Exam 1 Practice (Long Answer Questions) Flashcards
(25 cards)
a.) List the types of noncovalent interactions that are important in providing stability to the 3D structure macromolecules.
b.) Why is it important that these interactions be noncovalent, than than covalent bonds?
a.) Hydrogen bonds, Ionic interactions between charged groups, Van Der Waals interaction, and Hydrophobic interactions
b.) Because noncovalent interactions are weak, they can form, break, and re-form more rapidly and with less energy input that can covalent bonds. This is important to maintain flexibility needed in macromolecules.
Why is an asymmetric carbon atom called a chiral center?
An symmetric carbon has 4 different substituents attached, and cannot be superimposed on its mirror image–as a right hand cannot fit into a left glove.
Thus, a molecule with 1 chiral carbon will have 2 stereoisomers, which may be distinguishable from one another in a biological system.
Explain why living organisms are able to produce particular chiral forms of different biomolecules while laboratory chemical synthesis usually produces a racemic mixture.
Laboratory syntheses usually use achiral reagents and thus produce racemic mixtures of products. In contrast, because all enzymes are made of chiral precursors, all enzymes are inherently chiral catalysts.
Thus, they will show strong stereoselectivity in reactants and mechanisms, leading to the production of chiral products.
The free-energy change for the formation of a protein from the individual amino acids is positive and is thus an endergonic reaction. How, then, do cells accomplish this process?
The endergonic (thermodynamically unfavorable) reaction is coupled to an exergonic (thermodynamically favorable) reaction through a shared intermediate, so that the overall free-energy change of the coupled reactions is negative (the
overall reaction is exergonic).
Describe the “RNA world” hypothesis.
Initially, RNA molecules were both genes and catalysts. Self-replication of these molecules over long periods of time produced variants that were able to catalyze polymerization of amino acids to form peptides that assumed the function of catalysts. Eventually, genomic RNA was copied into DNA, which assumed the function of genetic information
storage.
What is meant by endosymbiotic association? How can this concept explain the evolution of eukaryotic cells that are capable of carrying out photosynthesis and/or aerobic metabolism?
An endosymbiotic association is the envelopment of one organism by another to form a relationship that is beneficial to both organisms. It is believed that primitive eukaryotic cells, which were incapable of photosynthesis or aerobic metabolism, formed endosymbiotic associations with photosynthetic and/or aerobic bacteria. The aerobic bacteria then evolved into the mitochondria found in modern eukaryotic cells, and the photosynthetic bacteria evolved into the chloroplasts found in plant cells.
. What is meant by feedback inhibition and why is it important in a living organism?
Feedback inhibition is the regulation of a biochemical pathway in which a reaction product inhibits an earlier (usually the first) step in the pathway. It is an important type of regulation because it ensures that energy is not wasted by an organism producing molecules it does not need.
Name and briefly define five types of noncovalent interactions that occur between biological molecules.
(1) Hydrogen bonds: weak electrostatic attractions between one electronegative atom (such as oxygen or nitrogen) and a hydrogen atom covalently linked to a second electronegative atom
(2) electrostatic interactions: relatively weak charge-charge interactions (attractions of opposite charges, repulsions of like charges) between two ionized groups
(3) hydrophobic interactions: the forces that tend to bring two hydrophobic groups together, reducing the total area of the two groups that is exposed to surrounding molecules of the polar solvent (water);
(4) Van Der Waals
interactions: weak interactions between the electric dipoles that two close-spaced atoms induce in each other
(5) tightly bound water molecules can form as an essential part of the binding site in a protein for its ligand.
Explain with an appropriate diagram why amphipathic molecules tend to form micelles in water.
What force drives micelle formation?
Micelle formation minimizes the area of the hydrophobic part of amphipathic molecules that contacts the polar solvent, water. Hydrophobic interactions between hydrophobic moieties are the driving force for micelle formation.
When amphipathic molecules form micelles in water, the entropy decrease due to the formation of ordered arrays of water molecules around the hydrophobic moieties is minimized. (See Fig. 2-7, p. 48.)
Define pKa for a weak acid in the following two ways: (1) in relation to its acid dissociation constant, Ka, and (2) by reference to a titration curve for the weak acid.
(1) pKa = –log Ka.
(2) See Fig. 2-17, p. 59; pKa is the value of pH at the inflection point in a plot of pH vs. extent of titration of the weak acid. At the pKa, the concentration of ionized acid equals the concentration of un-ionized acid.
If ice were denser than water, how would that affect life on earth?
Ice that formed at the surface of bodies of water would sink; hence, streams, ponds, lakes, and so on would freeze from the bottom up. With a reservoir of ice at the bottom, they would be perpetually cold, and in the limit they would freeze solid, precluding life as we know it.
What are the structural characteristics common to all amino acids found in naturally occurring proteins?
