Structures etc. Flashcards
Ketone
(Carbonyl)
RCHO
Aldehyde
(Carbonyl)
RCOOH
Carboxylic Acid
(Carbonyl)
RCOOR’
Ester
(Carbonyl)
RCONR’R’’
Amide
(Carbonyl)
Acid Chloride
(Carbonyl)
Acid Anhydride
(Carbonyl)
D or L Glucose?
D-Glucose
Hydrogenation
Halogenation
Hydrohalogenation
Hydration
Mechanism for Alkene Addition Reactions
The electron rich C=C double bond (nucleophile) is attacked by the H+ (electrophile), creating a carbocation intermediate. The electron rich X group is then attracted to the + carbon.
Tertiary Carbocation
Secondary Carbocation
Primary Carbocation
Phenol
Aniline
Benzoic Acid
Transferrin - Fe3+ Binding Site
The Porphyrin Ligand
(Haem Group)
Active Site of Carbonic Anhydrase
What is the Oxygen Cycle?
Biogeochemical Cycle of Sulphur
Biogeochemical Cycle of Nitrogen
Biogeochemical Cycle of Phosphorus
Biogeochemical Cycle of Carbon
Henry’s Law
The amount of gas dissolved in a solution is directly proportional to the pressure of the gas above the solution.
Henderson Hasselbach Equation
Buffering in Blood
How do amino acids change at different pH?
How does Carbonic Anhydrase convert CO2 to Carbonic Acid?
How does Carbonic Anhydrase convert Carbonic Acid back to CO2?
Ammine
Amide
Tell me about Nitrogen Gas
N2
10e- system with a very strong triple bond - very stable
Unreactive therefore difficult to incorporate into biological systems
How is nitrogen incorporated into biological systems?
N2 must be reduced to NH3
This is done by nitrogen fixing bacteria, who have an enzyme called nitrogenase (metal centres)
What are the hydrides of nitrogen?
Ammonia - NH3 is pyrimidal with sp3 hybridisation. IT behaves as a base and nitrogen has a -3 oxidation state
Hydrazine - N2H4 has sp3 hybridisation and lone pairs. N is in -2 oxidation state and the molecule exhibits strong hydrogen bonding.
What are the oxides of Nitrogen?
N2O - linear
NO - linear radical
NO2 - bent radical
N2O4 - planar dimar
What are the oxyacides and oxyanions of nitrogen?
Nitrous acid - HNO2 - is unstable and weak
Nitric Acid - HNO3 - is strong (three O bonded to central N)
What are the biological roles of NO?
- nerve function (acts as a neurotransmitter)
- regulation of blood pressure - dilation of blood vessels (implicated in nitroglycerin)
- inhiits blood clottine (mosquitoes)
- protection of Nasal sinuses
What effects do the oxides of nitrogen have on the atmosphere?
NO catalyses the degradation of ozone in the upper atmosphere
NO2 catalyses the formation of ozone in the lower atmosphere, where it reacts with hydrocarbons to form organic peroxides (photochemical smog)
What are the important patterns of the biogeochemical elements?
- oxidation states vary highest to lowest by 8
- highest oxidation state for each usually last digit of group number
- oxides of the non-metals generally acidic
- strength of acids generally correlates with the oxidation state
What are the two allotropes of oxygen?
O2 - dioxygen, oxygen gas - linear, functions as a ligand
O3 - ozone - v-shaped, polar, powerful oxidant, absorbs UV radiation
What is the gist of the oxygen cycle?
Redox
O2 is reduced to H2O in respiration
H2O is oxidised to O2 in photosynthesis
The reduction of O2 is a 4e- reduction with 4 redox states. It is very efficiently catalysed, but has toxic intermediates.
Sulphur in proteins
Sulphur is present in cysteine and methionine with an oxidation state of -2. The epg at the S atom is tetrahedral, with sp3 hybridisation
Oxidation of Sulphur containing compounds
Usually an energy favourable process
Forms compounds like SO2 and SO3
SO2 dissolves in water to produce weak diprotic acid H2SO3
SO3 dissolves in water to produce strong diprotic acid H2SO4
These are both implicated in acid rain
How is sulphur incorporated into biological systems?
SO42- is the soluble and oxidised form of S in nature. It is absorbed by cells and incorporated into cysteine and methionine and then into protens.
Plankton produce a zwitterion from methionine for osmotic and cryo-protection which decomposes upon cell death
What is phosphine?
PH3
Analogous to NH3 but is a much weaker base
A gas, used as a fumigant for stored grains
Phosphorus oxides
P4 (white phosphorus) reacts very strongly with oxygen to form oxides
First to P4O6
Then to P4O10
This then reacts with water to produce weak triprotic acid H3PO4
Phosphoric acid condenses on further heating to H4P2O7
This then undergoes polymerisation reactions nonspontaneously.
Polyphosphate acids react with bases to form polyanions
Phosphate esters
Phosphate esters are formed by condensation reactions between phosphoric acid and alcohols, and contain P-O-O bonds (mono, di and triesters can form)
Molecules containing polyphosphate and phosphate monoester links are involved in the storage and transport of energy, which is stored as P-O bond energy
ATP hydrolysis releases energy (high charge repulsion in triphosphate is partially relieved)
Phosphate mono and diesters are acidic (diesters relatively strong)
DNA backbone contains a phosphodiester link, fully ionised at pH7
Carbon Oxides
CO - odourless and colourless gas, neutral oxide, product of incomplete combustion, sp hybridisation with triple bond.
CO2 - colourless with some odour, non toxic, sublimes, product of respiration and complete combustion, soluble, sp hybrid, linear with two double bonds
ether
Ester
