Other Protein Functions - Biochemistry

Ribozymes are RNA molecules that catalyze specific biochemical reactions, so ribosomes (which catalyze the linking of amino acids) are indeed ribozymes. tRNA is complementary to ribosomal RNA in the sites where the two bind. Aminoacylation produces a tRNA with its 3’ end covalently linked to an amino acid. The sequence at the 3’ end is not ACA, however’ it is CCA.

The correct answer choice is isozymes, also called isoenzymes. Even though these enzymes can catalyze the same reaction, they often have differences in their kinetic parameters or in the way they're regulated. Coenzymes are a type of cofactor. They are generally complex organic molecules that are usually derived from vitamins, and they serve the purpose of assisting the enzyme to which they are bound. Examples include pyridoxal phosphate, biotin, coenzyme A, etc. Apoenzymes are enzymes that normally require a cofactor, but are in a state in which they lack that cofactor. Holoenzymes are apoenzymes that have their cofactor bound.

Heme normally binds to iron. Myoglobin is mostly concentrated in muscles, and after a muscle injury can be present in blood. Myoglobin has a higher affinity for oxygen than hemoglobin; myoglobin’s oxygen saturation curve is hyperbolic, whereas hemoglobin’s is sigmoidal. Hemoglobin F (fetal hemoglobin) has a higher oxygen affinity than hemoglobin A (adult hemoglobin). This improves the transfer of oxygen from the circulation of the mother to that of the fetus.

Chymotrypsin is a digestive enzyme that breaks down proteins (proteolysis). It has a catalytic triad of serine, histidine, and aspartate. The hydroxyl group on serine acts as a nucleophile and attacks the carbonyl group on the amino acid, forming a tetrahedral intermediate. Histidine acts as a base, which cleaves the peptide bond. Aspartate acts as an acid, which restores the active site. Since this catalytic triad has a defined nucleophile, base, and acid, we know that there will not be an additional thiol nucleophile. Thiol nucleophiles are found in cysteine proteases.

As stated in the question stem, proteins are super important because they perform an enormous variety of functions. Proteins can sometimes serve a structural role, such as the protein collagen which helps give some connective tissues their unique properties. They can also act as chemical messengers, as some protein hormones do such as growth hormone. Some proteins, such as antibodies, can even protect against infection by neutralizing invading pathogens such as bacteria. In addition, proteins can also exist as enzymes, which act to greatly increase the rate of specific reactions. Other proteins can act as carriers or transporters that help to facilitate the movement of some chemicals across an otherwise impermeable cell membrane. While it's true that proteins play a very important structural and functional role in the cell membrane, they are not the primary structural component. Rather, phospholipids serve as the most abundant component of cell membranes and helps to give them their unique role as "cellular barriers."

Myoglobin and hemoglobin are not the same molecule; their functions are similar but different in several ways. Myoglobin is an oxygen-binding protein of muscle tissues. In contrast, hemoglobin is the oxygen-transport protein found in blood. Hemoglobin can bind four oxygen atoms, while myoglobin can only bind one. Both hemoglobin and myoglobin contain heme groups, with hemoglobin containing four and myoglobin containing one. These iron-containing groups are responsible for binding the oxygen atom(s).

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.

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.

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.

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.

An oxygen dissociation curve for hemoglobin plots the percent saturation of oxygen on the -axis vs. the partial pressure of oxygen on the -axis. A rightward shift of the curve means that for a given oxygen saturation level, there needs to be a higher partial pressure of oxygen. Thus, a rightward shift is indicative of a decreased affinity of hemoglobin for oxygen.

