GRE Subject Test: Biochemistry, Cell, and Molecular Biology : Help with Proteins and Amino Acids

Study concepts, example questions & explanations for GRE Subject Test: Biochemistry, Cell, and Molecular Biology

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Example Questions

Example Question #1 : Macromolecules And Enzymes

Which of the following properties is NOT a feature of the genetic code?

Possible Answers:

Universal

Unambiguous

Overlapping

Degenerate

Correct answer:

Overlapping

Explanation:

The genetic code refers to the sequence of DNA that codes for genes and proteins in the body. The genetic code is composed of three-nucleotide codons, each used to recruit an amino acid during translation and protein synthesis. Each codon codes for one and only one amino acid, making the code unambiguous; however, some amino acids have more than one codon that can be used to recruit them. This feature of the genetic code is known as degeneracy. Finally, the genetic code is universal. All living organisms use the same genetic material (DNA) in their cells and produce proteins through transcription and translation. Though the processes may change slightly between organisms, the general genetic code is universal to all cells.

The genetic code is not overlapping, meaning that the code is linear. Transcription of DNA has a fixed starting point and proceeds in a linear fashion, as does translation of mRNA. There is no overlapping or reverse reading of the genetic code.

Example Question #1 : Macromolecules And Monomers

For amino acids, the phi () angle refers to the bond between __________ and the alpha carbon while the psi () angle refers to the bond between the alpha carbon and __________.

Possible Answers:

the carbonyl carbon . . . the R group's first carbon

the carbonyl carbon . . . the amine nitrogen

the amine nitrogen . . . the carbonyl carbon

the amine nitrogen . . . the R group's first carbon

Correct answer:

the amine nitrogen . . . the carbonyl carbon

Explanation:

These bonds are specifically referring to the invariable portions of the amino acid and, thus, do not involve the R group (functional group).

This is more of a definition-based answer. The phi angle refers to the bond between the amine nitrogen and the alpha carbon, while the psi angle refers to the bond between the alpha carbon and the carbonyl carbon of the carboxylic acid. These bonds play important roles in determining possible protein structures.

Example Question #2 : Macromolecules And Monomers

Which of the following amino acid sequences is most likely to form an alpha-helix?

Possible Answers:

GAADQAAPSAAEDAA

GQQGGCACTYFGGG

GAADEAAQSAATYP

GCCDPCQRRTSHM

Correct answer:

GAADEAAQSAATYP

Explanation:

Amino acid sequences with a lot of alanine (A) residues are higly likely to form alpha-helices. Glycine (G) and proline (P) residues often cap alpha-helices, though glycine can sometimes be found inside alpha-helices as well.

Proline is never found inside an alpha-helix due to the conformational hindrance caused by the hydrogen bonding within the residue. Proline is usually found in bends in a protein structure.

Example Question #3 : Macromolecules And Monomers

Which of the following is true regarding the protonation of histidine at a pH of 7?

Possible Answers:

The carboxyl group is protonated, the R-goup is protonated, and the amine group is protonated

The carboxyl group is deprotonated, the R-goup is deprotonated, and the amine group is protonated

The carboxyl group is deprotonated, the R-goup is protonated, and the amine group is protonated

The carboxyl group is deprotonated, the R-goup is deprotonated, and the amine group is deprotonated

Correct answer:

The carboxyl group is deprotonated, the R-goup is protonated, and the amine group is protonated

Explanation:

Histidine has the following pKa values:

COOH - 1.82

R-group - 6.00

NH3 - 9.17

Any pH below the pKa will cause the molecule to be protonated, while any pH above the pKa will cause the molecule to deprotonate. At a pH of 7, the COOH group to deprotonate, but the NH3 and R-group will remain protonated.

Example Question #4 : Macromolecules And Monomers

Which part of its amino acid mediates the interactions that form the tertiary structure of a protein?

Possible Answers:

The polypeptide backbone

The carboxyl groups

The alpha carbons

The R-groups

The amino groups

Correct answer:

The R-groups

Explanation:

Tertiary structure of a protein is determined by interactions between the R-groups of the amino acids that make up that protein. The secondary structure of a protein is mediated by the backbone atoms of the polypeptide chain which includes the carboxyl and amine groups. The alpha carbon are what the R-groups are attached to an do not directly contribute to any level of protein structure.

Example Question #5 : Macromolecules And Monomers

Interactions between which of these mediates the secondary structure of a protein?

Possible Answers:

The amino groups

The polypeptide backbone

The alpha carbons

The R-groups

Disulfide bonds

Correct answer:

The polypeptide backbone

Explanation:

Hydrogen bonds between repeating units of the polypeptide backbone (namely the amino groups and carboxyl groups) mediate secondary structure in proteins.

Example Question #7 : Macromolecules And Enzymes

Protein molecular structure can be described as a hierarchy. Which level of protein structure consists of spatial arrangements, such as alpha helices or beta sheets, that occur due to local folding in a polypeptide chain?

Possible Answers:

Secondary structure

Quarternary structure

Primary structure

Tertiary structure

Supramolecular structure

Correct answer:

Secondary structure

Explanation:

Primary structure simply describes the order of amino acids in a polypeptide chain. Tertiary structures describe global folding of the entire chain, which may be made up of a multitude of secondary structures like alpha helices or beta sheets. Quaternary structure describes the position of numerous subunits in a protein complex comprised of two or more smaller protein. Huge multiunit proteins are ordered by supramolecular structure. 

All GRE Subject Test: Biochemistry, Cell, and Molecular Biology Resources

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