Buffers, Carbon, Nitrogen and Phosphorous Flashcards
What are the 4 bulk elements?
Carbon, nitrogen, hydrogen and phosphorous
Where is carbon found?
- atmosphere - present as co2
- in biomolecules - carbohydrates, proteins and DNA
- geosphere - carbonate minerals and in sediments
How does the oxidation state of carbon change through the biogeochemical cycle?
oxidation state changes from -4 to +4
What is CO and what is it a product of?
- an odorless and colorless gas
- neutral oxide
- products of incomplete combustion of fossil fuels
Describe the structure of Carbon monoxide
Functions as a ligand for Fe in myoglobin and Hb
Co2 and water
produces carbonic acid - H2CO3
What is Henry’s law?
amount of gas dissolved in a solution is directly proportional to the pressure of the gas above the solution
What happens to gas solubility as pressure increases?
• as pressure increases, gas solubility also increases
How do you determine the solubility of a gas from KH value?
the larger the kH value, the more soluble the gas
How do the Ka values of polyprotic acids differ and why?
- Ka1 is much bigger which is typical of polyprotic acids
• this occurs because once a proton is lost. it gets harder and harder to lose protons
• ie. the greater the negative charge on the acid, the heart it is to REMOVE H+
Describe what happens in the carbon cycle (simplified)
- CO2 in the atmosphere is dissolved in the ocean
- Ocean life, when they die, end up as sediments (CaCO3, MgCO3)
- these sediments are burnt and used as duel
- burning of fuel releases CO2 into the atmosphere
What is a buffer solution?
One that resists a chnage in pH when either OH- ions or H+ ions are added
• prevents large changes in pH
e.g. blood, the sea
How can a buffer solution be made?
Mixing a weak acid with its conjugate base
What makes a good buffer?
once that has close to equal proportions of the acid and its conjugate base
What does the lewis structure allow us to predict?
• allows us to make predictions about shape
• make predictions about reactivity
- ie. will a given molecule be able to act as a ligand and bind to a transition metal
How do you calculate the formal charge?
Number of valence electrons in the atom - (non bonding electrons + 1/2 bonding electrons)
What elements are the exceptions to the octet rule?
- octet can be exceeded for elements in the third period and beyond
- elements with and odd atomic number (ie. N)
What is a radical?
- species that contain single unpaired electrons
- often very reactive
- typically contain an odd number of electrons
What are the steps to drawing a lewis structure?
- count the total no. of valence electrons
- draw the atoms and give everything a single bond
- give the outer atoms an octet
- put remaining valence electrons in the central atom
- turn lone pairs into double bonds to give every atom an octet
- assign formal charges
Ozone shape and function
- v-shaped
- powerful oxidant
- role in the upper atmosphere in UV absorption is critical to life on earth
- screens out UV radiation which damages DNA
The oxygen cycle
Respiration - reduction of O2
Photosynthesis - involved oxidation of H2O (this is the source of all oxygen on the planet)
What is superoxide?
- superoxide ion can damage cells and is involved in many disease states
- also causes ageing
How are the effects of superoxide ions minimised?
- Superoxide Dismutase (SOD) is abundant in aerobic organisms
- its task is to destroy superoxide ions (Radical species) and hence protect against radical damage
What is the oxidation state of Sulfur?
-2
SO2 and water
SO2 dissolves in water to produce the weak diprotic acid H2SO4
SO3 and water
SO3 dissolves in water to produce the strong diprotic acid H2SO4
How is acid rain produced?
- burning of fossil fuels lead to SO2 in the atmosphere
- SO2 and O2 react to form SO3
- SO3 dissolves in water to form H2S04 (sulfuric acid) - ACID RAIN
What are the consequences of acid rain?
- pH of natural waters decrease
- corrosion of structures and buildings
- marble limestone reacts with sulfuric acid (marble statues get destroyed)
In what form do we consume sulfur?
- Sulfate is absorbed by cells and incorporated in to the amino acids cysteine and methionine which then form proteins.
- we intake sulfur in the form of sulfate found in proteins
Nitrogen
- element exits in the atmosphere in the form N2 - one of the main gases
- very stable with strong triple bond
Why is nitrogen fixation necessary?
- N2 is a very unreactive molecule
- very difficult to incorporate into living systems
- must be reduced to NH3
What is nitrogen fixation? What enzyme is necessary?
- N2 is reduced to NH3 to be incorporated into biomolecules like amino acids, proteins and nucleic acids
- carried out by enzyme - nitrogenase enzyme
- nitrogen must be soluble for nitrogen fixation to occur
What roles does NO have in the body?
