Protein Structure - Lecture Flashcards
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
