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.
In the living cell, histone proteins pack DNA into a repeating array of DNA–protein particles called what?
Histones are responsible for the first and most fundamental level of chromatin packing: the formation of the nucleosome.
What are the specialized DNA sequences that are at the ends of most eukaryotic chromosomes called?
Telomeres contain repeated nucleotide sequences that are required for the ends of chromosomes to be fully replicated.
In an α helix, hydrogen bonds form between which of the following?
In an α helix, hydrogen bonds form between every fourth amino acid. An α helix is generated when a single polypeptide chain turns around itself to form a structurally rigid cylinder.
Shown here is a schematic of an interphase chromosome. Which region is most likely to contain the highest density of genes?
Heterochromatin tends to be relatively gene poor, whereas euchromatin is relatively gene rich. This is due to the gene expression machinery requiring access to the DNA in chromatin for transcription.
How does an allosteric inhibitor work?
To regulate enzyme activity, an allosteric inhibitor binds to a second site, causing a conformational change in the enzyme that makes the active site less accommodating to the substrate. Unlike competitive inhibition, allosteric inhibition cannot be overcome by experimentally elevating the concentration of the substrate.
What is the general name given to the most highly condensed form of chromatin?
“Heterochromatin” is the general name given to the most highly condensed form of chromatin, which can be observed under the light microscope.
The Michaelis constant (KM) of an enzyme is a measure of
Enzyme activity is measured using two values. The first is the rate at which the enzyme converts the substrate to product, which is called Vmax. This value is determined by measuring the rate of product formation in conditions where all enzyme binding sites are occupied by substrates. The Michaelis constant measures the relative binding strength of the enzyme to substrate, determined by the concentration of substrate at which the enzyme operates at half of its Vmax.
Is the following statement true, false, or impossible to determine? Phosphorylation is the only form of covalent modification that can affect a protein’s activity or location.
Can not be determined
Is the following statement true, false, or impossible to determine? Phosphorylation can only take place in the cell nucleus.
False
All of the following are true concerning enzymes except which statement?
They require an input of energy from ATP for activation.
Where is heterochromatin not commonly located?
Chromosomal regions carrying genes that encode ribosomal proteins are active in gene transcription; therefore, you would not expect to see heterochromatin in these areas.
Determine whether the following statement is true or false: Histones are an example of a sequence-specific DNA binding protein.
False - As the proteins that help package DNA into chromosomes, histones must interact with DNA of many sequences. Thus, they do not bind only to specific nucleotide sequences.
How does phosphorylation control protein activity?
Proteins are commonly controlled by phosphorylation and dephosphorylation. When added to the protein, the phosphate group induces a change in the protein’s conformation. Regulation of protein activity in this manner involves attaching a phosphate group covalently to one or more of the protein’s amino acid side chains.
Determine whether the following statements are true or false: “Eukaryotic chromosomes contain a single DNA replication origin.”
This statement is FALSE. “At an origin of replication, hydrogen-bonding between both strands of the double helix must denature/separate.” This statement is TRUE.
Eukaryotic chromosomes contain many DNA replication origins to allow the long DNA molecules to be replicated rapidly. - At an origin of replication, hydrogen-bonding between both strands of the double helix must denature/separate to reveal single-stranded DNA, which then serves as the template for the newly synthesized strand.
What kind of enzyme adds a phosphate group to another 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. The reverse reaction—removal of the phosphate group, or dephosphorylation—is catalyzed by a protein phosphatase.
The tails of the core histone proteins can be chemically modified by the covalent addition of what type of chemical group?
All - The tails of the core histone proteins can be chemically modified by the covalent addition of a methyl group, an acetyl group, or a phosphate group. Each modification alters the physiology of the histone, with some promoting or maintaining euchromatin and others promoting heterochromatin.
The human genome contains approximately how many genes?
The human genome contains approximately 30,000 genes. These include both protein-coding and non-protein-coding genes.
A binding site on the surface of a protein interacts specifically with another protein through
Covalent interactions are rarely used between protein molecules because they are difficult to break, often requiring an enzyme. Interactions between proteins and their partners need to be reversible but very specific. A specific interaction, but one that is able to be altered, can be achieved through formation of many weak noncovalent interactions between proteins and their binding partners.
Which of the following is true about “junk DNA”?
Portions of junk sequence are conserved between species and thus may be functional.
What structure in an interphase eukaryotic cell is the site of ribosomal RNA transcription?
During interphase, the parts of different chromosomes that carry genes encoding ribosomal RNAs come together to form the nucleolus.
A primary transcript (immature, non-processed) single-stranded RNA molecule has the following nucleotide composition: 30% A, 20% G, 24% C, and 26% U. What is the nucleotide composition of the double-stranded DNA molecule from which it was transcribed?
Because the DNA molecule is double-stranded, the nucleotide composition of both strands must be taken into account. The template DNA strand that encodes this RNA molecule would contain: 30% T, 20% C, 24% G, and 26% A. The nontemplate strand, sometimes called the “sense strand” of the DNA, which is complementary to the template strand, would contain: 30% A, 20% G, 24% C, and 26% T. The double helix would thus contain an average of these values: 28% A, 22% G, 22% C, and 28% T.
