Biology 1703 Exam 1 Set 4

Beta-sheets stabilization of abnormally folded proteins

Beta sheets can participate in the formation of amyloid fibers, which are insoluble protein aggregates. What drives the formation of amyloid fibers?

collagen

Coiled-coils are typically found in proteins that require an elongated structural framework. Which of the following proteins do you expect to have a coiled-coil domain?

hydrogen bonds

Cycle AMP (cAMP) is a small molecule that associates with it binding site with a high degree of specificity. Which type of noncovalent interactions are the most important for providing the "hand in a glove" binding of cAMP?

Allosteric activation

Energy required by the cell is generated in the form of ATP. ATP is hydrolyzed to power many of the cellular processes, increasing the pool of ADP. As the relative amount of ADP molecules increases, they can bind to glycolytic enzymes, which will lead to the production of more ATP. The best way to describe this mechanism of regulation ___________.

retinal

For some proteins, small molecules are integral to their structures and function. Enzymes can synthesize some of these small molecules, whereas others, called vitamins, must be ingested in the food we eat. Which of the following molecules is NOT classified as a vitamin but does require the ingestion of a vitamin for its production?

A hydrogen bond forms between a polar side and an aromatic side chain.

Fully folded proteins typically have polar side chains on their surfaces, where electrostatic attractions and hydrogen bonds can form between the polar group on the amino acid and the polar molecules in the solvent. In contrast, some proteins have a polar side chain in their hydrophobic interior. Which of the following would NOT occur to help accommodate an internal, polar side chain.

elastase

Globular proteins fold up into compact, spherical structures that have uneven surfaces. They tend to form multisubunit complexes, which also have a rounded shape. Fibrous proteins, in contrast, spam relatively large distances within the cell and in the extracellular space. Which of the proteins below is NOT classified as a fibrous protein?

This chamber serves to protect unfolded proteins from interacting with other proteins in the cytosol, until protein folding is completed.

Molecular chaperones can work by creating an "isolation chamber." What is the purpose of this chamber?

A conformational change is linked to ATP hydrolysis

Motor proteins use the energy in ATP to transport organelles, rearrange elements of the cytoskeleton during cell migration, and move chromosomes during cell division. Which of the following mechanisms is sufficient to ensure the unidirectional movement of a motor protein along its substrate.

absence of negative charges in the active site

Studies conducted with a lysozyme mutant that contains an Asp-->Asn change at position 52 and a Glue-->Gin change at position 35 exhibited almost complete loss in enzymatic activity. What is the most likely explanation for the decrease in enzyme activity in the mutant?

A change that decreases the rate of hydrolysis of GTP by Ras

The Ras protein is a GTPase that functions in many growth-factor signaling pathways. In its active form, with GTP bound, it transmits a downstream signal that leads to cell proliferation; in its inactive form, with GDP bound, the signal is not transmitted. Mutations in the gene for Ras are found in many cancers. Of the choices below, which alteration of Ras activity is most likely to contribute to the uncontrolled growth of cancer cells?

They form proteins aggregates

The correct folding of proteins is necessary to maintain healthy cells and tissues. Unfolded proteins are responsible for such neurodegenerative disorders as Alzheimer's disease, Huntington's disease, and Creutzfeldt-Jakob disease (the specific faulty protein is different for each disease). What is the ultimate fate of these disease-causing, unfolded proteins?

protein degradation

The phosphorylation of a protein is typically associated with a change in activity, the assembly of a protein complex, or the triggering of a downstream signaling cascade. The addition of ubiquitin, a small polypeptide, is another type of covalent modification that can affect the protein function. Ubiquitylation often results in _________.

Affinity

The process of generating monoclonal antibodies is labor-intensive and expensive. An alternative is to use polyclonal antibodies. A subpopulation of purified polyclonal antibodies that recognize a particular antigen can be isolated by chromatography. Which type of chromatography is used for this purpose?

ribbon

The three-dimensional coordinates of atoms within a folded protein are determined experimentally. After researchers obtain a protein's structural details, they can use different techniques to highlight particular aspects of the structure. What visual model best displays a protein;s secondary structure (alpha helices and beta sheets)?

sequence

The variations in the physical characteristics between different proteins are influenced by the overall amino acid compositions, but even more important is the unique amino acid __________.

