Protein Structure

Question 1

Ionisation state of amino acids

Answer 1

pH 0-2.5: both groups protonated
pH 2.5-9.5: zwitterionic
pH 9.5-14: both groups deprotonated

Question 2

Name the 8 categories amino acids are classified under

Answer 2

Hydrophobic, hydrophilic, polar, non polar, acidic, basic, aliphatic and aromatic

Question 3

Why are some amino acid residues charged?

Answer 3

Basic and acidic residues contain chemical groups that can either be protonated or deprotonated depending on environment and pH.

Question 4

What is Ka and pKa?

Answer 4

Ka= acid dissociation constant
pKa= -log 10Ka (smaller pKa, stronger the acid)

Question 5

What is the Henderson-Hasselbalch equation?

Answer 5

pH= pKa + log [deprotonated form]/[protonated form]
If pH <pKa, group is protonated
If pH> pKa, group is deprotonated

Question 6

What are the 3 features of peptide bonds?

Answer 6

Planar, rigid (partial double bond) and trans

Question 7

Name 2 key properties of proteins

Answer 7

Size (number of AA residues, molecular weight (kDa)
Isoelectric point (pH at which there is no overall net charge)

Question 8

Describe the alpha helix

Answer 8

H bonds between N-H and C=O stabilise structure
3.6 a/ turn
0.54nm pitch
Right handed helix

Question 9

Describe the beta pleated sheet

Answer 9

Extended b-strand structure
0.35nm between AAs
Adjacent b-strands stabilised by H bonds (anti parallel)

Question 10

Describe the AA residue distribution in a protein structure

Answer 10

Hydrophobic side chains are buried and polar, charged side chains on the outside

Question 11

How do proteins fold?

Answer 11

Localised folding ordered at each step to find and maintain the most stable conformation

Question 12

What is an amyloid fibre? What causes it?

Answer 12

A misfolded, insoluble form of a normally soluble protein. Caused by protein misfolding where the core b-sheet forms before the rest of the protein