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.
In principle, how many reading frames in an RNA molecule can potentially be translated into protein?
Three
This is because a codon is three consecutive nucleotides. However, only one reading frame correctly translates into the full protein sequence.
In eukaryotes, multiple genes can be expressed simultaneously by
the binding of a specific transcriptional regulator to several genes.
In eukaryotes, gene expression is often decided by a committee of transcriptional regulators. A single transcriptional regulator can act as the final voice in the committee to turn on expression by coordinated binding to several genes at once.
Determine whether the following statement is true or false: Even though control of eukaryotic gene expression is combinatorial, the effect of a single transcription regulator can still be decisive in switching any particular gene on or off.
True
Although the control of eukaryotic gene expression is combinatorial, a single transcription regulator can activate or repress a gene by completing the “combination” needed to control that gene’s activity.
Many transcriptional regulators function together to decide the expression level of a particular gene. This describes the concept of
combinatorial control
Transcriptional regulators work as a committee to determine the level of expression of a gene; this is called combinatorial control. Operons, on the other hand, are a set of genes under the control of a specific transcriptional regulator, a typical control mechanism in prokaryotes.
Although all of the steps involved in expressing a gene can in principle be regulated, what is the most important stage of control for most genes?
transcription initiation
Because transcriptional control is the first step in gene expression, regulation at this level has the most dramatic effects. If an RNA transcript is never synthesized, there is no way for that gene to ever be expressed.
Determine whether the following statement is true or false: All proteins are fully functional upon leaving the ribosome.
False
Not all proteins are fully functional upon leaving the ribosome. Some proteins require post-translational modifications in order to become active.
What is the name of the complex that degrades proteins that have reached the end of their lifespan, are damaged, or are misfolded?
Proteasome
Large molecular machines called proteasomes act as garbage disposals for degrading proteins that are old or damaged.
What is the best term for an RNA molecule that possesses catalytic activity?
Ribosome
RNA molecules, such as those that compose the ribosome, share features found in protein-based enzymes, including a complex three-dimensional conformation and the ability to recognize specific structures.
How do RNA templets work?
All nucleic acid, RNA included, is always polymerized in the 5’-to-3’ direction, and for different genes, opposite strands of DNA can serve as the template. That is, if one strand is the template for one gene, the other strand can be the template strand for a completely different gene.
Which of these is not a type of noncoding RNA?
mRNA
To reinforce cell identity, vertebrate cells can methylate which nucleotide?
Cytosine that falls next to guanine in the sequence CG
In vertebrates, this modification occurs on select cytosine (C) nucleotides that fall next to a guanine (G) in the sequence 5’-CG-3’.
Protein concentration can be regulated by all of the steps listed EXCEPT
DNA Replication - Protein levels can be tuned by changing the amount of processed mRNA available to ribosomes. Protein levels are not typically regulated by making more copies of the DNA instructions.
Protein concentration can be regulated by all
RNA processing.
nuclear export.
mRNA stability.
Determine whether the following statement is true or false: The general transcription factors that assemble at a eukaryotic promoter are different, depending on the specific gene being transcribed by polymerase II.
False
The general transcription factors that assemble at a eukaryotic promoter are not different, depending on the specific gene being transcribed by polymerase II.
Determine whether the following statement is true or false: Small interfering RNAs bind to the same RISC proteins that take up miRNAs.
True
Small interfering RNAs bind to the same RISC proteins that take up miRNAs. They are generated from larger, double-stranded foreign RNA precursor molecules by some of the same enzymes that process miRNAs.
Which form of post-transcriptional control is being widely exploited by scientists to “knock down” genes of interest?
RNA interference
RNA interference is a mechanism of post-transcriptional control that is widely exploited by scientists to “knock down” genes of interest. RNA interference (RNAi) is a biological process in which RNA molecules inhibit translation by degrading targeted mRNA molecules.
Which biochemical reaction is catalyzed by a ribozyme?
Peptide bond formation in protein synthesis is catalyzed by a ribozyme. The ribosome, along with its rRNA that composes the subunits, catalyzes the synthesis of the peptide bond in proteins.
Many antibiotics work by inhibiting bacterial protein synthesis. Investigators have isolated a promising new compound and wish to determine its mechanism of action. Using a cell-free translation system similar to the ones originally used to deduce the genetic code, the researchers incubate their drug with the synthetic polynucleotide 5’-AUGUUUUUUUUU.
