Lecture 1 2 3; universal, interactions, water

Question 1

how did the heavier elements that make up biological life come about

Answer 1

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

Question 2

What are the most common elements in biological systems and why

Answer 2

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

Question 3

What are the 3 features of the primordial earth that are necessary for life

Answer 3

Water needs to be able to condense to provide and aqueous environment. Reducing atmosphere which supports bond formation. Electrical discharges or high energy environments

Question 4

What did Urey and Millers experiment make

Answer 4

more than 20 amino acids from a simple recreation of primordial earth conditions. Ammonia, methane and H2 gas with water vapour and electrical charge

Question 5

What does the “modularity of biopolymers” mean

Answer 5

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

Question 6

How are monomers linked together in nature

Answer 6

condensation

Question 7

What is the difference between covalent bonding and non covalent bonding

Answer 7

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

Question 8

Why are non covalent bonds favoured in biology

Answer 8

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

Question 9

What is the order of the strongest non covalent bonds from strongest to weakest

Answer 9

charge- charge/// h bonding, charge-dipole, dipole-dipole, charge- induced dipole, dipole induced dipole, van de waals (dispersion)

Question 10

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

Answer 10

As the distance increases, the energy decreases- 1/r^(n).

H bonding is an exception with a fixed bond length.

Question 11

What is a dipole moment

Answer 11

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

Question 12

What is the minimum distance between two atoms for Van de Waals interactions

Answer 12

the radius of atom1 + radius of atom 2

Question 13

When atoms get really close together what happens to the attractive force vs the repulsive force

Answer 13

The repulsive force spikes and the attractive force dives

Question 14

What is a charged molecule

Answer 14

molecule with permanent charge-> NH3+, CO2-, PO43-

Question 15

what interaction is an ion pair/ salt bridge

Answer 15

charge to charge interaction

Question 16

What is a dipole molecule

Answer 16

A polar molecule with dipoles -> H2O

Question 17

What is an induced dipole

Answer 17

A non polar molecule that has its e- redistributed due to a strong charge nearby -> CH4,

Question 18

What molecules are van der Waals forces between and give eg

Answer 18

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

Question 19

What is the donor and the acceptor of the H bond and where are the charges involved in this bond

Answer 19

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

Question 20

what is the unique factor of H bonds

Answer 20

directionality -> (optimal angle 180) and partial covalent bond character-> can be very strong

Question 21

What are the properties of water that make it unique

Answer 21

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

Question 22

How do ionic compounds act in water

Answer 22

Dissolution, where ions dissociate from their ionic lattice and are surrounded by the opposite dipoles of water molecules and shields them from reassociating

Question 23

How do hydrophobic molecules act in water

Answer 23

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

Question 24

How do hydrophillic molecules act in water

Answer 24

They dissolve because of charge or polarity that has attraction/can form bonds with water

Question 25

How does amphipathic molecules relate to biological compartmentalisation

Answer 25

They produce vesicles, micelles, bilayers and monolayers

Question 26

What is the pH range of the human blood and what are the 3 buffers that do it

Answer 26

7.35-7.45, bicarbonate, phosphate and protein.

Question 27

How does the bicarbonate buffer work

Answer 27

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

Question 28

What is the structure of liquid vs solid water

Answer 28

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.

Question 29

What has a higher (less acidic pH) the tissues or the lungs

Answer 29

the lungs, so the tissues are slightly more acidic.

Question 30

Compare the timings for the 3 different systems that maintain blood pH

Answer 30

The bicarbonate buffer is instant, the respiratory system response is in min-hours, the renal system response is hours to days.

Question 31

What is the DNA phosphate protanated form

Answer 31

HPO3

Question 32

Is dissociation of HCl written using equilibrium arrows

Answer 32

no

Question 33

What is pKa measure of

Answer 33

The propensity of a weak acid to lose a proton at a given pH.

Question 34

What three rules do you use to predict the protanation at given pH

Answer 34

1. when the pH < pKa it is protanated form
2. when pH=pKa it is 50:50 mixture of acid and base form (50% chance)
3. when pH > pKa it is in de protanated form

Question 35

How is carbonic acid made

Answer 35

CO2 produced during exercise in blood stream + water.

Question 36

How can the respiratory system maintain the pH

Answer 36

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

Question 37

What does deprotanated vs protanated mean

Answer 37

Deprotanated (wants H) means base form

Protanated (with H) means acid form