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Enzymes & Metabolism > 1-2: ORGANIC CHEMISTRY (Def's & FG's) > Flashcards

1-2: ORGANIC CHEMISTRY (Def's & FG's) Flashcards

1
Q

Heteroatom

A

atom other than C or H in organic molecules

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2
Q

functional group

A
  • part of molecule containing heteroatom

- responsible for chemical reactivity

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3
Q

nucleophile

A

electronegative functional group with LP of e to form covalent bond

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4
Q

electrophile

A
  • e deficient functional group which can accept a pair of e to form a covalent bond
  • must have an empty orbital
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5
Q

polarised bonds

A

e not shared evenly between two joint atoms ie. bond has a dipole

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6
Q

polarisability

A

measure of ease of distortion of e distribution

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7
Q

electronegativity

A

measure of how strong the atom attracts e

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8
Q

H bonding

A

non-covalent bond resulting in electrostatic attraction between proton attached to heteroatom and electronegative atom in another functional group

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9
Q

leaving group

A

part of molecule which takes bonding e when the bond is broken

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10
Q

resonance

A
  • when more than one arrangement of double bonds needs to be drawn in order to show the electronic distribution
  • molecule exists as a resonance hybrid (e.g. aromatic compounds)
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11
Q

aromaticity

A

compound must be planar and cyclic and have (4n+2) delocalised pi e

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12
Q

tautomers

A

structural isomers that differ only in the position of a H and a double bonds (e.g. keto to enol; imine to enamine)

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13
Q

tautomerisation

A
  • conversion of one tautomer to its structural isomer

- its a reversible reaction

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14
Q

hybridisation

A
  • the mixing of atomic orbitals to make molecular orbitals

- the shape/orientation of hybrid orbitals is optimized for bond formation

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15
Q

determining hybridisation

A
  • AX2 = sp
  • AX3 = sp2
  • AX4 = sp3

of atoms bonded + # of lone pairs = 2,3,4 (sp, sp2, sp3)

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16
Q

sp3

A
  • 4 identical hybrid orbitals (1x2s + 3x2p)
  • tetrahedron
  • single bond by head-on overlap
  • if fewer than 4 bonds required to satisfy valence requirements, one or more of sp3 hybrid orbitals will not be involved in bonding but instead contains LP of e
  • LP is potentially basic and/or nucleophilic; frequently involved in H-bonding
17
Q

sp2

A
  • 3 identical hybrid orbitals (p-orbital not invovled in hybridisation is at right angle to plane of hybrid) (1x2s + 2x2p + 1x2p separate)
  • trigonal planar
  • single bond by head on overlap
  • double bond by sideways overlap of p orbital
  • always found in double bonds (also found in partial double bonds)
18
Q

Single bond O functional group

A
  • e.g. alcohol
  • tetrahedron
  • sp3
  • 2 LP on O usually involved in H-bonding
  • not a good base so does not protonate
  • nucleophile only when LP is not involved in H-bonding
19
Q

double bond O functional group

A
  • e.g. carboxylic acid
  • O in carbonyl is not reactive because proton is readily removed
  • carbonyl is sp2 trigonal planar
  • O is more electronegative so s- and C is s+
  • electrophilic carbonyl C; nucleophile can attack from top or bottom of plane
  • carboxylates are -ve charged at physiological pH so can behave as bases
  • Ca,Cc,=O,H are in the same plane
  • Ca is nucleophilic provided it has H that can be removed
20
Q

aldehydes vs ketones

A
  • aldehyde is R-C=H
  • ketone is R-C=R
  • in aldehyde, nucleophilic attack is v. easy as no hindrance
  • more reactive than ketone due to steric reasons
  • ketone less reactive due to electronic reasons as C is able via inductive effect (2 alkyl groups) to share e cloud with Cc which partly quenches s+ charge compared to having an H
21
Q

keto to enolate tautomerisation

A
  • Ca hybridisation changes from sp3 to sp2 as base removes H

- usually carbanion is v.unstable but in this case -ve charge can delocalise over carbonyl system to form enolate anion

22
Q

ester

A
  • carboxylic acid + alcohol
  • R-C=OR (-OR; -NR; -SR)
  • Ca in O ester is less acidic thus less reactive than in aldehyde/ketone
  • harder to remove the proton because the enolate anion is less stable because the O of the ester will be sharing its e in the carbonyl system so will be competing
  • sp2 not sp3 as it has most stable electronic configuration; trigonal planar shape
23
Q

amine

A
  • 1LP on N
  • R-NH2
  • sp3 tetrahedron
  • nucleophile only if proton is removed
  • acts as base when deprotonated
  • pka 8,9,10 so at physiological pH is protonated –this is why amino acid side chains act as acids in chemical reactions
24
Q

amide

A
  • R-C=ONH2
  • peptide bond is planar because N is sp2
  • sp2 hybridisation of N promotes delocalisation of LP and reduces electrophilicity of Cc so less reactive than aldehydes/ketones
25
Q

imine

A

-schiff base
-protonates v.readily so is v.reactive
-C is v.electrophilic
-protonated at physiological pH
-R1R2-C=N-R3
OR
-R1R2-C=N+-HR3

26
Q

thiol

A
  • RSH
  • e.g. cysteine, coA
  • no effective orbital overlap so no H-bonding
  • good leaving group
  • excellent nucleophile
  • v. reactive
  • can be oxidised to form S-S bridges
  • chemistry similar to alcohol but LP of e are in larger, more polarisable 3rd orbital
27
Q

thioester

A
  • CH3-C=O-SR
  • sp3 tetrahedron
  • S is better leaving group than O-ester
  • Ca is v. good nucleophile
  • S is not hybridized sp2 as no efficient orbital overlap
  • similar reactivity to aldehyde/ketone
  • Cc strongly electrophilic so favourable hydrolysis reaction
28
Q

thioether

A
  • e.g methionine

- can be oxidised to form sulphoxide and sulphone

29
Q

7 examples of good nucleophiles

A 
NH2-
OH-
SH-
RC- - - C-
Cl-
Br-
I-

Ca of thioester
Ca of ketone if it has H that can be removed

30
Q

7 examples of good electrophiles

A
  • H+
  • H3O+
  • HNO3
  • CO2
  • SO3
  • Cl2
  • Br2
  • I2

imine C
Cc of thioester
Cc

31
Q

examples of good leaving groups

A
  • H2O
  • HSO-4
  • NH3
  • COO-
  • Cl-
  • Br-
  • I-

thiol
thioester

32
Q

acids and bases (in terms of H)

A
  • acids donate H+ (e.g. carboxyl, phosphate)

- bases accept H+ (e.g. amino)

33
Q

effect of pH on functional groups and amino acids

A
  • if pH is below pKa = protonated

- hydrophobic prefers neutral side chains so -ve residues will protonate and +ve residues will deprotonate

Enzymes & Metabolism (17 decks)

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