Medical Cell Biology and Genetics - Amino Acids and Proteins

Question 1

What is the chiral centre of an amino acid?

Answer 1

The central alpha carbon of an amino acid

Question 2

How are amino acids classified?

Answer 2

According to:

• polarity (how they reach with water at pH 7)
• aromatic (contain benzene ring) or alipathic (no ring)
• whether they are positively or negatively charged

Question 3

What is a zwitterion?

Answer 3

A neutral molecule with both positive and negative charges
In the case of amino acids the amine group deprotonates the carboxylic group
NH3—-C—-COOH —> NH4+—-C—-COO-

Question 4

What are the 3 key properties of the peptide bond?

Answer 4

• all atoms are in the same plane
• although it is a single bond it has double bond characteristics therefore does not rotate
• the carbonyl oxygen and amide hydrogen are in the trans orientation

Question 5

What is the isoelectric point of a protein?

Answer 5

The pH at which the protein has no overall charge
eg Acidic proteins may have negatively charged amino acids therefore have a low pI
eg Alkaline proteins contain many charged amino acids and have a high pI

Question 6

Define the 4 levels of protein structure:

1. Primary structure
2. Secondary structure
3. Tertiary structure
4. Quaternary structure

Answer 6

Primary structure - the amino acid sequence
Secondary structure - folding of the peptide chain into alpha helices or beta pleated sheets
Tertiary structure - further folding to form the 3D structure of the protein
Quaternary structure - assembly of a large complex of MULTIPLE peptide chains eg Hb

Question 7

List the bonds associated with each level of protein structure

Answer 7

Primary structure - peptide bonds
Secondary structure - hydrogen bonds
Tertiary structure - H bonds, van der waals forces, ionic interactions, disulfide bridges, hydrophobic interactions
Quaternary structure - same as above

Question 8

In general what is the role of globular and fibrous proteins?

Answer 8

Globular proteins are mainly functional - such as enzymes and regulatory proteins eg Hb

Fibrous proteins tend to provide structure and support eg Collagen

Question 9

What is the role of molecular chaperones?

Answer 9

Ensure that protein folding is correct, therefore preventing disease states due to inefficeint damaged proteins

Question 10

What are the key features of the alpha helix ?

structure, and helix breakers and makers

Answer 10

Right handed helix
3.6 amino acids per turn

Pro acts as a helix breaker because the rotation around the N-C bond is impossible.
Gly acts as a helix breaker because the tiny H R group supports other conformations.

Small HPHOBIC amino acids are strong helix formers

Question 11

Describe the structure and bonds of a beta sheet

Answer 11

Can be parallel - run in same direction
Can be antiparallel - run in opposite directions

There are lots of inter-strand hydrogen bonds

Question 12

What is pK and how is it calculated?

Answer 12

NEED TO FINISH

pK = - Log [H+]