Organic Chemistry
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| Water is: | Highly cohesive (high affinity for one another)and polar.
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| Electronegativity: | The measure of the force of an atom's attraction for the electron it shares in a chemical bond with another atom.
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| Electronegativity in the periodic table | From left to right: increasing +ive charges in the nucleus
Bottom to top: decrease in the distance of valence electrons from the nucleus
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| Non-polar bonds: | < 0.5
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| Polar bonds | 0.5 - 1.9
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| Ionic bonds | > 1.9
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| ACID | proton donor, produces H3O+ ions in aqueous solutions.
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| BASE | proton acceptor, produces OH- ions in aqueous solutions.
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| Stron acid/base | ----> because equilibrium is far right.
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| pH | -log[H3O+]
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| The LARGER the pKa (small Ka) | the WEAKER the acid
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| The SMALLER the pK (large Ka) | the STRONGER the acid
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| LARGE pKb | STRONG base
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| SMALL pKb | WEAK base
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| When a base accepts a proton | it is converted to its conjugate acid
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| When an acid transfers a proton | it is converted to its conjugate base
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| Buffer solution | weak acid and conjugate base to resist changes in pH
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| Functional groups | - reactive parts of organic molecules
- essential for life
- same functional groups on compounds allows similar reactivity
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| Alkane | CnH2n+2
chair conformation most stable
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| Alkene | CnH2n
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| TRANS | OPPOSITE
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| CIS | SAME
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| Nomenclature | meth-
eth-
prop-
but-
pent-
hex-
...
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| Priority | higher atomic number determines priority
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| Alkyl | Alkane - H
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| Alcohol -ol | Hydrogen bonds are weaker than covalent but have a significant effect on properties:
- Higher bp than alkanes
- more soluble in water
both due to (-OH)
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| Amines | 1°, 2°, 3° depending on how many H's have been replaced.
-polar
- weak bases, aqueous solutions are basic
- aliphatic amines ~pKb 3-4
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| Aliphatic | A class of saturated or unsaturated carbon compounds, in which the carbon atoms are joined in open chains.
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| Aldehydes -al | H-C=O
Methanal: 2H's
Everything else: 1H & 1C
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| Ketones -one | 2C-C=O
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| Aldehyde & Ketone properties | - higher bp
- more soluble in H2O than nonpolar compounds of comparable size
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| Carboxylic Acids -CO2H | - high bp, very strong intermolecular hydrogen bonds
- solubility decreases and hydrophobic tail increases
- resonance increases acidity
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| Isomer: | different compounds with the same molecular formula
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| Constitutional isomer: | isomer with different connectivity
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| Stereoisomer: | same molecular formula, same connectivity but different orientation so that cannot be interconverted by rotation about a single bond.
(different atomic arrangement in space)
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| Enantiomers: | mirror images, non-superimposable.
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| Diastereomers: | non-mirror images.
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| Chiral: | non-superimposable on their mirror image.
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| Achiral: | are superimposable on mirror image.
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| Stereocentre: | Carbon with 4 different groups bonded to it.
2 stereocentres = 2^2
Therefore, 4 stereoisomers.
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| Oxidation: | REMOVAL of electrons or H from an atom and/or ADDITION of O
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| Reduction: | ADDITION of electrons or H to an atom or REMOVAL of O
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| ATP, ADP, AMP | universal carriers of phosphate groups, energy source
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| ATP: | Hydrolysis of terminal phosphate of ATP gives ADP + phosphate + energy
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| NAD/NADH FADH/FADH2 | coenzymes involved in oxidation/reduction of metabolic intermediates
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| NAD+ | an important coenzyme found in cells. It plays key roles as carriers of electrons in the transfer of reduction potential.
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| NADH | reduced form of NAD+
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| FADH/FADH2 | FADH and FADH2 are reduced forms of FAD. FADH2 is produced in the citric acid cycle.
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| β-oxidation | process by which FA, in the form of Acel-CoA, are broken down to form Acetyl-CoA, the entry molecule for the CAC.
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| β-oxidation [1] | oxidation of C-C to C=C by FAD
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| β-oxidation [2] | hydration of C=C, R enantiomer formed
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| β-oxidation [3] | oxidation of β-hydroxyl group to a carbonyl group by NAD+
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| β-oxidation [4] | cleavage of C chain by a reverse Claisen condensation (thiolysis)
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| Carbohydrates | - Natural monosaccharides are sweet
- Highly soluble MONOS due to the extensive hydrogen bonding between OH groups
- tri(number of C)ose(carbohydrate), tetrose, pentose
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| L - | OH LEFT
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| D + | OH RIGHT
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| Haworth projections | Anomeric carbon is the new stereocentre that is formed
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| OH RIGHT | F: down Haworth: α
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| OH LEFT | F: up Haworth: β
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| Mutarotation: | is the change in the rotation between two anomers, α & β.
