Biochemistry : Biochemistry

Study concepts, example questions & explanations for Biochemistry

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Example Questions

Example Question #34 : Macromolecule Structures And Functions

Which of these is not a function of membrane proteins?

Possible Answers:

Transport of substances into and out of the cell

Acting as a receptor

Catalysis

Energy storage

Correct answer:

Energy storage

Explanation:

Membrane proteins have several functions. They can act as catalysts, receptor proteins for different molecules attempting to enter/exit the cell, and also function in transport as channels or transporters. However, energy storage is a function that is carried out by carbohydrates and lipids.

Example Question #2 : Other Protein Functions

Which of the following correctly describes an allosteric enzyme?

Possible Answers:

It operates most optimally in a basic environment

It is versatile, in that it can act as either an anabolic enzyme or a catabolic enzyme

It operates most optimally in an acidic environment

It is regulated by binding to small molecules other than its substrate

It operates most optimally in a neutral environment

Correct answer:

It is regulated by binding to small molecules other than its substrate

Explanation:

Allosteric enzymes are enzymes that can be regulated by binding of a small molecule to an "allosteric site" on the enzyme. This is a location on the enzyme that is distinct from the active site, which is where the enzyme binds to its substrate.

Allosteric compounds can be either activators or repressors. Activators cause the enzyme's activity to increase, whereas repressors cause the enzyme's activity to decrease. This happens because binding of an allosteric molecule acts to change the enzyme's structural conformation, even if just slightly, which thus makes it either more active or less active.

For example, phosphofructokinase is an enzyme found in glycolysis, the metabolic pathway that breaks glucose down in cells for energy. This enzyme is a critical component of the pathway, because it is largely responsible for regulating the flux of glucose through this pathway. As such, there are many cellular metabolites that act to either increase or decrease this enzyme's activity. As an example, molecules like ATP and other intermediates of glycolysis and, subsequently, the citric acid cycle are able to decrease this enzyme's activity. Some of these metabolites include phosphoenolpyruvate and citric acid, in addition to ATP, all of which indicate that the cell has an abundant amount of energy available. AMP, on the other hand, acts to allosterically activate phosphofructokinase because it signals that the cell is low in energy. Thus, allosteric enzymes are an important component of how biochemical processes can be regulated.

Example Question #3 : Other Protein Functions

Where does steroid synthesis and detoxification of drugs and poisons occur in a cell? 

Possible Answers:

Nucleolus

Rough endoplasmic reticulum (RER)

Smooth endoplasmic reticulum (SER)

Golgi apparatus

Correct answer:

Smooth endoplasmic reticulum (SER)

Explanation:

Liver hepatocytes and steroid hormone producing cells of the adrenal cortex are rich in the SER. RER is the site of synthesis of secretory (exported) proteins. The golgi apparatus does many things, but in general, think of it as the distribution center and vesicular trafficking. It organizes and directs where everything should go. The nucleolus is unrelated to this topic, but it does produce ribosomes. 

Example Question #51 : Biochemistry

Which of the following reaction types is not catalyzed by cobalamin enzymes?

Possible Answers:

All of these are reaction types catalyzed by cobalamins

Reduction of ribonucleotides

Ligation of bonds between DNA bases

Intramolecular rearrangements

Methylations

Correct answer:

Ligation of bonds between DNA bases

Explanation:

Cobalamin enzymes are B12-dependent enzymes. This type of enzyme catalyzes methylations, intramolecular rearrangements, and reduction of ribonucleotides. However, it is not associated with the ligation of the hydrogen bonds between DNA bases.

Example Question #1 : Primary Structure

A protein's primary structure is determined by which of the following?

Possible Answers:

Beta-pleated sheets

The linear sequence of specific amino acids

R-group interactions

The hydrophobic effect

Alpha-helices

Correct answer:

The linear sequence of specific amino acids

Explanation:

A protein's primary structure is defined solely by its amino acid sequence, and is constructred by peptide bonds between adjacent amino acid residues.

Secondary structure results from hydrogen bonding along the polypeptide backbone, resulting in alpha-helices and beta-pleated sheets. Tertiary structure results from hydrogen bonding between R groups, hydrophobic interactions, and disfulide bridges; these interactions create the three-dimensional structure of the molecule. Finally, quaternary structure arises from the joining of multiple subunits to create a functional protein complex.

Example Question #2 : Primary Structure

Sickle cell anemia results from a missense mutation that replaces a glutamic acid residue with which of the following?