In the absence of the drug, this polynucleotide directs the synthesis of the peptide Met–Phe–Phe–Phe. When the drug is added, only the peptide Met–Phe is produced. Based on this observation, which is most likely the mechanism of action of this potential new antibiotic?
It blocks translocation of the large ribosomal subunit, preventing the movement of peptidyl-tRNA from the A site to the P site of the ribosome.
To have just a two-amino-acid peptide produced, there needs to be no translocation of the ribosome, so a translocation-blocking mechanism of action for this antibiotic is the most logical explanation. The methionine is present because the first codon is positioned in the P site, and the phenylalanine is present because another tRNA will enter at the A site, but then no further tRNAs can enter the ribosome.
In eukaryotes, where do transcription regulators bind?
upstream, downstream, or within the genes they control
In eukaryotes, transcription regulators bind upstream, downstream, or within the genes they control. More common in eukaryotes than prokaryotes, gene activation can occur at a distance.
Which of the following statements is false?
In a eukaryotic mRNA, the poly-A tail promotes longer-term stability of the molecule, not degradation.
True statements -
- The lifetime of a eukaryotic mRNA is controlled in part by nucleotide sequences in the mRNA itself.
- Many eukaryotic mRNAs have a longer lifetime than bacterial mRNAs.
- The longer the lifetime of an mRNA, the more protein it can produce.
What is the main function of the TATA-binding protein?
to promote initiation of transcription
Which of the following events occur when TATA-binding protein binds to the DNA?
An eight-stranded β-sheet domain of the TATA-binding protein lies on the DNA helix.
The DNA backbone is kinked nearly 90 degrees.
Binding leads to assembly of the rest of the transcription complex at the initiation site.
Which is not specifically targeted for destruction by the proteasome?
phosphorylated proteins
Although phosphorylation can trigger ubiquitin modification of a protein and its subsequent degradation, the phosphorylation itself is not directly recognized by the proteasome. Phosphorylation is regularly used to modify activity of proteins and in some cases can lead to ubiquitination.
Which does not affect gene expression at the post-transcriptional level?
DNA methylation
Because DNA methylation takes place on DNA, it does not affect the steps that occur after transcription.
Translation takes place in a series of four steps. Which of these best describes this four-step cycle during elongation?
An aminoacyl-tRNA binds to the vacant A site on the ribosome; a peptide bond forms; the large subunit of the ribosome translocates, moving the bound tRNAs to the E and P sites; the small subunit of the ribosome translocates, ejecting the tRNA from the E site.
Researchers assayed the activity of enzyme F in three different types of tissue from the same mouse by determining the amount of enzyme product produced per milligram of tissue per unit time. As shown in the graph below, results indicate more product generation in the liver compared to the kidney and muscle samples.
Which of the following factors might explain the different results among the three tissues?
differences in the translation of the mRNA encoding the protein among the tissue types
differences in the post-translational modifications of the enzyme among the tissue types
differences in the transcription of the gene encoding the enzyme among the tissue types
An RNA molecule (for example, rRNA or tRNA) within a cell can fold into complex three-dimensional shapes for which reason?
The product of transcription is a single-stranded RNA molecule that can form hydrogen bonds with itself.
Which of the following statements most accurately describes the expression of the repressor protein of the tryptophan operon?
The gene for the tryptophan repressor is expressed constitutively.
The gene for the tryptophan repressor is expressed constitutively. The Trp repressor protein must always be present so as to constantly respond to the levels of tryptophan in the cell.
Proteasomes act primarily on proteins that have been marked for destruction by the attachment of which small protein?
ubiquitin
Proteasomes act primarily on proteins that have been marked for destruction by the attachment of ubiquitin. In fact, multiple rounds of ubiquitination must happen before the protein is accepted into the proteasome.
MicroRNAs regulate the activity of protein-coding genes by doing which of the following?
promoting the degradation of mRNAs
inhibiting the translation of mRNAs
Determine whether the following statement is true or false: In eukaryotes, individual transcription regulators are often involved in controlling the expression of multiple genes. Thus, their interactions with DNA must be weak and relatively non-specific.
