Amino acids, Proteins and DNA

Question 1

Zwitterions

Answer 1

The no charge form of an amino acid never occurs. The amino acid exists as a dipolar zwitterion.

Amino acids are often solids

The ionic interaction between zwitterions explains the relatively high melting points of amino acids as opposed to the weaker hydrogen bonding that would occur in the no charge form.

Question 2

High pH

Answer 2

H2N

CO2 -

Question 3

Neutral pH

Answer 3

H3N+

CO2 -

Question 4

Low pH

Answer 4

H3N+

CO2H

Question 5

Chromatography of amino acids

Answer 5

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.

Question 6

Secondary structure: alpha helix

Answer 6

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

Question 7

Secondary structure: beta pleated sheet

Answer 7

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 .

Question 8

Tertiary structure

Answer 8

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.