Protein Structure and Functions - Biochemistry

The induced fit model explains one method by which an enzyme's active site can accept some specific substrate. Initially, the active site might not be a perfect match for the substrate, however, when the substrate enters into the site, it can change the conformation of the enzyme just enough that it now fits perfectly and can be acted upon by the enzyme.

To answer this question, we need to have a general understanding about amino acid properties. For instance, at physiological pH, some amino acid side chains will carry a negative charge, some will carry a positive charge, and others will be neutral. Thus, we'll need to take note of which amino acid characteristics each position has, and then evaluate each answer choice to see if the new amino acid being substituted has different characteristics.

At position is arginine, which carries a positive charge. At position is valine, which has an aliphatic side chain that is neutral and relatively hydrophobic. At position is the amino acid glutamate, which is negatively charged due to the carboxyl group on its side chain. Finally, we have glycine at position , which contains a lonely hydrogen atom as its side chain.

Now that we have the characteristics of the amino acid residues in the enzyme, let's compare them to the substitutions listed in the answer choices.

Substituting an aspartate residue into position would mean replacing valine (neutral) with a positively charged amino acid. Hence, this would likely result in disruption of enzyme activity.

Substituting a tryptophan residue into position would replace glycine. In contrast to the extremely small side chain of glycine, the side chain of tryptophan is very large. This great size discrepancy could potentially lead to steric effects that could interfere with the binding of substrate to the enzyme.

Substitution of an asparagine residue into position would replace glutamate. Because glutamate is negatively charged, whereas asparagine is neutral, this substitution would likely interfere with enzyme activity.

Finally, let's consider the substitution of arginine at position with a lysine. In this case, a positively charged arginine would be replaced by another positively charged amino acid, lysine. Because of the similarity between these two amino acids, this substitution would be the least likely to cause a disruption in the enzyme's activity.

In a globular protein, the amino acid chain can twist in a way that polar groups lie at the protein's surface. This allows the protein to interact with water and enhances the protein's solubility in water. This does not occur in fibrous proteins, so fibrous proteins are insoluble in water.

Actin chain growth occurs at the (+) end of the chain, and nucleotide hydrolysis promotes dissociation of actin chains. 2 microfilaments of G-actin monomers make 1 filament of F-actin. However, actin filament assembly is powered by ATP, not GTP.

An O-linked glycoprotein is a protein that has a sugar attached to it. It is called O-linked because the sugar is attached to an oxygen atom on either a threonine residue or a serine residue within the protein.

A peptide bond is formed via the condensation of one amino acid's alpha-carboxy group with the alpha-amino group of another amino acid. Thus, the joining together of two amino acids results in the loss of one water molecule. Likewise, joining three amino acids together results in the loss of two water molecules. Following this pattern, we can conclude that the number of water molecules lost is equal to the number of amino acids joined together, minus 1. Therefore, the joining together of 100 amino acids results in the loss of 99 water molecules.

A peptide bond connects two amino acids. This is the result of a condensation reaction (water is lost) and a new nitrogen-carbon bond forms between two amino acids. Note that amino acid synthesis occurs in the direction. Peptide bonds are covalent bonds that are responsible for the primary structure of amino acids.

For this question, we are presented with three different amino acids and are asked how many possible ways they can be arranged. One way to do this is to list out all the various ways they can be connected.

1. Gly-Leu-Glu

2. Gly-Glu-Leu

3. Leu-Gly-Glu

4. Leu-Glu-Gly

5. Glu-Leu-Gly

6. Glu-Gly-Leu

Alternatively, we could use the mathematic expression to determine the number of combinations of three separate things, which is equal to .

The peptide bond within a polypeptide creates planarity, while other parts of the polypeptide are free to rotate. This occurs because of a delocalization of the electrons on the nitrogen of the amino group (resonance), forming a partial double bond.

While there is a slight difference in electronegativity between carbon and nitrogen, this does not effect the planarity of a polypeptide. Additionally, while a small and insignificant amount of hydrogen bonding may occur between side chains and water, it would not effect planarity regardless.

A cis conformation is so rare due to steric clashes between side chains in different amino acid residues. The Van der Waals forces are simply to great for two side chains to occupy nearby spaces. However, proline is a very unique amino acid. Proline has a unique ring structure, in which its side chain is attached to its amino backbone group. Because of this, there is actually some steric clash in the trans conformation, in addition to the cis conformation. Overall, it is estimated that 10-30% of proline exists in the cis conformation, which is far greater than any other amino acid.

A Ramachandran plot, also referred to as a dihedral plot, tells us about what bond angles are favorable for an amino acid residue. The colored regions are favorable, while the uncolored (white) regions are not favorable. Additionally, each colored regions also corresponds to a different secondary structures (alpha helix, beta sheet, etc.).

These plots can't tell us much about the specific residue order within a polypeptide chain, or the energy required to break an amide bond.

The lysosome is the "stomach" of the cell. It contains many hydrolytic enzymes to digest and recycle the monomers used to form old polymers. Remember the opposite of dehydration/condensation synthesis is hydrolysis. Hydrolysis reactions use water to break bonds in polymers, yielding monomers that can be recycled and reused in anabolic pathways.

Lysozymes speed up by many times the hydrolysis of polysaccharides, by adding the water molecule to sugars linked in its enzyme-substrate complex. If left alone without the lysozyme, this hydrolysis would occur relatively infrequently, because it requires a large activation energy which would be supplied only by rare random collisions. The amino acid cleavage enzyme which uses the ping-pong mechanism is chymotrypsin. The enzyme which breaks nucleic acid phosophodiester bonds is phosphodiesterase. Fats are hydrolyzed by lipases, not lysozymes.

Phosphoglucomutase is responsible for altering the position of the phosphate on the glucose from the "1" position to the "6" position. However, notice how the molecular formula for the product and the substrate are the same. Enzymes that rearrange the structure of a molecule in this manner are referred to as isomerase enzymes.

Mammalian DNA ligase I has this function, and there are other DNA ligases which perform it in other animals and eukaryotes (prokaryotes also have their own DNA ligases). All the other functions mentioned are done by other classes of enzymes, not ligases (i.e. hydrolases, aminotransferases, oxidoreductases, etc.).

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.