The solvents break all noncovalent interactions

To study how proteins fold, scientists must be able to purify the protein of interest, use solvents to denatured the folded protein, and observe the process of refolding at successive time points. What is the effect of the solvents used in denaturation process?

hydrophobic

Two or three alpha helices can sometimes wrap around each other to form coiled-coils. The stable wrapping of one helix around another is typically driven by _________ interactions.

tubulin

Which of the following globular proteins is used to form filaments as an intermediate step to assembly into hollow tubes>

They can interact with unfolded polypeptides in a way that changes the final fold of the protein.

Which of the following is NOT TRUE of molecular chaperones?

left-handedness

Which of the following is NOT a feature commonly observed in alpha helices?

coiled-coil patterns

Which of the following is NOT a feature commonly observed in beta sheets?

by speeding up the rate at which water molecules collide with the substrate

Which of the following mechanisms best describes the manner in which lysozyme lowers the energy required for its substrate to reach its transition-state conformation?

nuclear magnetic resonance

Which of the following methods used to study proteins is limited to proteins with a molecular mass of 50 kD or less?

western blot analysis

Which of the following methods would be the most suitable to assess levels of expression of your target protein in different cell types?

gel electrophoresis

Which of the following methods would be the most suitable to assess the relative purity of a protein in a sample you have prepared?

gel-filtration chromatography

Which of the following methods would be the most suitable to assess whether your protein exists as a monomer or in a complex.

Allosteric regulators are often products of other chemical reactions in the same biochemical pathway.

Which of the following statements about allostery is TRUE?

Disulfide binds stabilize but do not change a protein's final confirmation.

Which of the following statements is TRUE?

Nonpolar amino acids tend to be found in the interior proteins

Which of the following statements is TRUE?

The loss of a binding site on the mutant-protein surface through which protein Y normally forms dimers.

You have two purified samples of protein Y: the wild-type (nonmutated) protein and a mutant version with a single amino acid substitution. When washed through the same gel-filtration column, mutant protein Y runs through the column more slowly than the normal protein. Which of the following changes in the mutant protein is more likely to explain this result?

globular

globular or fibrous protein molecule: actin

fibrous

globular or fibrous protein molecule: collagen

fibrous

globular or fibrous protein molecule: elastin

globular

globular or fibrous protein molecule: hemoglobin

fibrous

globular or fibrous protein molecule: keratin

globular

globular or fibrous protein molecule: lysozyme

Enzyme

protein function for carboxylase

Storage

protein function for ferritin

special purpose

protein function for green fluorescent protein

Transport

protein function for hemoglobin

gene regulatory

protein function for homeodomain proteins

Signal

protein function for insulin

motor

protein function for myosin

Receptor

protein function for rhodopsin

structural

protein function for tubulin

True

true for false: the relative distribution of polar and nonpolar amino acids in a folded protein is determined largely by hydrophobic interactions, which favor the clustering of nonpolar side chains in the interior.

True

true or false: A large number of noncovalent interactions is required to hold two regions of a polypeptide chain together in a stable conformation.

False There is a single, final fold for every polypeptide. The fold adopted is the "best" conformation, for which the free energy (G) of the molecule is at a minimum.

true or false: A single polypeptide tends to adopt 3-4 different conformations, which all have equivalent free-energy values (G).

False. ATPases hydrolyze ATP; they do not produce it. These enzymes enable the cell to harness the chemical energy stored in the high-energy phosphate bonds.

true or false: ATPases generate ATP for the cell.

False. Although antibodies are Y-shaped, they are composed of four, not six, polypeptide chains. There are two heavy chains and two light chains.

true or false: Antibodies are Y-shaped and are composed of six different polypeptide chains.

False. Collagen fibers and elastin fibers are very different in structure and function. Collagen fibers are highly organized, triple-strand coiled-coils that provide strength to hold tissue together. Elastin molecules are linked together in a loose network with disulfide bonds; this allows the fibers (and tissues) to stretch without tearing.

true or false: Collagen fibers and elastin fibers serve similar functions, which is expected because the structure of these two types of fibers is quite similar.

