Organic Chemistry 1 Flashcards
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.
pH
-log[H3O+]
The LARGER the pKa (small Ka)
the WEAKER the acid
The SMALLER the pK (large Ka)
the STRONGER the acid
LARGE pKb
STRONG base
SMALL pKb
WEAK base
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
TRANS
OPPOSITE
CIS
SAME
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
L -
OH LEFT
D +
OH RIGHT
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
5-Apr
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
organic chemistry
chemistry related to the compounds containing carbons
funcational group
an atom or group of atoms within a molecume that shows a characterisitic set of predictable physical and chemical behaviors
alcohol group
a compund containing an -OH group bonded to a tetrahedral carbon atom
hydroxyl group
an -OH group bonded to a tetrahedral carbon atom
amine
an organic compund in which 1,2 or 3 hydrogens of ammonia are replaced by carbon groups of RNH2 OR R2NH OR R3N
amino group
an -NH2, RNH2, OR R3N group
carbonyl group
a C=O group
aldehyde
a compound containing a carbonyl group bonded to a hydrogen a -CHO group
ketone
a compound containing a carbonyl group bonded to 2 carbon groups
carboxyl group
a -COOH group
ester
a derivation of carboxylic in which the H of the carbon group
alkane
a saturated hydrocarbon whose carbon atoms are arranged in a chain
hydrocarbon
a compound that contains only carbon and hydrogen atoms
saturated hydrocarbon
a hydrocarbon that contains only C-C bonds
aliphatic hydrocarbon bonds
an alkane
line angle formula
an abbreviated way to draw structure formulas in which each vertex and line terminus represents a carbon atom and each line represents a bond
consitutional isomers
compounds with the same molecular formula but a different connectivity of their atoms
alkyl groups
a group derived by removing a hydrogen from an alkane given the symbol R
R-
a symbol used to represent an alkyl group
cycloalkane
a saturated hydrocarbon that contains carbon atoms boned to form a ring
conformations
any 3-D arrangement of atoms in a molecule that results from rotation about a single bond
equatorial position
a position on a chair conformation of a cyclohexane ring that extends from the ring roughly perpendicular to an imaginary axis of the ring
axial position
a position on a chair confromation of a cyclohexane ring that extends from the ring prallel to the imaginary axis of the ring
cis-trans
isomers that have the same connectivity of their atoms but a different arrangement of their atoms in space due to the presence of either a ring or a C=C
sterocenter
tertahedral atoms most commonly carbon at which exchange of 2 groups produces a stereoisomer
configuration
refers to the arrangment o fatoms about a stereocenter that is the reative arrangment of parts of a molecule in space
stereoisomer
isomer that have the same connectivity of their atoms but different orientation of their atoms in space
alkene
an unsaturated hydrocarbon that contains a C=C
alkyne
an unsaturated hydrocarbon that contains a triple C C bond
Termal Cracking
a saturated hydrocarbon that is converted into an unsaturated hydrocarbon plus H2
cycloalkenes
number of carbon atoms of the ring = bond 1 and 2
Terpene
a compund whose carbon skeleton can be divided into two or more units identical to 5 carbon skeleton of isoprene
Essential oils
highly fragrant oils from plants (rose, fressia, etc)
regioselective reaction
a reaction in which one direction of bond formation or bond breaking occurs in preference to all other directions
markovinkov’s rule
in the addition of HX or H2O to alkene Hydrogens add to the carbon of the C=C having a greater humber of Hydrogens
reaction mechanism
a step by step description of how a chemical reaction occurs
carbocation
a species containing carbon atoms with only 3 bonds to it and bearing a positive charge
hydration
addition of water
oxonium ion
an ion in which oxygen is bonded to 3 other atoms and bears a positive charge
catalytic reducation/ catalytic hydrogenation
the conversion of an alkane involves reducation by hydrogen in teh presence of a catalyst
polymer
many parts any long chain molecule synthesized by bonding together many single parts called monomers
monomer
single part, simplest nonredundant unit from which a polymer is synthesized
peroxide
any compund that contains an -O-O- bond as for example hydrogen peroxide H-O-O-H
aromatic compunds
benzene or one of its derivatives
arene
a compund contian one or more benzene rings
aryl group
a group derived from an arene by removal of an H and given the symbol Ar-
Ar-
The symbol fused for aryl group
Resonance hybid
a molecule best decribed as a composite of 2+ Lewis structures
contributing structure
each individual lewis structure
phenyl group
C6H15 aryl group derived by removing an Hydrogen atom from a benzene
Autoxidation
ocidation requiring oxygen and no other reactant
Active figure
autoxidation is a radical chain reaction vonverting hydrocarbons to a a hyroperoxide
Chain length
number of times the cycle of chain propagation steps repeats
Diol
a compound containing 2 -OH groups
Triol
a compound containing 3 -OH groups
Glycol
a compound with hydroxyl groups on adjacent carbons
hydrogen bonding
Dipole-Dipole bond, between electronegative atoms and a hydrogen bonded to another electronegative atom
dehydration
elimination of molecule of water from an alcohol, OH is removed from 1 C and H is removed from the adjacent C
ether
a compund containing an oxygen between 2 atoms
cyclic ether
an ether in which the ether oxygen is one of the atoms of the ring
thiol
an -SH (sulfhydroyl group) bonded to a tetrahedral carbon atom
mercaptan
a common name for any molecule containing an -SH group
polarity
how equally bonding electons are shared between atoms, effects solubility, melting and boiling points
covalent bonding
sharing of pairs of electrons
ionic bonding
electrostative bond between 2 oppositely charged ions
sigma bonding
2 atoms are held together by the forces operating between them and a pair of elections shared by them the electon pair occupies an orbital
pi bond
a conhesive interaction between to atoms and a pair of elections that occupy and an orbital located in 2 regions parallel
free radical
a compound containing an unpaired electron
Diradical
a compound that contains 2 unpaired electrons (oxygen)
Monoterpene
2 Isoprenes
Sesquiterpenes
3 Isoprenes
Diterpenes
4 Isoprenes
Triterpenes
6 Isoprenes
Tetraterpenes
8 Isoprenes
Wohler
Made an organic out of 2 inorganics
Fredrick.Kekule
Redefined organics how we know know it and found the benzene ring
Markovinkov
rule of bonding H go towards more H’s in reaction for stability
L. Pauling
motion within benzene rings
