amino acids, proteins, DNA Flashcards
do amino acids rotate plane of polarised light
yes - as they are chiral
if an AA has an extra CA/amine grp what is it classed as
+ CA grp = acidic
+ amine grp = basic
why do AA have relatively high MPs
- AA exists as dipolar zwitterion - ionic interaction bw zwitterions explains high MPs of AAs as opposed to the weaker hydrogen bonding that would occur in the no charge form.
AA Species in alkaline solution High pH
has CO2-
what links 2 AAs to form dipeptide
one amide (peptide) link.
Hydrolysis of di-peptides/proteins
If proteins are heated with concentrated hydrochloric acid or concentrated strong alkalis they can be hydrolysed and split back into their constituent amino acids.
how to determine composition of the protein molecule
TLC chromatography
how to do Thin-layer chromatography
a) Wearing gloves, draw a pencil line 1 cm above the bottom of a TLC plate and mark spots for each sample, equally spaced along line.
b) Use a capillary tube to add a tiny drop of each solution to a different spot and allow the plate to air dry.
c) Add solvent to a chamber or large beaker with a lid so that is no more than 1cm in depth
d) Place the TLC plate into the chamber, making sure that the level of the solvent is below the pencil line. Replace the lid to get a tight seal.
e) When the level of the solvent reaches about 1 cm from the top of the plate, remove the plate and mark the solvent level with a pencil. Allow the plate to dry in the fume cupboard.
f) Spray paper with ninhydrin and put in oven Draw around them lightly in pencil.
g) Calculate the Rf values of the observed spots.
why need PENCIL line
will not dissolve in the solvent
why need tiny drop of sample
too big a drop will cause different
spots to merge
why should solvent depth be lower than start line
if the solvent is too deep it will dissolve the sample spots from the plate
why wear plastic gloves
prevent contamination from the hands to the plate
why use a lid
to prevent evaporation of toxic solvent
primary structure of proteins
sequence of the 20 different naturally occurring amino acids joined together by condensation reactions with peptide links.
Secondary Structure of a Protein.
The 3D arrangement of amino acids with the polypeptide chain in a corkscrew shape is held in place by Hydrogen bonds between the H of –Nδ- —Hδ+ group and the –O of Cδ+=Oδ- of the fourth amino acid along the chain
The R-groups on the amino acids are all pointed to the outside of the helix
The secondary structure can also take the form of a β– pleated sheets
The protein chain folds into parallel strands side by side
The protein chain is held into a the pleated shape by Hydrogen bonds between the H of –N-H group and the – O of C=O of the amino acid much further along the chain in the parallel region .
Tertiary Structures of Proteins
The tertiary structure is the folding of the secondary structure into more complex shapes. It is held in place by interactions between the R- side groups in more distant amino acids . These can be a variety of interactions including hydrogen bonding, sulfur-sulfur bonds and ionic interactions.
what is the active site pod an enzyme
usually a hollow in the globular protein structure into which a substrate molecule can bond to the amino acid side chains through a variety of interactions including:
Hydrogen bonding
Van der waals forces Permanent dipole-dipole forces Ionic interactions
what happens if substrate is chiral
Stereospecific active site
If the substrate is chiral then its likely that only one enantiomer will have the correct stereochemistry to fit in the active site of the enzyme and so only one isomer will be catalysed.
what can be used to help design drugs as enzyme inhibitors
computers
how does cisplatin x DNA replication in cancer cells
by a ligand replacement reaction with DNA in which a dative covalent bond is formed between platinum and a nitrogen atom on guanine
