Organic Chemistry : Biological Molecules

Study concepts, example questions & explanations for Organic Chemistry

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Example Questions

Example Question #5 : Help With Organic Proteins

What is the D/L configuration and the absolute (R/S) configuration of the following amino acid (cysteine)?

Screen shot 2015 11 16 at 1.06.26 pm

Possible Answers:

Cysteine is achiral

D, S

L, S

L, R

D, R

Correct answer:

L, R

Explanation:

Cysteine is an unusual amino acid. Although each of the normal biological amino acids have the L configuration (with the exception of glycine, which is achiral), meaning they can be drawn with the Fischer projection as shown:

 Screen shot 2015 11 16 at 1.10.31 pm

the fact that cysteine contains a sulfur group makes the side chain a higher priority than the carboxylic acid. Therefore, the absolute configuration of cysteine will be R, and not S like the other amino acids.

Example Question #1 : Help With Organic Proteins

Consider L-glutamate, which is shown below.

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Using the pKa information provided, what is the isoelectric point (pI) of the given molecule?

Possible Answers:

Correct answer:

Explanation:

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.

Screen shot 2015 11 16 at 1.44.03 pm

Given the pKa values shown, calculate the pI of lysine.

Possible Answers:

Correct answer:

Explanation:

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 #1 : Help With Organic Proteins

Treatment of a peptide with Edman's reagent yielded the following phenylthiohydantoin (PTH) derivative:

Screen shot 2015 11 18 at 8.23.34 pm

What is the side chain of the amino acid at the N-terminus of the peptide?

Possible Answers:

sec-Butyl

Hydrogen

Isobutyl

Benzyl

Amide

Correct answer:

sec-Butyl

Explanation:

Treatment of a peptide with Edman's reagent () will remove the N-terminal amino acid. The PTH derivative will look as follows:

 Screen shot 2015 11 18 at 8.40.08 pm

In the molecule in the question, a sec-butyl replaces the R group. This is the amino acid isoleucine.

Example Question #9 : Help With Organic Proteins

What is the amino acid that is synthesized from the malonic ester synthesis shown?

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Possible Answers:

Valine

Alanine

Leucine

Isoleucine

Lysine

Correct answer:

Valine

Explanation:

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.

Screen shot 2015 11 18 at 10.00.44 pm

Example Question #31 : Biological Molecules

Which of the following can be classified excluisively as pyrimidines?

Possible Answers:

Adenine and thymine

Adenine and guanine

Cytosine and thymine

Cytosine and guanine

Correct answer:

Cytosine and thymine

Explanation:

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 #32 : Biological Molecules

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Consider the DNA bases cytosine and guanine. Which interaction allows for these bases to pair up and form a double helix?

Possible Answers:

Nitrogen bonding

Covalent bonding

Hydrogen bonding

Dipole-dipole interactions

Correct answer:

Hydrogen bonding

Explanation:

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 #3 : Help With Other Biological Molecules

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A chair flip of the pictured cyclohexane would result in __________.

Possible Answers:

all three substituents in the equatorial position

the bromine in the equatorial position and both the chlorine and alcohol in the axial position

the bromine in the axial position and both the chlorine and alcohol in the equatorial position

all three substituents in the axial position

Correct answer:

the bromine in the equatorial position and both the chlorine and alcohol in the axial position

Explanation:

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?

Possible Answers:

Phosphorous

Nitrogen

Carbon

Oxygen

Correct answer:

Carbon

Explanation:

By definition, an organic compound is a compound that contains carbon. Organic chemistry is the study of carbon-containing molecules.

Example Question #33 : Biological Molecules

Which of the following compounds are isomers?

Possible Answers:

1-butanol and 2-butanol

Methane and methanol

Ethane and ethanol

Benzene and hexane

Correct answer:

1-butanol and 2-butanol

Explanation:

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.

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