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| Mattose (di) | α-1,4 - glucosidic bonds
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| Sucrose (di) | α- 1, 2 - glucosidic bonds
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| Unbranched polys | 1,4 α glucosidic bonds
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| Branched polys | 1,4 α glucosidic bonds & 1,6 α glucosidic bonds
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| Starch | 1,4 α glucosidic bonds & 1,6 α glucosidic bonds
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| Cellulose | 1,4 β glucosidic bonds
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| Lipids | -insolubility in H2O due to large hydrocarbon component
- saturated: solid/semi-solid
- unsaturated: liquid
- storage of energy
- made of glycerol + 3 FAs
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| Saturated lipids | DECREASE mp as C increases
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| Unsaturated lipids | INCREASE mp as C decreases & C=C decrease
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| Micelle: | spherical arrangement of lipids in water so that hydrophilic head points out, hydrophobic in.
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| Waxes: | are esters formed from long chains of carboxylic acids and alcohols.
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| Phospholipids: | Glycerol + 2FA + phosphoric acid
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| Saponification: | The reaction of an ester with a metallic base and water.
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| Fatty Acids | usually C12-20, unbranched, C-C, C=C (must be cis)
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| Amino acids | Side chains determine their behaviour in water,
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| Isoelectric point (pI): | is pH at which majority of molecules in solution have no nett charge.
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| Electrophoresis | Electrical potential applied, move towards opposite charge. Higher charge density move faster that those with lower charge density. At pI don't move.
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| Peptides read.. | from N terminal
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| Peptides have | trans configuration
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| Peptide or amide bond | -(O=)C-H-N-
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| Primary protein structure | aa sequence
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| Secondary protein structure | folds, α-helices, β-sheets... hydrogen bonding
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| Tertiary protein structures | held together by S-S linkages and other bonds. 3D
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| Quaternary protein structures | Tertiary put together. The arrangement of polypeptide chains into a non covalently bonded aggregation.
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| Hydrophobic effect: | non-polar groups cluster in a way that they are shielded from contact with aqueous environment.
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| Competative inhibition | to active site.
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| Uncompetative inhibition | seperate site to active site but only binds to ES complex.
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| Mixed inhibition | either one, may not affect active site.
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| Precedence | ...........
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| Amino acids | Nitrogen-containing compounds that are the building blocks of proteins.
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| Saccharides | draw..
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| Saccharides | (Greek σάκχαρον meaning "sugar") are simple molecules that are straight-chain aldehydes or ketones with many hydroxyl groups added, usually one on each carbon atom that is not part of the aldehyde or ketone functional group.
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| Carbohydrates | (CH2O)n
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| Oligosaccharide | 3-6 joined monosaccharides
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| Monosaccharides | ALPHA opposite. BETA same. as CH2OH
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| Cycloalkanes | hex-chair pent-envelope hex-chair
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| Biochemistry of alcohol | Liver oxidises the alcohol to an aldehyde which is toxic. Aldehyde can then be converted into a carboxylic acid which can be used as a source of energy.
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| Amines | are slightly stronger bases than amonia.
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| Carbonyl group | is polar as the oxygen is more electronegative that the carbon
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| Carboxylic acids pKa | 4-5
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| Carboxacids reaction with bases | whether soluble or insoluble in water react with NaOH, KOH and other strong bases to form WATER-SOLUBLE SALTS.
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| Carboxyl Derivatives - Esters | (R1-C(=O)OR2) condensation bw corboxacid and alcohol.
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| Carboxyl Derivatives - Amides | organic functional group characterized by a carbonyl group (C=O) linked to a nitrogen atom (N), or a compound that contains this functional group
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| Fates of pyruvate: | reduction to lactate or ethanol. oxidation and decarboxylation to acetyl-CoA.
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| Activation of FAs | begins in the cytoplasm with the formation of a thioester. involves a reaction with ATP and then a reaction with coenzyme A,
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| Penultimate carbon: | stereocentre of monosaccharide farthest from carbonyl group
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| Anomer: | pair of cyclic diastereoisomers of a sugar where the position of the OH differs.
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| Cellulose breakdown | humans do not have a β-glucosidase to break cellulose's bonds
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| Glycogen | energy storage in animals. 1,6 or 1,4 α
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| Glycerol | C3H8O3
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