Cell Biology Learning Curve Chapter 3

______ are commonly found in β turns. Glycine and lysine Lysine and serine Glycine and proline Glycine and alanine Serine and valine

Glycine and proline

Which factor limits the number of conformations a polypeptide can have? the planar structure of the peptide bond the number of hydrogen bonds within the structure the number of oxygen molecules within the structure There are no limitations to the number of conformations a polypeptide can have. None of the answers is correct.

the planar structure of the peptide bond

Why would someone utilize a pulse-chase experiment in the laboratory? to measure the charge of a protein to visualize how much antibody a cell has made against a protein to detect the amount of protein in a cell's membrane to decrease the transfer of proteins from the cytoplasm to the nucleus to trace the changes in the intracellular location of a protein

to trace the changes in the intracellular location of a protein

In some proteins, _____ form part of the hydrophobic core of the protein. α helices β sheets β turns All of the answers are correct. None of the answers is correct.

β sheets

The average molecular weight of an amino acid in proteins is 113, taking into account their average relative abundances. Calculate the number of amino acid residues in a protein whose molecular weight equals 52,728. 941 932 466 1112 233

466

The rates of enzyme-catalyzed reactions vary enormously, with turnover numbers (numbers of substrate molecules converted to product at a single active site at substrate saturation) ranging from fewer than 1 to: 1 x 105. 2 x 105. 4 x 105. 6 x 105. The range cannot be determined.

6 x 105.

Which statement regarding the 19S cap complexes in proteasomes is FALSE? A two-cap complex is always referred to as 30S. 19S cap complexes regulate the 20S core of the proteasome. A 19S cap has 16—18 protein subunits. The 19S cap is responsible for hydrolyzing ATP for protein unfolding. All of the statements about the 19S cap complexes are true.

A 19S cap has 16—18 protein subunits.

Which method could be used to study the function of enzymes in a cell? Add an enzyme inhibitor to the cell. Introduce the cell to an environment that has the optimal temperature for enzyme function. Introduce the cell to an environment that has the optimal pH for enzyme function. Add more coenzymes to the cell. Add more cofactors to the cell.

Add an enzyme inhibitor to the cell.

Liquid chromatography techniques separate proteins based on: mass. charge. affinity for a specific binding partner. All of the answers are correct. None of the answers is correct.

All of the answers are correct.

Proteasomes are very large protein-degrading molecular machines that influence many different cellular functions including: the cell cycle. transcription. DNA repair. apoptosis. All of the answers are correct.

All of the answers are correct.

Proteomic studies can tell you: what fraction of the whole proteome is expressed. what is the relative abundance of a protein in a sample. what is the relative amount of chemically modified proteins in a sample. which proteins are present in a large multiprotein complex. All of the answers are correct.

All of the answers are correct.

Serine proteases hydrolyze peptide bonds in substrate proteins using the side chains of _____ within the protease as catalytic groups. Ser-195 His-57 Asp-102 All of the answers are correct. None of the answers is correct.

All of the answers are correct.

The exceptional conformational flexibilities of intrinsically disordered proteins contribute to their functions as: flexible links between well-organized regions of protein. sites of post-translational protein modifications. autoinhibitors. signals for intracellular protein sorting. All of the answers are correct.

All of the answers are correct.

To what can proteins bind? All of the answers are correct. themselves small molecules ions other macromolecules

All of the answers are correct.

Which feature of natively well-ordered proteins limits their folding from many potential conformations to just a few? size of side chains hydrophobicity of side chains ability of side chains to form hydrogen bonds ability of side chains to form ionic bonds All of the answers are correct.

All of the answers are correct.

_____ bind to the active sites of some enzymes and play an essential role in enzyme catalysis. Cofactors Prosthetic groups Coenzymes Nonpolypeptide small molecules or ions All of the answers are correct.

All of the answers are correct.

Which statement is TRUE? Any particular protein adopts only one or just a few very closely related confirmations called the native state. The native state is the most stably folded form of a protein. The native state permits a protein to function normally. The native state is the confirmation with the lowest free energy. All of the statements are true.

All of the statements are true.

Which statement is TRUE? In allostery, the noncovalent binding of one ligand molecule, the allosteric effector, induces a conformational change that alters a protein's activity. In allostery, the noncovalent binding of one ligand molecule, the allosteric effector, induces a conformational change that alters a protein's affinity for other ligands. The allosteric effector can be identical or different in structure from the other ligands, whose binding it affects. The allosteric effector can be an activator or an inhibitor. All of the statements are true.

All of the statements are true.

Which statement regarding protein structure is TRUE? The linear sequence of amino acids linked together by peptide bonds is the primary structure. Folding of peptide chains into local alpha helices or beta sheets represents secondary structure. Secondary structural elements together with various loops and turns in a single polypeptide chain packed into a larger, independently stable structure represents tertiary structure. Some proteins consist of more than one polypeptide associated together in a quaternary structure. All of the statements are true.

All of the statements are true.

What is the significance of FG repeats in nuclear pore complex proteins? They block the passage of large molecules that do not have affinity for phenylalanine or glycine. They have affinity for the negative charges of mRNA molecules. They have affinity for nuclear transporter proteins that shuttle cargo in and out of the nucleus. Both the first and the third answers are correct. All of the answers are correct.

Both the first and the third answers are correct.