All amino acids found in naturally occurring proteins have an alpha carbon to which are attached a carboxylic acid, an amine, a hydrogen, and a variable side chain. All the amino acids are also in the L configuration.
As more OH– equivalents (base) are added to an amino acid solution, what titration reaction will occur around pH = 9.5?
Around pH = 9.5, the —NH3+ group will be titrated according to the reaction:
—NH3+ + OH– –> —NH2 + H2O.
What is the uniquely important acid-base characteristic of the histidine R group?
Only the imidazole ring of the histidine R group has a pKa near physiological pH (pKa = 6.0), which suggests that histidine may provide buffering power in intercellular and intracellular fluids.
Why do smaller molecules elute after large molecules when a mixture of proteins is passed through a size-exclusion (gel filtration) column?
The column matrix is composed of cross-linked polymers with pores of selected sizes. Smaller molecules can enter pores in the polymer beads from which larger molecules would be excluded. Smaller molecules therefore have a larger three-dimensional space in which to diffuse, making their path through the column longer. Larger molecules migrate faster because they pass directly through the column, unhindered by the bead pores.
What factors would make it difficult to interpret the results of a gel electrophoresis of proteins in the absence of sodium dodecyl sulfate (SDS)?
Without SDS, protein migration through a gel would be influenced by the protein’s intrinsic net charge—which could be positive or negative—and its unique three-dimensional shape, in addition to its molecular weight. Thus, it would be difficult to ascertain the difference between proteins based upon a comparison of their mobilities in gel electrophoresis.
As a protein is purified, both the amount of total protein and the activity of the purified protein decrease. Why, then, does the specific activity of the purified protein increase?
Specific activity is the units of enzyme activity (mol of product/min) divided by the amount of protein (mg). As the protein is purified, some of it is lost in each step, resulting in a drop in activity. However, other contaminating proteins are lost to a much greater extent. Therefore, with each purification step, the purified protein constitutes a greater proportion of the total, resulting in an increase in specific activity. (See also Table 3-5, p. 88.)
Conjugated proteins contain chemical substituents in addition to amino acids. List three classes of conjugated proteins and identify the type of prosthetic group associated with each one.
Any of the following are acceptable answers:
Lipoproteins, with lipid groups
Glycoproteins, with carbohydrate groups
Phosphoproteins, with phosphoryl groups
Hemoproteins, with heme groups
Flavoproteins, with flavin nucleotide groups
Metalloproteins, with metal ions (zinc, iron, calcium, etc.)
Name four factors (bonds or other forces) that contribute to stabilizing the native structure of a protein, and describe one condition or reagent that interferes with each type of stabilizing force.
Any of the following forces stabilize native protein structures and are disrupted by the listed conditions or reagents:
(a) disulfide bonds by reducing conditions or mercaptoethanol or dithiothreitol
(b) hydrogen bonds by pH extremes
(c) hydrophobic interactions by detergents or urea or guanidine hydrochloride
(d) ionic interactions by changes in pH
or ionic strength
(e) van der Waals interactions by any unfolding condition.
When a polypeptide is in its native conformation, there are weak interactions between its R groups. However, when it is denatured there are similar interactions between the protein groups and water. What then accounts for the greater stability of the native conformation?
In the unfolded polypeptide, there are ordered solvation shells of water around the protein groups. The number of water molecules involved in such ordered shells is reduced when the protein folds, resulting in higher entropy.
Hence, the lower free energy of the native conformation.
Why are glycine and proline often found within a Beta turn?
A Beta turn results in a tight 180° reversal in the direction of the polypeptide chain. Glycine is the smallest and thus most flexible amino acid, and proline can readily assume the cis configuration, which facilitates a tight turn.
In superhelical proteins, such as collagen, several polypeptide helices are intertwined. What is the function of this superhelical twisting?
The superhelical twisting of multiple polypeptide helices makes the overall structure more compact and increases its overall strength.
Describe a reservation about the use of x-ray crystallography in determining the three-dimensional structures of biological molecules.
To obtain an x-ray picture of a biomolecule, the molecule must be purified and crystallized under laboratory conditions far different from those encountered by the native molecule. Biomolecules in the cell also have more flexibility and freedom of motion than can be accommodated in a rigid crystal structure. Therefore, the static picture obtained from an x-ray analysis of a crystal may not provide a complete or accurate representation of the biomolecule in vivo.
Once a protein has been denatured, how can it be renatured? If renaturation does not occur, what might be the explanation?
Because a protein may be denatured through the disruption of hydrogen bonds and hydrophobic interactions by salts or organic solvents, removal of those conditions will reestablish the original aqueous environment, often permitting the protein to fold once again into its native conformation. If the protein does not renature, it may be because the denaturing treatment removed a required prosthetic group, or because the normal folding pathway requires the presence of a polypeptide chain binding protein or molecular chaperone. The normal folding pathway could also be mediated by a larger polypeptide, which is then cleaved (e.g., insulin). Denatured insulin would not refold easily.
