the iron atom is bonded (liganded) to four nitrogen atoms which in turn form part of the aforementioned heterocyclic rings (rings containing both carbon and another atom)

    This leaves an axial sites that can ligand to oxygen for transport around the body (or carbon monoxide or any other reasonable ligand)
    http://www.thepaperbank.co.uk/papers...2007_jan_w.pdf

    if you could please help me with question 3 d please, i am stuck on it and is really annoying me. Thanks in advance.
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    (Original post by boromir9111)
    http://www.thepaperbank.co.uk/papers...2007_jan_w.pdf

    if you could please help me with question 3 d please, i am stuck on it and is really annoying me. Thanks in advance.
    [OH-] is 100 x greater than [H+]

    and you know that [H+][OH-] = 1 x 10-14

    So substitute [OH-] = 100 x [H+] into the equation

    Therefore: [H+] x 100 x [H+] = 1 x 10-14

    so [H+]2 = 1 x 10-16

    and [H+] = 1 x 10-8

    pH = 8
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    (Original post by charco)
    [OH-] is 100 x greater than [H+]

    and you know that [H+][OH-] = 1 x 10-14

    So substitute [OH-] = 100 x [H+] into the equation

    Therefore: [H+] x 100 x [H+] = 1 x 10-14

    so [H+]2 = 1 x 10-16

    and [H+] = 1 x 10-8

    pH = 8
    BOOM, that's where it was getting me.... i had to sub it in, now i understand so thanks for that mate!!!!! i have given you +rep thanks once again!!!
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    (Original post by Loz17)
    For A, you just need to translate each base into its constituant. I haven't done this for a while (I did it in AS biology, I so wish we had a biochemistry module though :emo:) I think it Goes, A-->T, T-->A, C-->G and G--> C

    I will double check this.

    Your anser to b) is correct, Its 15

    EDIT: Just looked at the mark scheme, you don't use the base change durng protein synthesis

    Now give it a try and I will check with the MS that it is correct.

    2nd Edit: Ok I'm getting mixed up a bit lol. The stuff in the 1st part of this post is correct, but in the 2nd part (part c) (DNA --> mRNA) A is paired with U
    Cheers mate for your reply but i figured out why they changed around the sequence for the DNA strand just by applying a little logic in there.... thanks anyway, much appreciated your message!!!
 
 
 
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