Cell Bio Exam 2 Flashcards
What type of bond connects base pairs?
A double-stranded DNA molecule is composed of two polynucleotide chains (DNA strands) held together by hydrogen bonds between the paired bases.
How does binding of GTP to a GTP-binding protein affect its activity?
Proteins in the GTP-binding protein family are always in their active conformation when GTP is bound, in contrast to phosphorylation of a protein, which can activate or inactivate a protein. The hydrolysis of GTP to GDP returns the protein to the inactive state.
What kind of enzyme removes a phosphate group from a protein?
Protein phosphorylation involves the enzyme-catalyzed transfer of the terminal phosphate group of ATP to the hydroxyl group on a serine, threonine, or tyrosine side chain of the protein. This reaction is catalyzed by a protein kinase. However, the reverse reaction—removal of the phosphate group, or dephosphorylation—is catalyzed by a protein phosphatase.
How does the GTP-bound form of a GTP-binding protein switch to a GDP-bound form?
The GTP-bound form of a GTP-binding protein switches to a GDP-bound form by hydrolyzing GTP, releasing a phosphate. When this happens, the protein retains the GDP and changes to the inactive conformation.
What is the definition of a protein-binding site?
A protein-binding site is any region on a protein’s surface that interacts with another molecule through noncovalent bonding. A protein can contain binding sites for a variety of molecules, large and small.
Investigators decide to analyze the purity of a preparation of antibody molecules using SDS polyacrylamide-gel electrophoresis (SDS-PAGE). On Lane 1 of the gel, they load a sample of the antibody. On Lane 2, they load an antibody sample that has been treated with a reducing agent called mercaptoethanol, which breaks disulfide linkages. Following electrophoresis, they see distinct bands representing polypeptides with molecular weights of 50 kD and 25 kD in Lane 2 and only one band weighing 150 kD in Lane 1. What can the investigators conclude about their antibody based on the results of this experiment?
Their antibody is composed of subunits (50 kD and 25 kD in molecular weight) that each must include at least one cysteine residue. The untreated antibody in Lane 1 of the gel migrates as a single, distinct band with a molecular weight of 150 kD. Thus, the preparation is pure. Treatment with mercaptoethanol, Lane 2, reduces the disulfide linkages that hold together the subunits (those of 50 kD and 25 kD) that are part of the mature antibody molecule. Disulfide linkages only form between cysteine residues.
Which amino acid is involved in the formation of disulfide bonds?
Two cysteine side chains can be involved in the formation of a disulfide bond. Disulfide bonds help stabilize a favored protein conformation.
What can happen if heterochromatin spreads inappropriately into an area with active genes?
Due to its compact nature, genes in heterochromatin are often inactive because they are not accessible. Heterochromatin can sometimes accidentally spread into regions where it is not meant to and cause silencing of genes in that region.
Mutations in the nucleic acid sequence of a gene can sometimes direct the substitution of one amino acid for another in the encoded protein. Which amino acid substitution would be most likely to severely disrupt the normal structure of a protein?
Arginine and methionine have different chemical properties. Methionine has a nonpolar side chain that would likely be buried in the protein’s interior; arginine, on the other hand, is a positively charged amino acid that would likely be facing the protein’s exterior. Replacing methionine with arginine would likely disrupt a protein’s structure.
What evidence suggests that the large amount of excess “junk” DNA in a genome may serve an important function?
Genetic conservation is a significant indicator that there is an important function of a particular sequence.
How many different polypeptide chains are possible from a sequence that is 10 amino acids long?
The number of combinations is represented by the expression 20n, where the n represents the number of amino acids, which is 10 in this example. This demonstrates the great combinatorial diversity that just 20 amino acids can generate.
What does the primary structure of a protein refer to?
The primary structure of a protein refers to the linear amino acid sequence of the protein. The chain of linear polymers of amino acids that compose proteins is termed a polypeptide. The primary structure determines the secondary and tertiary structures.
Protein molecules that have a quaternary structure must have two or more of which of the following?
Protein molecules that have a quaternary structure must have two or more polypeptide chains. If a protein molecule exists as a complex of more than one polypeptide chain, then these interacting polypeptides form its quaternary structure.