NO is a radical and is an essential regulatory molecule in:
• nerve function
• regulation of blood pressure - involved in the dilation of blood vessels
• inhibits blood clotting
• protection of the nasal sinuses
however excess levels are toxic
What effect does NO2 have on the upper atmosphere?
NO2 catalyses ozone depletion - degrades the protective ozone layer
Effect of NO2 in the lower atmosphere?
Catalyses the formation of Ozone
What is the net result of NO2 pollution?
- O3 produced in lower atmosphere - production of photochemical smog
- O3 lost in the upper atmosphere - degradation of ozone layer which absorbs UV rays that are damaging to life
Hydride of Phosphorous
- phosphine - pH3
- weaker base than NH3
- pyramidal
Allotropes
Different physical forms in which an element can exist
e.g. carbon can exist as graphite, charcoal and diamond
What is the most reactive allotrope of phosphorous?
- P4
* tetrahedral molecules which is highly strained = reactive
How are phosphate esters formed?
Condensation reactions between phosphoric acid and alcohols and contain P-O-C bonds
Why is ADP lower in energy than ATP?
- think about negative charges
- highest energy state when like charges are close together - more works needs to be done to keep like charges together
- ATP has 4 -ve charges kept in close proximity (ADP is 3 -ves)
Why is the DNA backbone negatively charged?
Phosphodiesters are relatively strong acids
• at pH 7 - diesters will essentially carry a full negative charge (pKa ~1/2)
• dna backbone contains phosphodiester link
Oxidation states of phosphorous
does not change
• always +5
What are the 2 requirements for Hydrogen bonding?
- electron deficient H atom - found in compounds containing OH, NH or HF
- small highly electronegative atom with an electron pair available to interact with the H atom (O, N, F etc)
What is enterobactin structure?
EbH6
• cyclic ester with amide links to catechol type ligands
how many irons can enterobactin bind?
- six
* hexadentate ligand
What produces enterobactin?
Aerobic bacteria
What are siderophores?
Chelating molecules secreted by micro-organisms able to bind to Fe ions very strongly
• e.g. enterobactin
can enterobactin cross cell membrane?
- lipophilic which means it is able to cross cell membranes
* transfers Fe into cells
How many redox states does oxygen have and what are they?
- dioxygen - O2
- superoxide - O2- (Radical)
- peroxide - O2^2-
- oxide - o^2-
formation of P4O6
P4 + O2 –> P4O6
Formation of P4O10
P4O6 +O2 –> P4O10
Equation for the formation of Phosphoric acid
P4O10 + 6H2O —> 4H3PO4
- Weak triprotic acid
Describe the Ka values of the dissociation of H3PO4
- as the ion becomes more negative - Ka becomes smaller
* it is harder to remove H+ as ionic charge becomes more negative
Describe the polymerisation reactions H3PO4 undergoes
- 2H3PO4 –> H4P2O7 + H2O
* requires heat
What happens when further heat is applied (polymerisation of H3PO4)
- H4P2O7 + H3PO4 –> H5P3O10 +H2O
* G>0 : This is a non-spontaneous reaction and to proceed requires the energy supplied by heating
What complexes are used to ‘soften’ water
- Polyanion attracts Mg2+ and Ca2+ strongly, softening water
* Na+[P3O10]5- is used widely in detergents
How is energy stored in ATP
- energy is supplied by respiration and photosynthesis - stored in P-O bond energy
- ADP3- + [H2PO4]- –> ATP4- + H2O
- Catalysed by ATPase enzymes
What is the equation for ATP formation
- ADP3- + [H2PO4]- –> ATP4- + H2O
- Catalysed by ATPase enzymes
- G>0 = non-spontaneous
Equation showing how energy is released from ATP
ATP4- + H2O –> ADP3- + [H2PO4]
• G<0 (spontaneous)
• catalysed by phosphatase enzyme
• energy is released for metabolic purposes
what is Solvation and give an example
stabilises ions in solution with strong ion-dipole attraction for both anions and cations
• ie. Water overcomes the strong electrostatic attraction bw oppositely charge ions such as Na+ and Cl-
What does a nucleotide consist of?
- deoxyribose sugar
- purine/pyrimidine
- phosphate group
Summarise the formation of H3PO4 from P4
- P4(s) + 5O2(g) –> P4O10 (s)
* P4O10 (s) + 6H2O (l) –> 4H3PO4 (aq)
Does the temperature affect the pH of a buffer?
- yes
- pH of a buffer is given by pH = pKa + log [B]/[A].
- As Ka is a function of temperature, so too is pKa.