To crack the genetic code, researchers introduced synthetic messenger RNAs into in vitro translation systems and determined which proteins were produced from these synthetic mRNAs. mRNAs consisting of poly-UUC led to production of three different proteins: poly-Phe, poly-Ser, and poly-Leu. What best explains this result?
The synthetic mRNA was read in all three reading frames.
In a cell, specific start signals initiate translation from a particular nucleotide. However, in a test tube, ribosomes can be forced to translate any RNA molecule and will translate the message in all three possible reading frames.
Export of RNA from the nucleus requires the RNA to have which characteristic(s)?
To be exported, RNAs must have the features of a processed mRNA. This includes being properly spliced (no introns), having a 5’ cap and a poly-A tail.
The splicing of introns out of an mRNA molecule is catalyzed by
RNA molecules that base pair with the splice sites to promote intron removal.
Splicing is actually an RNA-catalyzed reaction. The RNA molecules in the snRNPs base pair with regions of the RNA that are to be spliced. This base pairing helps promote the rearrangement of bonds to remove the intron.
What is true of bacterial mRNAs?
Transcription and translation can occur simultaneously in bacteria because there is no nucleus. Therefore, DNA is located in the cytoplasm where ribosomes are also already present. Once the ribosomal binding site near the 5’ end of the mRNA is transcribed, it is available for ribosomal binding, and translation can begin even while transcription is still underway.
Which macromolecule(s) is/are critical in the active site of the ribosome for catalysis of peptide bond formation?
ribosomal RNA
Translation proceeds in a series of steps in the active site of the ribosome. Which of the following are important steps in polypeptide formation?
Hydrogen bonds with the ribosomal RNA are used to position both the A site and P site tRNAs and to position the amino acids for catalysis of peptide bond formation.
What structure is responsible for selecting and transporting only properly processed eukaryotic mRNAs into the cytoplasm?
Properly processed mature mRNAs will bind a collection of proteins that aid in their delivery to and through the nuclear pore complex.
The transcription initiation site of a eukaryotic gene is found at which location?
The transcription initiation site of a eukaryotic promoter is where RNA synthesis first begins, and this location is “downstream” of the core promoter region. where RNA synthesis begins
At any given time, a typical differentiated human cell will express how many of its approximately 19,000 protein-coding genes?
Experimental examination of mRNAs in different cell types suggests that differentiated human cells express about this number of genes.
from 5000 to 15,000
Which of the following statements about eukaryotic activator proteins is false?
FALSE - They stimulate transcriptional initiation by opening up the double helix.
TRUE -
They stimulate transcription initiation by recruiting proteins that modify chromatin structure.
They stimulate transcription initiation by promoting the assembly of a transcription initiation complex at the promoter.
They stimulate transcription initiation by aiding in the assembly of general transcription factors and RNA polymerase at the promoter
In eukaryotes, which parts of a gene are transcribed into RNA?
introns and exons
In eukaryotes, the introns and the exons of a gene are transcribed into RNA. Introns are spliced out by the activity of the spliceosome, leaving only exons in the mature mRNA.
To begin transcription, eukaryotic RNA polymerase recognizes nucleotide sequences in what region of the DNA?
The promoter region is within the 50 or so nucleotides that are before, or upstream of, the transcription start site.
Which of the following statements concerning leucine zipper protein dimerization and DNA binding is correct?
Leucine zipper proteins function as a dimer with both subunits making contact with the sequence-specific DNA site.
Which of the following mutations would be least likely to disrupt the function of the leucine zipper protein in the animation? The structures of relevant amino acids are provided below.
mutation of a leucine to valine in the dimerization domain of the protein
When a transcription regulator binds to DNA, its most important interactions occur with which of the following?
nucleotide pairs in the major groove of the double helix
Proteins that recognize a specific nucleotide sequence do so because the surface of the protein fits tightly against the surface features of the DNA double helix in that region.
What recognizes the stop codons in an mRNA?
release factors
When the ribosome encounters a stop codon, instead of a tRNA binding, a protein called release factor binds and catalyzes the addition of a water molecule to the carboxyl end of the polypeptide and releases it.
The assembly of general transcription factors at a eukaryotic promoter typically begins at what site?
The TATA box is a key component of many promoters used by RNA polymerase II, and it is typically located about 30 nucleotides upstream from the transcription start site.
Which would be more deleterious: the loss of a single nucleotide from the protein-coding region of a gene or the loss of three nucleotides in that same region?
The loss of a single nucleotide would be more deleterious than the loss of three nucleotides in that same region. Removing a single nucleotide from the protein-coding region of a gene would alter the reading frame in the mRNA, resulting in a vastly different amino acid sequence or even a premature stop codon.
What is true of eukaryotic mRNAs?
They are translated after they are exported from the nucleus.
This is because transcription happens inside the nucleus, and translation occurs at ribosomes, which are located in the cytosol.
