2.7 Reaction Mechanisms

Question 1

What does the mechanism of an organic reaction show?

Answer 1

How electrons move around to break bonds and make new ones
(Can be single or multiple steps)

Question 2

What is a kinetic product?

Answer 2

The one with the lowest Ea

Question 3

What is the thermodynamic product?

Answer 3

The most stable

Question 4

What mechanism is where bonds break involving the movement of a single electron?

Answer 4

Free radical mechanisms
Produce radical intermediates (1 unpaired electron) - very reactive

Question 5

How is the movement of a single electron shown?

Answer 5

A curly arrow with a single head (fish hook arrow)

Question 6

What are the characteristics of bonds that break into radicals?

Answer 6

Tend to be non-polar
Energy input required to break bond
This can be in form of heat or light (uv)

Question 7

How is two radicals pairing up illustrated in a mechanism?

Answer 7

Two single headed arrows come together to create an electron pair

Question 8

What are the steps of a free radical mechanism?

Answer 8

Initiation: free radical formation - more radicals on right of equation

Propergation: same number of radicals on either side of reaction

Termination: when 2 radicals pair to form an unreactive molecule

Question 9

What enzymes use free radicals in their mechanisms to functionalise biological molecules?

Answer 9

Prostaglandin - start from arachidonic acid - tyrosine side chain radical

Fatty acids double bonds - introduced with iron cofactor

Metabolism of drugs/steroids - rely on iron cofactor (which creates radical)

Question 10

How does water form radicals

Answer 10

OH bonds split to give hydroxy radical - causes aging

Question 11

Give an example of a vitamin that uses free radicals

Answer 11

Vitamin E - antioxidants

Question 12

What does a polar/Ionic mechanisms show?

Answer 12

Movement of pairs of electrons - indicated by double headed curly arrow

Question 13

What direction do electrons tend to go in?

Answer 13

Direction of most electronegative atom

Question 14

What are electrophiles?

Answer 14

Electron-loving
Short of electron - what to gain
Will have a + charge or a partial positive charge

Eg. Cations, carbonation

Question 15

What are nucleophiles?

Answer 15

Electron rich
Might be - charged, partially negativity charged, or have lone pair of electrons

Eg. Anions, carbanions
O, N

Question 16

What is an adition reaction?

Answer 16

Where a small molecule is incorporated into a larger starting material

Question 17

What is a classic feature of addition reactions?

Answer 17

Pi bond broken in starting material
2 new sigma bonds formed as reagent added to starting material

(Happens in molecules with double bonds)

Question 18

What are electrophilic and nucleophilic addition reactions?

Answer 18

Electrophilic - double bond is attached by electrophilic agent

Nucleophilic - double bond attached by a nuceophilic agent

Question 19

Give an example of a nucleophic addition reaction

Answer 19

fumaric acid ——-> malic acid

O: in water acts as nuceophile
Catalysed by fumarase

Question 20

What is an elimination reaction?

Answer 20

The reverse of an addition reaction
2 sigma bonds are broken to form a pi bond

Question 21

Give an example of an elimination reaction

Answer 21

2-phophoglycerate ——->phosphoenolpyruvate

Water is being removed
Catalysed by Enolase enzyme

Question 22

What 2 type of reactions can be seen as special cases of addition and elimination?

Answer 22

Oxidation and reduction

Reduction - usually addition of a hydrogen (H2) molecule

Oxidation - usually elimination/removal of H2 molecule

Question 23

What are condensation reactions?

Answer 23

Joining 2 molecules together. Often involves removal of small molecule.

Biologically usually H20
Chemistry can be things like HCl

Question 24

Give examples of condensation reactions

Answer 24

1. Formation of peptides/proteins
2. Formation of esters (carboxylic acid + alcohol)
3. Formation of nucleosides
4. Formation of phosphate esters

Question 25

What is a substitution reaction?

Answer 25

Where a functional group is directly replaced by another one

Question 26

What are the 2 types of substitution reactions?

Answer 26

Nucleophilic - more biological relevant - happens on sp3 hybridised C atoms - polar bond is attacked by nucleophile and replaces

Electrophilic - characteristic reaction of aromatic rings - allows to maintain stability

Question 27

What is a rearrangement (isomerisation) reaction?

Answer 27

Formula of molecule doesn’t change, but arrangement of atoms in space does

Question 28

Example of rearrangement reaction

Answer 28

Succinyl CoA ——-> (R)-Methylmalonyl CoA

Catalysed by methylmalonyl-CoA mutase