lecture 2

Question 1

Proteins are synthesized as what?

Answer 1

Linear unbranched polymers of amino acids

Question 2

Lysozyme cleaves what

Answer 2

Polysachharide chains in the cell walls of bacteria

Question 3

Proteins adopt what stable structure?

Answer 3

Folded stable structure

Question 4

The native conformation is the fold with the lowest what?

Answer 4

Lowest free energy

Question 5

What bond allows free rotation and what type of bond has limited rotation and why?

Answer 5

Single bonds allow free rotation. Multiple bonds so double bonds are planar and there is very limited rotation

Question 6

Cationic is what?

Answer 6

Positive charged

Question 7

Anionic is what?

Answer 7

Negatively charged

Question 8

Zwitterionic is what?

Answer 8

Neutral, no net charge

Question 9

Peptide bond is formed with removal of what?

Answer 9

Removal of water

Question 10

What is the peptide bond

Answer 10

CO-NH

Question 11

Why is there limited rotation about peptide bonds?

Answer 11

Peptide bond has partial double bond character due to resonance. The groups are also co-planar

Question 12

Peptide bond is shorter than what bond and longer than what bond?

Answer 12

Shorter than average C-N and longer than average C-N bond

Question 13

Is cis or trans favoured for peptide linkages? and why?

Answer 13

The trans form is favoured. Both Calpha atoms are on opposite sides so there is less steric hindrance

Question 14

Omega (w) is defined by what four atoms?

Answer 14

Calpa - C - N - Calpha

Question 15

Omega (w) describes the angle between what bonds?

Answer 15

Between the Calpha-C bond and the N-Calpha bond.

Question 16

A trans peptide bond has what omega angle?

Answer 16

-180, Calpha atoms on opposite side of double bond

Question 17

A cis peptide bond has what omega angle

Answer 17

0

Question 18

The N-Calpha bond is called what angle?

Answer 18

Phi angle. Circle with line

Question 19

Phi is defined by what 4 atoms

Answer 19

C - N - Calpha - C

Question 20

Phi describes the angle between which bonds?

Answer 20

C - N bond

Calpha - C bond

Question 21

Rotation about the calpha - C bond is described by what angle?

Answer 21

Psi angle. W with line

Question 22

Psi is defined by what 4 atoms?

Answer 22

N - Calpha - C - N

Question 23

Psi describes the angle between what bonds?

Answer 23

N - Calpha

C - N

Question 24

What makes the psi and phi angles so important?

Answer 24

Assuming all peptide bonds are trans, the conformational freedom in the backbone of a polypeptide is due to these two rotations.

Question 25

Ramachandran plot show what 3 main clusters?

Answer 25

Beta sheet, alpha helical and left handed turns

Question 26

Alpha helical structures are mostly what type of turns

Answer 26

Right handed turns

Question 27

Left handed turns are mostly what amino acid

Answer 27

Glycine

Question 28

Describe the location of the 3 main clusters

Answer 28

Alpha cluster is bottom left
Beta cluster is top left
L turn is top right