Lecture 5 - Protein Strucutre

Question 1

Are structural proteins usually drug targets?

Answer 1

No

Question 2

Which structural protein has been useful in drug design?

Answer 2

Tubulin

Question 3

What are the three main drug target proteins?

Answer 3

Receptors, enzymes and transporters

Question 4

What do transport proteins do (3)?

Answer 4

• Transport chemical building blocks (polar) across the cell membrane
• Transport neurotransmitters back into the neuron

Question 5

What can go wrong with receptors?

Answer 5

• Over-activation of the cell due to too much messenger

- Under-activation of the cell due to tell little messenger

Question 6

How do we fix over-activation and under-activation?

Answer 6

• Introduce antagonists

- Introduce agonists

Question 7

What are the three families of receptors?

Answer 7

Ion channels
G-protein coupled
Kinase-linked

Question 8

What is signal-transduction

Answer 8

The chain of events that involve secondary messengers, proteins and enzymes

Question 9

What is the difference between the 3 types of protein drug targets?

Answer 9

1) Enzymes - there is a chemical transformation of the LMW compound
2) Receptors - there is a message and the LMW compound leaves unchanged
3) The LMW is moved into the cell unchanged after binding

Question 10

What do all amino acids have? (4)

Answer 10

Carboxylic acid groups (Co2H)
Amino group (NH2)
Functional group (R)
Central C-H motif

Question 11

What is special about the structure of proline

Answer 11

The side chain is bonded to both the amino and carboxylate groups

Question 12

Where is proline normally found in the protein?

Answer 12

protein ‘bends’

Question 13

Why is proline also termed an imino acid

Answer 13

It has a 2° amino group instead of a 1° amino group

Question 14

What are the two S-containing amino acids

Answer 14

Cysteine (SH)

Methionine (S-CH3)

Question 15

Do charged amino acid residues stabilise protein conformations?

Answer 15

Yes

Question 16

What are two non-standard amino acids?

Answer 16

Selenocysteine and pyrrolysine

Question 17

What is a peptide bond

Answer 17

CO-NH with water spat out

Question 18

Is the carbonyl atom usually cis or trans to the amino acid H atom

Answer 18

trans

Question 19

Does the amide bond undergo rotation?

Answer 19

No it has some double bond character

Question 20

What is primary protein structure?

Answer 20

The order in which amino acids are linked together

Question 21

What is secondary protein structure?

Answer 21

Ordered regions within the protein, from specific hydrogen-bonding patterns

Question 22

What is the tertiary protein structure?

Answer 22

The spatial arrangements of all atoms (including side chains and formation of disulfide bonds)

Question 23

What is quaternary protein structure

Answer 23

The arrangement of two or more subunits

Question 24

What are some examples of secondary structure

Answer 24

alpha helix, parallel beta sheet, anti-parallel beta sheet

Question 25

Parallel beta sheets have what two groups on the same side?

Answer 25

Amino group

Question 26

What is a key contributor to tertiary structure?

Answer 26

Van der waals

Question 27

What amino acid residues will be located at the surface of proteins?

Answer 27

Polar

Question 28

What is the result of the polar amino acid residues located at the surface?

Answer 28

They are less able to participate in the maintenance of the tertiary structure

Question 29

What are the two similarities between enzymes, receptors and transporters?

Answer 29

1. All are protein-based biomolecules

2. They have recognition-based interactions with LMW compounds