Which kind of reaction is involved in peptide bond formation?
dehydration reaction
Which two amino acids with almost ALWAYS be positively charged?
Arginine and Lysine
In peptide bonds, the ______ group might act as a nucleophile for the carboxyl group which is ______.
amino; electrophilic
To accomplish peptide bond formation, the reaction must first be “activated”. How might the reaction be activated?
It must be coupled with another favorable reaction
After a peptide bond has been formed, it is relatively stable. How could the bonds become cleaved?
- Hydrolysis using enzymes
- strong acid
- strong base
Is the dehydration reaction thermodynamically favorable?
no
How can we drive an unfavorable reaction into a favorable one?
Using Heiss’s law which states a dehydration reaction is the counter-reaction to a hydrolysis reaction.
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.
extended strand conformation
Which protein structure consists of a single string of amino acids?
primary structure
Which protein structure consists of beta-pleated sheets or alpha-helices?
secondary structure
Which protein structure consists of a mixture of both beta-pleated sheets and alpha helices?
tertiary structure
Which protein structure consists of multiple bundles of alpha-helices and beta-pleated sheets in a macromolecule?
quarternary structure
What are the two enantiomer classifications of generic amino acids?
L isomer & D isomer
Which amino acid enantiomer is the most common conformation?
L isomer
List one example of where a D isomer could potentially be used.
In the cell walls of some bacteria
What determines the difference between L and D isomers?
- 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!!
Describe the mnemonic for C-O-R-N when dealing with conformations.
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
Which component of the amino acid deterines it’s identity? Which amino acid does not follow this, and how?
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.
What is it called when an amino acid has both poitive and negative charges?
Zwitterionic form
At what pH range is an amino acid considered neutral?
4-7 pH