There are several factors that can influence hemoglobin's affinity for oxygen. One such factor is pH. At lower pH levels, hemoglobin has a more difficult time holding onto oxygen. Physiologically this makes sense, because the blood is likely to be slightly more acidic in regions where tissues are metabolically active, hence they are going to need more oxygen to sustain their metabolism. Likewise, carbon dioxide is also capable of lowering hemoglobin's affinity for oxygen. And again, this makes sense physiologically, because tissues with a high metabolism are going to be generating more carbon dioxide, which serves as a signal to allow hemoglobin to drop off more oxygen for these active tissues. And finally, an additional regulatory factor is a glycolytic intermediate called 2,3-bisphosphoglycerate (2,3-BPG). Binding of this compound to hemoglobin lowers oxygen affinity, thus higher concentrations of 2,3-BPG also cause a rightward shift of the curve.

Also note that oxygen binds hemoglobin in a cooperative fashion. This means that when one molecule of oxygen binds to hemoglobin, the other three oxygen binding sites on hemoglobin gain subsequently increased affinity for oxygen. And when a second oxygen molecule binds, the other binding sites gain more affinity, and so on. Thus, when the partial pressure of oxygen increases, hemoglobin's affinity for oxygen becomes greater.

Ribozymes are RNA molecules that catalyze specific biochemical reactions, so ribosomes (which catalyze the linking of amino acids) are indeed ribozymes. tRNA is complementary to ribosomal RNA in the sites where the two bind. Aminoacylation produces a tRNA with its 3’ end covalently linked to an amino acid. The sequence at the 3’ end is not ACA, however’ it is CCA.

The correct answer choice is isozymes, also called isoenzymes. Even though these enzymes can catalyze the same reaction, they often have differences in their kinetic parameters or in the way they're regulated. Coenzymes are a type of cofactor. They are generally complex organic molecules that are usually derived from vitamins, and they serve the purpose of assisting the enzyme to which they are bound. Examples include pyridoxal phosphate, biotin, coenzyme A, etc. Apoenzymes are enzymes that normally require a cofactor, but are in a state in which they lack that cofactor. Holoenzymes are apoenzymes that have their cofactor bound.

Heme normally binds to iron. Myoglobin is mostly concentrated in muscles, and after a muscle injury can be present in blood. Myoglobin has a higher affinity for oxygen than hemoglobin; myoglobin’s oxygen saturation curve is hyperbolic, whereas hemoglobin’s is sigmoidal. Hemoglobin F (fetal hemoglobin) has a higher oxygen affinity than hemoglobin A (adult hemoglobin). This improves the transfer of oxygen from the circulation of the mother to that of the fetus.

Chymotrypsin is a digestive enzyme that breaks down proteins (proteolysis). It has a catalytic triad of serine, histidine, and aspartate. The hydroxyl group on serine acts as a nucleophile and attacks the carbonyl group on the amino acid, forming a tetrahedral intermediate. Histidine acts as a base, which cleaves the peptide bond. Aspartate acts as an acid, which restores the active site. Since this catalytic triad has a defined nucleophile, base, and acid, we know that there will not be an additional thiol nucleophile. Thiol nucleophiles are found in cysteine proteases.

As stated in the question stem, proteins are super important because they perform an enormous variety of functions. Proteins can sometimes serve a structural role, such as the protein collagen which helps give some connective tissues their unique properties. They can also act as chemical messengers, as some protein hormones do such as growth hormone. Some proteins, such as antibodies, can even protect against infection by neutralizing invading pathogens such as bacteria. In addition, proteins can also exist as enzymes, which act to greatly increase the rate of specific reactions. Other proteins can act as carriers or transporters that help to facilitate the movement of some chemicals across an otherwise impermeable cell membrane. While it's true that proteins play a very important structural and functional role in the cell membrane, they are not the primary structural component. Rather, phospholipids serve as the most abundant component of cell membranes and helps to give them their unique role as "cellular barriers."

Myoglobin and hemoglobin are not the same molecule; their functions are similar but different in several ways. Myoglobin is an oxygen-binding protein of muscle tissues. In contrast, hemoglobin is the oxygen-transport protein found in blood. Hemoglobin can bind four oxygen atoms, while myoglobin can only bind one. Both hemoglobin and myoglobin contain heme groups, with hemoglobin containing four and myoglobin containing one. These iron-containing groups are responsible for binding the oxygen atom(s).

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.

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.