Lecture 1 2 3; universal, interactions, water Flashcards
Lecture 1 to 3
how did the heavier elements that make up biological life come about
After the big bang 14 bya, H + He condensed over millions of years to form stars, 7 bya H + He fused under heat and pressure to form heavier elements. Unstable stars supernova and spread across the universe to make 2nd gen stars and planetary systems
What are the most common elements in biological systems and why
C, H, O, N because they have the strongest tendency to form strong covalent bonds, Water means that O and H abundant with C being the scaffold for organic molecules due to different ways it can bond
What are the 3 features of the primordial earth that are necessary for life
Water needs to be able to condense to provide and aqueous environment. Reducing atmosphere which supports bond formation. Electrical discharges or high energy environments
What did Urey and Millers experiment make
more than 20 amino acids from a simple recreation of primordial earth conditions. Ammonia, methane and H2 gas with water vapour and electrical charge
What does the “modularity of biopolymers” mean
Biology builds complex things (macromolecules) from simple subunits.
This is efficient because the monomers are already pre made and then they can be joined together to make biopolymers
How are monomers linked together in nature
condensation
What is the difference between covalent bonding and non covalent bonding
Covalent bonding is where the electrons are shared between the two atoms, resulting in a polar bond which is stronger than weak non covalent bonds that exist because of weak electrostatic forces of attraction
Why are non covalent bonds favoured in biology
Covalent bonds require much more energy to break and form, but weak bonds easily break and reform for processes that only require temporary bonding- like enzyme, receptors, signalling etc and they can still be strong when there are many points of intermolecular forces- hold the 3D shape of macromolecules
What is the order of the strongest non covalent bonds from strongest to weakest
charge- charge/// h bonding, charge-dipole, dipole-dipole, charge- induced dipole, dipole induced dipole, van de waals (dispersion)
What is the relationship between the energy required to break the bond and the distance between atom and the type of bonding that is an exception to this
As the distance increases, the energy decreases- 1/r^(n).
H bonding is an exception with a fixed bond length.
What is a dipole moment
Vector quantity showing the dipole from the S- to the S+ from the Electronegative atom to each atom its bonded to. These are added together to give the vector sum
What is the minimum distance between two atoms for Van de Waals interactions
the radius of atom1 + radius of atom 2
When atoms get really close together what happens to the attractive force vs the repulsive force
The repulsive force spikes and the attractive force dives
What is a charged molecule
molecule with permanent charge-> NH3+, CO2-, PO43-
what interaction is an ion pair/ salt bridge
charge to charge interaction
What is a dipole molecule
A polar molecule with dipoles -> H2O
What is an induced dipole
A non polar molecule that has its e- redistributed due to a strong charge nearby -> CH4,
What molecules are van der Waals forces between and give eg
non polar molecules due to temporary fluctuations in the distribution of electrons lead to mutually attractive induced dipoles. Seen in the stacking of benzene rings or dna base pairs
What is the donor and the acceptor of the H bond and where are the charges involved in this bond
Acceptor is the Ea that doesn’t have an H bonded to it and Donor is the Ea that has the H bonded to it. The charges are between the positive dipole on H and the negative dipole of the acceptor
what is the unique factor of H bonds
directionality -> (optimal angle 180) and partial covalent bond character-> can be very strong
What are the properties of water that make it unique
Unlike other molecules of the same size, water has a higher boiling point and heat of vaporisation because of its polar O-H bonds and two lone pairs on O which allow 4 H bonds to be made. It is a heat buffer
How do ionic compounds act in water
Dissolution, where ions dissociate from their ionic lattice and are surrounded by the opposite dipoles of water molecules and shields them from reassociating
How do hydrophobic molecules act in water
Have limited solubility, can’t form H bonds. So water cages/clatharate structures form similar to ice, in that the water H bonds to itself
How do hydrophillic molecules act in water
They dissolve because of charge or polarity that has attraction/can form bonds with water
How does amphipathic molecules relate to biological compartmentalisation
They produce vesicles, micelles, bilayers and monolayers
What is the pH range of the human blood and what are the 3 buffers that do it
7.35-7.45, bicarbonate, phosphate and protein.
How does the bicarbonate buffer work
The dissolution of CO2 in water is catalysed by carbonic anhydrase, and this produces Carbonic acid H2CO3. This weak acid dissociates to make HCO3 and H30+ to buffer addition of CO2 or bicarbonate addition into the blood
What is the structure of liquid vs solid water
Solid water has 4 full H bonds being formed, forming ordered structure that expands and therefore is less dense than liquid. Liquid makes 3.6 H bonds per molecule, with bonds continually being broken and reformed.
What has a higher (less acidic pH) the tissues or the lungs
the lungs, so the tissues are slightly more acidic.
Compare the timings for the 3 different systems that maintain blood pH
The bicarbonate buffer is instant, the respiratory system response is in min-hours, the renal system response is hours to days.
What is the DNA phosphate protanated form
HPO3
Is dissociation of HCl written using equilibrium arrows
no
What is pKa measure of
The propensity of a weak acid to lose a proton at a given pH.
What three rules do you use to predict the protanation at given pH
- when the pH < pKa it is protanated form
- when pH=pKa it is 50:50 mixture of acid and base form (50% chance)
- when pH > pKa it is in de protanated form
How is carbonic acid made
CO2 produced during exercise in blood stream + water.
How can the respiratory system maintain the pH
The receptors in the brain sense the drop in pH due to increased CO2 and this increases the breathing rate, removing more CO2 so pH can raise
What does deprotanated vs protanated mean
Deprotanated (wants H) means base form
Protanated (with H) means acid form
