1. introduction
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Biological molecules
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Carbon based life forms are made form molecules using carbon atoms
A carbon atom has 6 protons6 neutrons and 6 electrons
This gives 4 electrons in the outer shell so a carbon atom will make 4 covalent bonds to have a stable 8 electrons
Here carbon (blue) has made a covalent bond with each of 4 hydrogens (red)This makes a molecule called methane with a chemical formula of CH4
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Methane is a 3-dimensional structure like this:
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Which can be drawn like this: Or more simply like this:
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Carbon can share an electron with another carbon, forming a covalent bond
Notice that there are now only 3 hydrogen atoms on each carbon CH3CH3 or C2H6
This is ethene
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By forming covalent bonds between carbon atoms long carbon chains can be built
Notice that each carbon makes 4 bonds so the terminal carbons have 3 hydrogens, the central ones have 2
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Other atoms like oxygen and nitrogen can also form covalent bonds with carbon
Oxygen requires 2 more electrons to form a stable shell so often forms a double bond, sharing 2 electrons with carbon which also shares 2 electrons
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Double BondsThese can form between 2 carbons or between other atoms
Each carbon still has 4 bonds, but there are 2 bonds between the carbonsSo there is only space for 2 hydrogen atoms to attach to each carbonThis is EthyleneCH2CH2 or C2H4
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There can even be a triple bond between carbon molecules
Notice that sometimes we simply draw a line without showing Hydrogen on the end – it is implied
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Double Bonds can form between carbon and other
moleculesOr as part of a ring structure
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Functional groupsThe order in which atoms attach to a carbon chain will determine the properties
of the molecule
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Aldehyde group - CHO
This attaches to a carbon chain
This is a carbonyl group
Aldehydes often smell aromaticAcetone and some vitamins are aldehydes
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Keto group - CO
A central carbon bonds to oxygenThis is another carbonyl group
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Hydroxyl group - OH
This attaches to a carbon
Molecules with this group are called alcohols
Hydroxyl groups are important in making bonds by condensation
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Molecules are named according to the position of the hydroxyl group
Hydroxyl is terminal
Hydroxyl is in the middle
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Carboxyl group - COOH
These are called acidsThe hydrogen will dissociate and become a proton (H+) in solution – making the solution acidic
The oxygen left becomes positively charged giving the molecule an overall charge
Charged molecules are called polar molecules
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Saturated Carbon chains have no double bonds
Unsaturated carbon chains have one or more double bonds and therefore fewer hydrogen
molecules
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OPTICAL ISOMERISMThis may occur when 2 molecules have the same
molecular formula but different arrangements in space, forming mirror images.
If a central carbon has FOUR DIFFERENT groups attaches it will be asymmetrical, and may exist in two different forms.
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The central black carbon has 4 different groups attachedBy rearranging these we can form isomers which are mirror images
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Like a left and a right hand
This is important in biology because molecules must fit into enzymesIf the shape is wrong it would be like trying to put your left hand into a right-hand glove
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Isomers change the angle of plane-polarised light;Bending it either right or leftThey are named accordingly
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Molecules are actually based on the properties of the isomers of glyceraldehyde
D = rightL = left