Biochem: water Flashcards
Why do polar molecules dissolve in aqueous environments?
Hydrogen bonds between water molecules attribute water liquid form at RT and solid at cold Ts. polar molecules readily replace the weak hydrogen interaction with more energetically favourable water-solute interactions
The angle of hydrogen-oxygen bond in water
104.5º
The lifetime of a hydrogen bond
1 to 20 picoseconds (and when 1 bond breaks another one forms within 0.1 ps)
What is the difference in number of h-bonds between liquid water (RT) and ice (cold T)?
in liquid water the molecules are in continuous motion and disorganised so each H2O molecule forms a bond with ~ 3.4 other molecules, whereas in ice water molecules are fixed in space and are organised so each water molecule can form H bond with 4 molecules
When are hydrogen bonds the strongest?
when the H atom and the atoms that share it are in a straight line; so when the sharing atom is in line with the covalent atom
How can we determine the strength, or
force (F), of ionic interactions in a solution
F = Q1Q2/er (Q = the charge, e = dielectric constant and r = the distance between the charged groups)
dielectric constant of water and benzene
For water at 25ºC, e is 78.5, and for the very nonpolar solvent benzene e is 4.6.
What are amphipathic compounds ?
Amphipathic compounds contain regions that are polar (or charged) and regions that are nonpolar
What are micelles?
micelle are aggregates of amphipathic compounds in aqueous solotuin. the non polar head groups together in a circle with other non polar heads to present the smallest hydrophobic area to the solution and the hydrophilic polar head points outwards
How are micelles achieving strong hydrophobic interactions?
1. intrinsic attraction between molecules
2. thermodynamic stability via minimised interaction with water
3. high Gibbs free energy
4. large distance between non polar compounds
- thermodynamic stability via minimised interaction with water
hydrophobic interactions are achieved via the system’s achieving the greatest thermodynamic stability by minimizing the number of ordered water molecules required to surround hydrophobic portions
of the solute molecules
What is the advantage of storing sugar fuel as polysaccharides (e.g. glucagon)?
It prevents an enormous increase in osmotic pressure of the cell (as the effect of solutes on osmolarity depends on the number of dissolved particles, not their mass, so 1 g of glucagon made of 1000 units of glucose would have the same effect as 1 molecule of glucose)
What happens to hydrogen ions formed in water ?
they are immediately hydrated to generate a hydronium ion (H3O+)
how is pH defined?
pH = 1/log[H] = -log[H]
How is the pKa defined?
pKa = -logKa (analogous to the pH and is the log transformed value of the ionisation constant)
Which method is used to determine the amount of acid in a solution?
Titration:
measured volume of the acid is
titrated with a solution of a strong base, usually sodium hydroxide (NaOH), of known concentration. The NaOH is added in small increments until the acid is consumed (neutralized), as determined with an indicator dye or a pH meter
What is a buffer?
Buffers are aqueous systems that tend to resist changes in pH when small amounts of acid (H1) or base (OH2) are added. A buffer system consists of a weak acid (the proton donor) and its conjugate base (the proton acceptor)
What can be determined by the Henderson-Hasselbalch equation?
The ionisation constant:
pH = pKa + log[A/HA]
Calculate the fraction of histidine that has its imidazole side chain protonated at pH 7.3. The pKa values for histidine are pK1 5 1.8, pK2 (imidazole) 5 6.0, and pK3 5 9.2
pH = pKa + log[A/HA]
7.3 = 6 + log[His/HisH+] // -6
1.3 = log[His/HisH+] // antilog
antilog[1.3] = His/HisH+
= 2 + 10^1
Why is the bicarbonate buffer system a good buffer in the blood?
The bicarbonate buffer system is an effective
physiological buffer near pH 7.4, because the
H2CO3 of blood plasma is in equilibrium with a large reserve capacity of CO2(g) in the air space of the lungs
what is the pH of blood plasma?
7.4
What is a hydrolysis reaction
Hydrolysis are reactions where a molecule is broken/cleaved by adding water molecule to it. These reactions are also responsible for the enzymatic depolymerization of proteins, carbohydrates, and nucleic acids. Hydrolysis reactions, catalyzed by enzymes called
hydrolases, are almost invariably exergonic; by producing two molecules from one, they lead to an increase in the randomness of the system
What is a condensation reaction
the opposite from hydrolysis, it is a reaction where a molecule is built, and water molecule is formed as byproduct. (e.g. ADP + Pi = ATP + H2O)
