Water, Acids and Bases Flashcards
Describe the structure of water?
V-Shaped = 104.5° angles
The oxygen atom has 4 sp3 hybrid orbitals that extend roughly toward the corners of a tetrahedron
Due to having two lone pairs their is greater repulsion than a tetrahedral shape
Why do biological molecules need water?
Most biological molecules assume their shape in response to the properties of water
The medium for most biochemical reactions is water
Water itself participates in many life sustaining chemical reactions
What are some properties of water based on it’s structure?
Water is polar due to the O-H bond (0.958 A)
Each H atom carries 0.33 positive charge with the O atom carrying 0.66 negative charge = electronegativity is biased towards the oxygen
Water can H-bond, due to the lone pairs on neighbouring molecules
Each molcules can participate in a max of 4 H bonds (due to 2H and 2 lone pairs)
Describe ice?
Ice forms at the triple point when all contacts are satisified
Ice is a crystal of hydrogen-bonded water molecules
1 molecules is tetrahedrally surrounded
Water expands on freezing = lower density than liquid water 0.92 g ml-1, this is why ice floats on water
Describe the structure of liquid water?
15% less H bonded than ice
As liquid water reorientates once every 10^-12 s they form networks of linked rings of 3-7 that break and reform every 2x10^-11 s
Increase in entropy drives the processes
What is significant about the water and Coulomb’s law?
Water has a very large dielectic constant (D)
How does water interact with charged/polar groups?
- The charged groups are stabilised, making water an excellent solvent for ionic substances
- The interaction between charged groups is reduced e.g. the polar and ionic molecules are described as hydrohphillic
Describe how water dissolves polar molecules?
An ion attracts oppositely charged ends of the solvent dipoles
The ion becomes surrounded by many concentric shells of orientated water molecules - to spread the ionic charge
How does water interact with non-polar groups?
Hydrophobic effect:
Non-polar molecules in water get coated with water molecules, leading to decrease in entropy of water causing non-polar molecules to clump together
Very few water molecules are trapped by the hydrophobic molecules as they form a boundary layer
This leads to a smaller overall surface area which is energetically more favourable
Describe the hydrophobic effect?
The tendency of water to minimize its contacts with hydrophobic molecules
To maximize their number of hydrogen bonds, water molecules form a “cage” around the solute
The aggregation of the nonpolar groups, minimizes the surface area of the cavity and therefore maximizes the entropy of the entire system
What do amphiphilic/amphipathic molecules form in water?
Water hydrates the hydrohphillic areas and also excludes the hydrophobic portion
This forms micelles (spheroidal) and bilayers (planar)
How does water move?
Via osmosis
The net movement of a solvent across a semi-permeable membrane from a region of high concentration to a region of lower concentration
What is osmotic pressure?
The pressure that must be applied to the solution to equalize the flow of water across the membrane in both directions
It is proportional to the concentration of the solute
Describe dialysis?
Diffusion of small solutes through small pores in a membrane until equilibrium
The larger molecules e.g. nucleic acids, remain within the membrane
A useful technique for separation
What are some log rules?
Log(a^b) = b* log(a) Log(ab) = log(a) + log(b) Log(1/a) = log(a^-1) = -log(a)
What does water ionise to form?
H20 ⇌ H+ + OH-
Derived from:
2H20 ⇌ H30+ + OH-
H30+ is the hydronium ion as there is no such thing as a free proton H+ in solution
What is the Grotthuss mechanism?
AKA: Proton jumping
Where protons/hydroxides interact over large distances
Protons diffuse through the hydrogen bond network of water molecules via formation and cleavage of covalent bonds
Protons can therefore diffuse rapidly fast
This is why acid/base reactions are among the fastest in aqueous solution
What is Kw?
Kw = [H+][OH-]
Kw of water = 10^-14 M^2 (at 25 degrees and 1 bar)
What are the concentrations of neutral, acidic and basic solutions?
Neutral: [H+] = 10^-7 M
Acidic: [H+] > 10^-7 M
Basic: [H+] < 10^-7 M
However, we use pH as it’s easier to see
What is pH?
A property of the environment not a true reflection of the number of H+ ions
pH = -log[H+]
What is pKw?
pKw = pH + pOH
pKw = 14
What is an acid and what is a base?
Acid - a substance that can donate a proton
Base - A substance that can accept a proton
What equation shows the acid-base reaction?
HA ⇌ H+ + A-
HA acid
A- conjugate base
HB+ ⇌ H+ + B
HB+ base
B conjugate acid
What is Ka?
Weak acid/base dissociation constant
Ka = [H+][A-]/[HA]
Ka = [H+][B]/[HB+]
How to move between pKa and Ka
pKa = -log(Ka) Ka = 10^-pKa
What is the Henderson-Hasselbach equation?
pH = pKa + log [A-]/[HA]
If HA and A- have the same concentration log(1) = 0 and the pH = pKa
What does pKa indicate?
It indicates to what extent an acid (HA) dissociates
Low pKa = strong acid and weak base
High pKa = weak acid and strong base
What do buffers do?
Resist changes in pH
What are some factors of titration curves?
The pH at the midpoint of each titration (flat bit) is equal to the pK of its corresponding acid - [HA]=[A−]
At this point described the solution is relatively insensitive to addition of strong acid/base = the buffer works best here
What can acids be in relation to protons?
Mono/di/polyprotic
Losing varying numbers of protons
A polyprotic acid has multiple pKa values for each ionisation step
e.g. H3PO4
What is the equivalence point?
The vertical line on a titration curve
The point where moles of acid = moles of base
What is pI?
Isoelectric point:
The pH at which a molecule (containing acids/bases) carries no net electric charge
What is significant about the pI of amino acids?
Amino acids at neutral pH are zwitterions
How to workout the pI of an amino acid?
If no ionisable side chain (pK of carboxyl group + pK of amino group) x0.5
If positive ionisable side chain (pK of ionisable side chain + pK of amino group) x0.5
If negative ionisable side chain (pK of ionisable side chain + pK of carboxyl group) x0.5
