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Example Questions
Example Question #1 : Help With Organic Proteins
Consider L-glutamate, which is shown below.
Using the pKa information provided, what is the isoelectric point (pI) of the given molecule?
The isoelectric point is the average of the two pKa values around which the molecule has an overall neutral charge. In the case of glutamate, the amino acid is in its neutral (zwitterion) form in between the lower two pKa values. Taking the average of the two values gives the pI.
Example Question #1 : Help With Organic Proteins
Consider the amino acid L-lysine, shown below.
Given the pKa values shown, calculate the pI of lysine.
The isoelectric point is the average of the two pKa values around which the molecule has an overall neutral charge. In the case of lysine, the amino acid is in its neutral (zwitterion) form in between the higher two pKa values. Taking the average of the two values gives the pI.
Example Question #2 : Help With Organic Proteins
Treatment of a peptide with Edman's reagent yielded the following phenylthiohydantoin (PTH) derivative:
What is the side chain of the amino acid at the N-terminus of the peptide?
Hydrogen
Amide
sec-Butyl
Benzyl
Isobutyl
sec-Butyl
Treatment of a peptide with Edman's reagent () will remove the N-terminal amino acid. The PTH derivative will look as follows:
In the molecule in the question, a sec-butyl replaces the R group. This is the amino acid isoleucine.
Example Question #3 : Help With Organic Proteins
What is the amino acid that is synthesized from the malonic ester synthesis shown?
Alanine
Lysine
Leucine
Isoleucine
Valine
Valine
First step: Deprotonation of alpha hydrogen and formation of the malonic ester enolate.
Second step: bimolecular nucleophilic substitution, resulting in addition of the isopropyl group to the alpha carbon.
Third step: hydrolysis of amide and ester bonds, followed by decarboxylation
The synthesis forms valine, because the alkyl halide that is attacked is an isopropyl group (Valine's side chain is an isopropyl group). A more detailed mechanism is shown below.
Example Question #1 : Help With Other Biological Molecules
Which of the following can be classified excluisively as pyrimidines?
Adenine and thymine
Cytosine and thymine
Adenine and guanine
Cytosine and guanine
Cytosine and thymine
Pyrimidine is one classification of a nucleotide base that is formed of only one six-membered heterocyclic ring. Cytosine and thymine (of DNA) and uracil (of RNA) are all pyrimidines while adenine and guanine are classified as purines. One way to help you remember this is that pyrimidines, like pyramids, are "sharp." Sharp things "CUT" Cytosine, Uracil, Thymine.
Example Question #2 : Help With Other Biological Molecules
Consider the DNA bases cytosine and guanine. Which interaction allows for these bases to pair up and form a double helix?
Dipole-dipole interactions
Covalent bonding
Nitrogen bonding
Hydrogen bonding
Hydrogen bonding
The correct answer is hydrogen bonding. The hydrogens on the amine groups of each base can hydrogen bond with the nitrogens and oxygens in the adjacent base. Three hydrogen bonds are formed between cytosine and guanine, and these three bonds are what make up the "rungs" of the ladder, that is the DNA double helix.
Example Question #1 : Help With Other Biological Molecules
A chair flip of the pictured cyclohexane would result in __________.
all three substituents in the equatorial position
the bromine in the equatorial position and both the chlorine and alcohol in the axial position
all three substituents in the axial position
the bromine in the axial position and both the chlorine and alcohol in the equatorial position
the bromine in the equatorial position and both the chlorine and alcohol in the axial position
Originally, bromine is in the axial position and the other two substituents are equatorial. During a chair flip, all substituents become inverted in their positions. Therefore, the bromine will be found in the equatorial position and both the chlorine and alcohol will be found in the axial position.
Example Question #4 : Help With Other Biological Molecules
Which element is present in all organic compounds?
Nitrogen
Oxygen
Carbon
Phosphorous
Carbon
By definition, an organic compound is a compound that contains carbon. Organic chemistry is the study of carbon-containing molecules.
Example Question #1 : Help With Other Biological Molecules
Which of the following compounds are isomers?
Ethane and ethanol
Benzene and hexane
Methane and methanol
1-butanol and 2-butanol
1-butanol and 2-butanol
By definition, isomers are compounds that share the same molecular formula but have differing molecular structures. 1-butanol and 2-butanol share the same formula, but the hydroxyl group can be located on either the first or second carbon on the molecule, yielding two different structures that share the same molecular formula. The other answers have different molecular formulas and are thus not isomers.
Example Question #5 : Help With Other Biological Molecules
By which characteristic do resonance structures of a molecule differ?
Rotation around sigma bonds
Molecular formula
Hybridization
The position of the electrons
The position of the electrons
By definition, resonance structures are multiple Lewis structures that depict the same molecular compound. The only difference pertains to the way in which electrons are shared by atoms in the molecule. Molecules are weighted averages of their most stable resonance contributors.
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