lecture 1 and 2: the basics

what does a reaction mechanism describe

the flow of electrons during the reaction pathway

rules of curly arrows

• the base of the arrow begins at the original location of the pair of electrons

• the head points to the destination of the electrons

• 2 barbs on the head denotes the movement of the electron pair

alpha helix formation

• the C=O group of 1 amino acid forms a H bond with the NH group of a residue that is located 4 residues down the chain

• the R groups points outwards so that they don’t interfere with the backbone’s stability

beta sheet formation

the C=O group of 1 strand and the NH group of an adjacent strand forms H bonds

lewis structure rules

• write the molecular skeleton

• assume all bonds are covalent

• count the available valence electrons

• add sigma bonds and give each atom 8 electrons (2 for H)

• introduce pi bonds if necessary

formal charge on atom =

valence electrons - number of electrons that contributes to the system

resonance structures must have:

• same relative positions of all atoms in the compound

• same number of paired and unpaired electrons

• all important structures have similar energies

lewis acid

can coordinate with lone pairs of electrons

lewis base

lone pairs of electrons available for sharing

bronsted acid

proton donor

bronsted base

proton acceptor

Henderson-Hasselbalch equation

pH = pKa + log₁₀([A-]/[HA])

pKa

how good an acid the amino acid is (the larger the pKa, the less likely it is to donate electrons)

factors that determine acidity of an organic compound (Y-H):

• strength of Y-H bonds

• electronegativity of Y

• the nature of the solvent

• factors that stabilise Y-(conjugate base) compared to Y-H

what does pKa depend on

• the temperature

• ionic strength of the solvent

• microenvironment of the ionisable group

the more electronegative an element is…

the stronger its negative charge is, hence the stronger it attracts a positive charge (less likely to donate protons → weaker acid)

why are tautomers not resonance structures

because the atoms move

acid-base catalysis

when a H+ is transferred in, going to or from the transition state during the chemical reaction

acid-base catalysis in ribonuclease A

RNAse acts as an endonuclease to cleave ssRNA into smaller nucleotide fragments via hydrolysis, cutting after a pyrimidine base

how did researchers find out where the H2O ended up when the RNA strand was cut

they used water labelled with O18 to identify the key intermediate, 2’-3’-cyclic nucleotide

how was the active site of RNAse A identified

when idoacetate was applied, the enzyme would stop working and bonded to His12 and His229. because they block each other, it proves they are physically close in the 3D space of the active site

1. transesterification in the 2 step mechanism of RNAse A

• His12: general base → pulls H+ away from the 2’-OH of the ribosome, making the O nucelophilic causing it to attack the nearby P

• His119: general acid → donates H+ to the RNA chain and gets cut away to stabilise it

2. hydrolysis in the 2 step mechanism of RNAse A

His119: base → pulls H+ away from the water, turning it into a hydroxide ion to attack the P

His12: acid → donates H+ back to 2’-O of the ribose

tertiary structure of RNAse A

• polypeptide folds into a 3-stranded V-shaped, anti-parallel beta sheet and 3 short alpha helices

• cross-linked with 4S-S bridges

active site residues of RNAse A

• HIs12 and His119 → involved in the mechanism

• lys41 → stabilises the negatively charged PO4 in the intermediate

• Phe120 → forms vab der waals contact with RNA base

• ser123 and Thr45 → hydrogen bonding