Protein Structure - Lecture

Question 1

Which kind of reaction is involved in peptide bond formation?

Answer 1

dehydration reaction

Question 2

Which two amino acids with almost ALWAYS be positively charged?

Answer 2

Arginine and Lysine

Question 3

In peptide bonds, the ______ group might act as a nucleophile for the carboxyl group which is ______.

Answer 3

amino; electrophilic

Question 4

To accomplish peptide bond formation, the reaction must first be “activated”. How might the reaction be activated?

Answer 4

It must be coupled with another favorable reaction

Question 5

After a peptide bond has been formed, it is relatively stable. How could the bonds become cleaved?

Answer 5

• Hydrolysis using enzymes
• strong acid
• strong base

Question 6

Is the dehydration reaction thermodynamically favorable?

Answer 6

no

Question 7

How can we drive an unfavorable reaction into a favorable one?

Answer 7

Using Heiss’s law which states a dehydration reaction is the counter-reaction to a hydrolysis reaction.

Question 8

What is common in b-sheets (secondary structure), instead of a flat sheet, the side chains alternate up and down or into and out of the plane, and the amino H and carbonyl O point in the same direction and also alternate up and down but parallel to the plane of the backbone.

Answer 8

extended strand conformation

Question 9

Which protein structure consists of a single string of amino acids?

Answer 9

primary structure

Question 10

Which protein structure consists of beta-pleated sheets or alpha-helices?

Answer 10

secondary structure

Question 11

Which protein structure consists of a mixture of both beta-pleated sheets and alpha helices?

Answer 11

tertiary structure

Question 12

Which protein structure consists of multiple bundles of alpha-helices and beta-pleated sheets in a macromolecule?

Answer 12

quarternary structure

Question 13

What are the two enantiomer classifications of generic amino acids?

Answer 13

L isomer & D isomer

Question 14

Which amino acid enantiomer is the most common conformation?

Answer 14

L isomer

Question 15

List one example of where a D isomer could potentially be used.

Answer 15

In the cell walls of some bacteria

Question 16

What determines the difference between L and D isomers?

Answer 16

• L isomers: chiral, has an S-configuration, counter-clockwise
• D isomers: non-chiral (due to hydrogen side chain), has an R-configuration, clockwise

With the exception of glycine which is neither!!

Question 17

Describe the mnemonic for C-O-R-N when dealing with conformations.

Answer 17

This is the order in which we follow the groups in a S-conformation or L isomer. It follows as:
C - carbon
O - oxygen
R - R-group
N - nitrogen group

Remember, S-confirmations go counter-clockwise

Question 18

Which component of the amino acid deterines it’s identity? Which amino acid does not follow this, and how?

Answer 18

The R-group determines the identity of the amino acid. Glycine does not follow this rule as there is a hydrogen group in the place of the R-group.

Question 19

What is it called when an amino acid has both poitive and negative charges?

Answer 19

Zwitterionic form

Question 20

At what pH range is an amino acid considered neutral?

Answer 20

4-7 pH