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Organic Chemistry

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