False. Feedback inhibition occurs when an enzyme acting early in a metabolic pathway is inhibited by the accumulation of a product late in the pathway. The inhibitory product binds to a site on the enzyme that lowers its catalytic activity.

true or false: Feedback inhibition is defined as a mechanism of down-regulating enzyme activity by the accumulation of a product earlier in the pathway.

True

true or false: GTP-binding proteins typically have GTPase activity, and the hydrolysis of GTP transforms them to the "off" conformation.

True

true or false: Hexokinase recognizes and phosphorylates only one of the glucose stereoisomers.

True

true or false: If an enzyme's allosteric binding site is occupied, the enzyme may adopt an alternative conformation that is not optimal for catalysis.

False. Although phosphorylation of a protein can change its conformation, this modification may be either as a positive or a negative regulator of enzyme activity, depending on the protein in question.

true or false: Protein phosphorylation is another way to alter the conformation of an enzyme and serves exclusively as a mechanism to increase enzyme activity.

False. Peptide bonds are planar amide bonds that are central to the polypeptide backbone formation. The atoms in the amino acid side chains are not considered to be part of the backbone.

true or false: The "polypeptide backbone refers to all atoms in a polypeptide chain, except for those that form the peptide bonds.

False. The interior amino acids form a structural scaffold that maintains the specific orientation for those that directly interact with the ligand. Changes to these interior amino acids can change the protein shape and render it nonfunctional.

true or false: The amino acids in the interior of a protein do not interact with the ligand and do not play a role in selective binding.

True

true or false: The assembly of both collagen and elastin fibers requires the formation of disulfide bonds.

True

true or false: The chemical properties of amino acids side chains include charged. uncharged polar, and nonpolar.

False. Van der Waals attractions are weakly attractive forces that occur between all atoms. Hydrophobic interactions are only observed between nonpolar molecules in the context of an aqueous solution.

true or false: Van Der Waals interactions and hydrophobiv interactions are two ways to describe the same type of weak forces that help proteins fold.

False. Collagen is not used inside the cell; it is secreted and incorporated into the existing collagen fibers in the extracellular matrix.

true or false: collagen is a protein that participates in both the cytoskeleton and the extracellular matrix.

False. The order in which amino acids are linked is unique for each protein and is the most important factor in determining overall protein structure.

true or false: generally, the total number of non polar amino acids has a greater effect on protein structure than the exact order of amino acids in a polypeptide chain

hydrolase

Lysozyme is an enzyme that specifically recognizes bacterial polysaccharides, which renders it an effective antibacterial agent. Into what classification of enzymes does lysozyme fall?

Hydrogen bonds along the protein backbone

Although all protein structures are unique, there are common structural building blocks that are referred to as regular secondary structures. Some proteins have alpha helices, some have beta sheets, and still others have a combination of both. What makes it possible for proteins to have these common structural elements?

systemic temperature increase

Antibody production is an indispensable part of our immune response, but it is not the only defense our bodies have. Which of the following is observed during an infection that is NOT a result of antibody-antigen interactions?

proteomics

Instead of studying one or two proteins or protein complexes present in the cell at any given time, we can now look at a snapshot of all proteins being expressed in cells being grown in specific conditions. This large-scale, systemic approach to the study of proteins is called _________.

a water molecule

Polypeptides are synthesized from amino acid building blocks. The condensation reaction between the growing polypeptide chain and the next amino acid to be added involves the loss of ________.

The polypeptide returns to its original conformation

Protein folding can be studied using a solution of purified protein and a denaturant (urea), a solvent that interferes with noncovalent interactions. Which of the following is observed after the denaturant is removed from the protein solution?

a protein segment that folds independtly

Protein structures have several different levels of organization. The primary structure of a protein is its amino acid sequence. The secondary and tertiary structures are more complicated. Consider the definitions below and select the one that best fits the term "protein domain."

inside a cavity on the protein surface

Proteins bind selectively to small-molecule targets called ligands. The selection of one ligand out of a mixture of possible ligands depends on the number of weak, noncovalent interactions in the protein's ligand-binding site. Where is the binding site typically located in the protein structure?

translation of protein components

Proteins can assemble to form large complexes that work coordinately, like moving parts inside a single machine. Which of the following steps in modulating the activity of a complex protein machine is least likely to be DIRECTly affected by ATP or GTP hydrolysis?