To identify genes coding for essential proteins, researchers can create temperature-sensitive mutations. These mutations allow proper protein folding and cell proliferation at the permissive temperature of 22ºC, but they cause protein misfolding and reduced cell proliferation at a higher restrictive temperature, such as 37ºC. Which of the following mutations might increase protein flexibility and lead to a temperature-sensitive phenotype?
Protein folding is maintained by both noncovalent interactions (electrostatic attractions, hydrogen bonds, and van der Waals attractions) and covalent disulfide bonds. Loss of any of these will contribute to proteins unfolding at a temperature lower than they otherwise would. Generation of temperature-sensitive mutations in the yeast S. cerevisiae helped uncover genes involved in the cell division cycle and in protein secretion through the endomembrane system.
Which of the following correctly describes phosphorylation of a protein?
The phosphorylation of a protein can either increase or decrease the protein’s activity, depending on the site of phosphorylation and the structure of the protein. Binding sites can either be exposed to or hidden by these conformational changes.
Determine whether the following statement is true or false: The majority of human DNA does not code for genes.
TRUE - Only a couple percent of human DNA is known to contain genes that encode proteins. Even accounting for regulatory sequences required for controlling gene activity, the usefulness of the rest of the DNA has not yet been demonstrated.
Cylindrical α helices and planar β sheets can be formed by what bonding?
hydrogen-bonding of many different sequences. Both α helices and β sheets result from hydrogen bonding of backbone atoms within the protein. Disrupting hydrogen bonding will cause both structures to unfold.
Which important intramolecular force for polypeptide folding is demonstrated by the clustering of green side chains?
Which of these amino acids could be represented by the green side chains that are clustered in the center of the folded protein?
Hydrophobic forces help proteins fold into compact conformations. In a folded protein, nonpolar amino acid side chains are buried on the inside to form a tightly packed hydrophobic core of atoms hidden from water. In this figure, the hydrophobic nonpolar amino acids are shown in green.
Valine, leucine, and phenylalanine are all nonpolar amino acids that would be expected to cluster in the center of a folded protein. In an aqueous environment, the nonpolar side chains of these amino acids tend to be forced together to minimize their disruptive effect on the polar interaction network formed by the surrounding water molecules.
Ras is a GTP-binding protein involved in cell proliferation (division). In its active form, with GTP bound, Ras activates cell signaling pathways that promote cell division. Mutations in the gene that encodes Ras can lead to cancer. How might mutations in the gene encoding Ras lead to the uncontrolled proliferation characteristic of cancer cells?
A mutation that decreases the rate at which Ras hydrolyzes GTP would be a logical mutation in the gene encoding Ras that could lead to the uncontrolled proliferation characteristic of cancer cells. Ras is a G protein that is activated upon GTP binding. If a mutation happened that caused a decrease in the ability of Ras to hydrolyze that GTP, then cell-proliferative Ras signaling would lead to cancer.
Imagine that this experiment uses a mutant version that increases the enzyme’s affinity, or ability, to bind its substrate. Using the graph as a comparison, what effect would the mutant version of the enzyme likely have on the KM?
If a mutant version of the enzyme used to generate these data increased its ability to bind substrate, then we would expect the new KM to move to the left of this graph, meaning that it decreases. In general, a small KM indicates that a substrate binds very tightly to the enzyme (due to a large number of noncovalent interactions).
Many proteins are regulated by the binding of GTP or GDP. Which form is the active state of the protein?
A GTP-binding protein requires the presence of a tightly bound GTP molecule to be active. The active protein can shut itself off by hydrolyzing its bound GTP to GDP and inorganic phosphate (Pi), which converts the protein to an inactive conformation.
Which is true of prion proteins?
Prions are misfolded forms of normal proteins and can spread from one organism to another. The aggregates formed by prion proteins are insoluble and very stable, thanks in part to the tight stacking of their β sheets. Therefore, prion proteins form very stable protein aggregates.
How do chromatin-remodeling complexes work?
Changing the conformation of chromatin is an energy-intensive process and can result in making a segment of DNA more or less accessible to proteins involved, for example, in transcription.
Which statement is true about the association of histone proteins and DNA?
Peripheral arginine and lysine side chains, which are positively charged, interact with the phosphate groups of DNA.
Histone proteins have a high proportion of positively charged amino acids, which bind tightly to the negatively charged DNA backbone.