Proteins and Radicals

Question 1

How do you describe the chirality of stereogenic amino acids?

Answer 1

Use D/L

L=S
D=R

Question 2

What are enzymes?

Answer 2

Catalysts for biological reactions -> they speed up reactions by lowering the activation energy barrier

Question 3

What is the mechanism of enzymes?

Answer 3

E + S -> E.S -> E.P -> E + P

Question 4

How do you name amimo acids?

Answer 4

From the N-terminus of the amino acid on the left to the C-terminus of the amino acid to the right

Question 5

What is the reactivity of amide bond?

Answer 5

Low because the lone pair of electrons on the nitrogen donate to the carbonyl group essentially forming a double bond

Question 6

What is the shape around a amide bond?

Answer 6

Planar -> N-H is oriented at 180 degrees to the C=O

Question 7

What is the primary structure of a protein?

Answer 7

Sequence of amino acids in the peptide chain

Question 8

What is the secondary structure of a protein?

Answer 8

Hydrogen bonding between N-H of one amide and the C=O of another amide to form a helix or b pleated sheet

Question 9

How is an alpha helix formed?

Answer 9

Hydrogen bonding between N-H of an amide bond to the C=O of an amide bond 5 amino acids ahead in the primary structure

Question 10

How is a beta pleated sheet formed?

Answer 10

Parallel:
Hydrogen bonding between the C=O and N-H bond of two peptide chains both in the same direction (e.g. N to C)

Anti-parallel:
Hydrogen bonding between the C=O and N-H bonds of two peptide chains running in the opposite direction

Question 11

What is the tertiary structure of a protein?

Answer 11

The overall 3D shape of the protein when the protein folds due to R group interactions

Weak non-covalent bonds:
Ionic
Van der waals
Hydrophobic interactions

Strong covalent bonds:
Disulfide bonds between two cysteine amino acid R groups

Question 12

What is the quarternary structure of a protein?

Answer 12

When difference proteins (peptide chains) come together (aggregate) to form new structures

Question 13

What is a free radical?

Answer 13

An atom, molecule, or ion that has one or more unpaired electrons

Question 14

How are free radicals generated?

Answer 14

Due to homolytic bond cleavage - even sharing of a pair of electrons upon bond breakage

Question 15

What are the steps of a radical reaction?

Answer 15

1) initiation
2) propagation
3) termination

Question 16

What is the initiation step?

Answer 16

Homolytic bond cleavage of a weak bond to form two radicals

Usually facilitated by light or heat

Question 17

What is the propagation step?

Answer 17

Reaction between a free radical with a molecule that has no unpaired electrons to generate a new radical

NO CHANGE IN NO. OF RADICAL SPECIES

Question 18

What is the termination step?

Answer 18

The pairing of two radicals forming a species with no unpaired electrons

Question 19

What does it mean for a radical to be more stable?

Answer 19

It will more likely to survive long enough to encounter another radical and react via a termination pathway

Question 20

What are the factors that affect radical stability?

Answer 20

Delocalisation - ability to form resonance hybrids by movement of electrons within the molecule

Question 21

What happens when you have a build up of free radicals in the body?

Answer 21

Biological molecules become damaged

-> can cause DNA oxidation, denature proteins and disrupt lipid membranes

Question 22

What is the role of vitamin E?

Answer 22

Antioxidant -> reacts with hydroxyl radicals to form more stabilised radical