Which statement is NOT a way that cells can regulate protein activity? There can be a change in location or concentration within the cell of the protein itself. Cells do not change the intrinsic activity of the protein. Cells can change the affinity of substrate binding. Cells can increase or decrease the steady-state level of the protein by altering its rate of degradation. Cells can increase or decrease the steady-state level of the protein by altering its rate of synthesis.

Cells do not change the intrinsic activity of the protein.

Which statement describes how inhibitors of proteasome function can be used therapeutically? Full inhibition of proteasomal activity allows for cancer cells to live. Decrease in the number of proteasome inhibitors in order to increase the rate of apoptosis. Partial inhibition of proteasomal activity decreases levels of IκB, allowing pro-survival activity of cancer cells. Controlled administration of proteasome inhibitors can allow for killing of cancer cells, but not normal cells. Full inhibition of proteasomal activity increases NFκB activity allowing pro-survival activity of cancer cells.

Controlled administration of proteasome inhibitors can allow for killing of cancer cells, but not normal cells.

Which statement is FALSE? The disruption of a protein's structure is called denaturation. Denaturation can be induced by thermal energy from heat. Denaturation cannot be induced by extreme pH values that alter the charges on amino acid side chains. Treatment with reducing agents that break disulfide bonds can further destabilize disulfide bond-containing proteins. All of the statements are true.

Denaturation cannot be induced by extreme pH values that alter the charges on amino acid side chains.

A protein's function does not depend on its ability to bind to ligands. True False

False

Which statement is FALSE? Some individual polypeptides associate into multi-chain complexes. Proteins have a hierarchical structure. A polypeptide's linear sequence of amino acids linked by peptide bonds folds into helices or sheets. Protein function arises from the specific binding interactions and conformational changes in the structure of an improperly folded protein. Proteins can provide a cell with structure.

Protein function arises from the specific binding interactions and conformational changes in the structure of an improperly folded protein.

Which statement is TRUE about sodium dodecyl sulfate (SDS)? SDS disrupts the tertiary structure of a protein by breaking disulfide bonds. SDS provides or coats proteins with a uniform positive charge. SDS is denser than water, allowing the sample to sink to the bottom of the well. SDS eliminates the mass-to-charge ratio from factoring into the protein's migration. All of the statements are true.

SDS eliminates the mass-to-charge ratio from factoring into the protein's migration.

Which techniques CANNOT be used to obtain the 3D structure of a protein? x-ray crystallography cryoelectron microscopy NMR spectroscopy SDS-PAGE All of these techniques can be used to obtain the 3D structure of a protein.

SDS-PAGE

The ligands of enzymes are called: substrates. light chains. antibodies. ribozymes. heavy chains.

substrates.

_____ refers to the ability of a protein to bind one molecule or a very small group of molecules in preference to all other molecules. Specificity Affinity Molecular complementarity Epitope None of the answers is correct.

Specificity

_____ determine the shapes of cells and their extracellular environments and serve as guide wires or rails to direct the intracellular movement of molecules and organelles. Structural proteins Regulatory proteins Scaffold proteins Membrane transport proteins Enzymes

Structural proteins

Enzymes increase the reaction rate by lowering the energy of the transition state, and therefore the activation energy required to reach it. True False

True

Like α helices, β strands have a directionality defined by the orientation of the peptide bonds. Therefore, in a pleated sheet, adjacent β strands can be oriented in alternating opposite (antiparallel) directions or in the same (parallel) direction. True False

True

The molecule to which a protein binds is called its ligand. True False

True

Calculate the rate of formation of a product (Vo) for a reaction whose [S] = 15, Vmax = 12, and Km = 4. 7.5 10.5 11.5 9.5 8.5

V0=Vmax * [S]/[S] + Km 9.5

Which result will NOT occur if there is an accumulation of misfolded proteins? a large concentration of proteins that function normally in the cell development of degenerative diseases formation of plaques in organs, including the liver and brain loss of normal protein function marking of misfolded proteins for proteolytic degradation

a large concentration of proteins that function normally in the cell

Which type of side chain is needed for two helices to form the coiled-coil structural motif? hydrophobic hydrophilic aliphatic aromatic None of the answers is correct.

aliphatic

Ubiquitination can control all of the following EXCEPT: cell cycle progression. metabolism. catabolism. repair of damaged DNA. protein degradation.

catabolism.

Which technique is used to detect protein bands that have been transferred to a membrane? secondary antibody only primary antibody only chromogenic reaction GFP polyacrylamide

chromogenic reaction

Proteins that catalyze chemical reactions are called: substrates. antibodies. ribozymes. enzymes. None of the answers is correct.

enzymes.

A peptide _____ is the list of the molecular weights of peptides that are generated from a protein by digestion with a specific protease. mass fingerprint index glossary menu None of the answers is correct.

mass fingerprint

Which technique CANNOT be used to determine the mass of a protein? SDS-PAGE native protein electrophoresis ES ionization MALDI-TOF mass spectrometry All of these techniques can be used to determine the mass of a protein.

native protein electrophoresis

The amino acid _____ is usually not found in α helices because the covalent bonding of its amino group with a carbon in the side chain prevents its participation in stabilizing the backbone through normal hydrogen bonding. alanine lysine valine proline serine

proline

Proteasomes influence all of the following cell functions EXCEPT: retaining properly functioning proteins. infection response. transcription. cell cycle. apoptosis.

retaining properly functioning proteins.