Possible Answers:

Lysine

Aspartic acid

Arginine

Glutamine

Asparagine

Correct answer:

Lysine

Explanation:

A single amino acid substitution from glutamic acid to lysine is responsible for sickle cell anemia. The mutation occurs in the gene that codes for hemoglobin and causes misfolding that results in a lower oxygen affinity.

Example Question #1 : Primary Structure

The __________ structure of a protein corresponds to the linear order of amino acids in a given polypeptide chain.

Possible Answers:

Primary

None of these answers

Tertiary

Quaternary

Secondary

Correct answer:

Primary

Explanation:

With regard to protein structure, primary structure refers to the order of the amino acids, which are held together by peptide bonds. Secondary structure refers to the presence of beta pleated sheets and alpha helices within a protein. Tertiary structure refers to a protein's geometric shape as a result of the interactions between the sidechains of the amino acids in the peptide chain. Quaternary structure concerns side chain interactions within a multiple polypeptide chains.

Example Question #1 : Protein Folding

What type of bonds are found in the primary structure of a protein?

Possible Answers:

Hydrogen bonds

Van der Waals interactions

Sulfide bonds

Peptide bonds

Ionic bonds

Correct answer:

Peptide bonds

Explanation:

Primary structure consists of amino acids joined by peptide bonds. Peptide bonds are between the alpha-carboxyl of one amino acid, and the alpha-amine of the next amino acid. A peptide bond is an example of an amide bond. Hydrogen bonds are found in secondary structure, tertiary structure exhibits Van Der Waals interactions.

Example Question #1 : Protein Folding

When a protein is transferred to a solution with a pH that is much lower than its optimal range, which of the following levels of protein structure is or can be affected?

Possible Answers:

Secondary only

Tertiary only

Primary only

Secondary, tertiary, and quaternary

Primary, secondary, tertiary, and quaternary

Correct answer:

Secondary, tertiary, and quaternary

Explanation:

This question is presenting us with a scenario in which a protein is being transferred to a highly acidic solution that is outside of the protein's optimal pH range. In such a situation, we would expect the protein to undergo conformational changes that would alter its function. The question, however, is which levels of protein structure would be altered by such a change in pH.

The first level of structure worth considering is primary structure. The primary structure of a protein refers to the sequence of individual amino acids that make up the protein. Upon being transferred to an acidic solution, the protein does indeed unfold, but it doesn't break apart into individual amino acids. Therefore, the unfolded protein remains as a single, long chain, but its sequence of amino acids is still intact. Thus, there is no change in primary structure.

The secondary structure of a protein refers to local conformations found within the folded protein. Such local conformations include certain commonly found structural motifs, such as alpha-helices and beta-pleated sheets. These local conformational structures are held together by various intramolecular bonds between the amino acid residues. These intramolecular interactions include hydrogen bonding and van der Waals forces, among others. When transferred to an acidic solution, these intramolecular forces are disrupted and, as a result, cause a disruption in the protein's secondary structure.

The third level of protein structure is tertiary structure, which refers to the overall conformation of a single chain of amino acids, sometimes referred to as a polypeptide. The overall three-dimensional conformation of a polypeptide is held together by some of the same intramolecular forces involved with secondary structure, such as hydrogen bonding, van der Waals interactions, and disulfide bonds. Because a highly acidic solution interferes with these interactions, the tertiary level of protein structure is indeed affected by pH changes.

And finally, the last level of protein structure to consider is quaternary structure. Not all proteins possess this level of structure, because in order to have this level of structure, two or more polypeptide chains need to come together and interact via intermolecular bonding to form the final, finished protein. An example of this level of structure can be seen in the protein hemoglobin, in which two alpha-chains and two beta-chains come together and interact to form hemoglobin. Just as with secondary and tertiary structures, the introduction of a highly acidic solution can disrupt these intermolecular interactions, thus causing a disruption in the quaternary structure of a protein composed of two or more polypeptide chains.

Example Question #2 : Primary Structure

What is the primary structure of a protein?

Possible Answers:

The complete folding of a protein. 

Alpha and beta folding patterns created by amino acid interactions. 

The interaction of one polypeptide sub-unit with another.

The sequence of amino acids and the initial folding of the protein.

The sequence of amino acids. 

Correct answer:

The sequence of amino acids. 

Explanation:

The primary structure is only composed of the sequence of amino acids in a protein. The secondary structure is the alpha or beta folding that occurs due to amino acid interaction. The tertiary structure is the three dimensional folding that occurs within a protein. Finally, quaternary structure occurs when a protein has two or more polypeptide sub-units. A perfect example of quaternary structure is found in hemoglobin. 

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