False Transcription regulators recognize nucleotide sequences by fitting tightly to the surface features of the DNA double helix, allowing multiple weak interactions such as hydrogen bonds to form, yet resulting in a tight interaction.
c-Met is an oncogene that contributes to the development of certain cancers by triggering cell division and tumor growth. In a 2009 article, Yan and colleagues found regions in the 3’ untranslated region of c-Met mRNA complementary to microRNA-1/206. In addition, higher levels of microRNA-1/206 were associated with slower cell proliferation. What is a likely explanation for the inverse correlation between microRNA-1/206 and cell proliferation?
MicroRNA-1/206 targets c-Met mRNA for destruction via RISC.
MicroRNAs are noncoding regulatory RNAs that regulate gene expression by binding complementary mRNAs, leading to the destruction of the targeted mRNAs.
Introns are removed by which of the following?
RNA splicing in the nucleus
To produce an mRNA in a eukaryotic cell, an RNA transcript of the entire gene, which often includes introns and exons, is made. Splicing to remove the introns takes place in the nucleus, even while transcription of the gene is still occurring.
How does the tRNA synthetase enzyme charge a tRNA with the correct amino acid?
Each different tRNA synthetase has one region that recognizes the tRNA anticodon and a second region that attaches the matching amino acid to the CCA at the 3’ end of the tRNA.
At what site do all charged tRNAs (with the exception of the initiator tRNA) first bind on the ribosome?
A Site
All charged tRNAs (with the exception of the initiator tRNA) first bind on the ribosome at the A site. To add an amino acid to a growing peptide chain, a charged tRNA enters the A site by base-pairing with the complementary codon on the mRNA molecule.
What is an operon?
a set of genes transcribed as a single mRNA from a single promoter
Operons are defined by the coordination of expression of their resident genes under the direction of a single promoter. Each operon produces a single mRNA that encodes multiple proteins.
A reporter gene is an experimentally engineered regulatory DNA sequence from a gene of interest that has been fused to a gene that encodes a protein that is easily observed experimentally. Why is this approach useful?
It provides information into where and when a gene is expressed.
Reporter genes make it easy to view the location and timing of a gene’s expression because the regulatory sequences drive the expression of a gene product that is easily monitored.
Which of the following does not increase the stability of eukaryotic mRNAs?
an intron
Does
a poly-A tail
a 5’-end cap
Researchers often want to isolate a certain type of RNA. For some RNA species, this can be accomplished via affinity chromatography, using beads coated with chains of poly-deoxythymidine (poly-dT). The desired RNA will stick to the beads while unwanted RNAs will flow through the column. The retained RNA can then be eluted.
What RNA species can be purified using this method?
eukaryotic mRNA
Eukaryotic mRNAs end with a long series of adenine residues, which will bind via complementary base-pairing to the thymidine oligomer.
In a patch of animal cell membrane about 10 μm in area, which will be true?
There will be more lipids than proteins.
Proteins constitute about half the mass of an animal cell membrane. Therefore, in terms of mass, proteins and lipids provide an equal share.
However, lipids are much smaller than proteins, so a cell membrane typically contains 50 times more lipid molecules than protein molecules.
Which proteins bind to nuclear localization signals on newly synthesized proteins?
nuclear import receptors
The nuclear localization signal on proteins destined for the nucleus is recognized by cytosolic proteins called nuclear import receptors. These receptors help direct a newly synthesized protein to a nuclear pore by interacting with the tentacle-like fibrils that extend from the rim of the pore into the cytosol.
are the most abundant molecules in the animal cell membrane, whereas ________ make up 50% of the membrane by mass.
Lipids, proteins
Lipids are the most abundant molecule in the cell membrane. Proteins, however, are much more massive and thus, by mass, make up about 50% of the mass of the plasma membrane.
If a signal sequence is removed from an ER protein, what happens to the altered protein?
It remains in the cytosol.
Deleting the signal sequence from an ER protein converts it into a cytosolic protein.
Detergent molecules are ___________ in nature and bind with membrane proteins and membrane lipids to disrupt their interactions and release the proteins from the membrane.
amphipathic
Detergents have a hydrophobic portion that disrupts the hydrophobic interaction of lipids with membrane proteins. They also have a hydrophilic region that stabilizes the protein in solution by interacting with the aqueous environment.
Lysosomes contain ____________ enzymes that can break down diverse macromolecules, cell parts, and microorganisms.
hydrolytic
Lysosomes are a compartment in the cell where ingested cell particles, organelles, or macromolecules can be digested for recycling. The macromolecules from ingestion or from these cell parts are broken down into their building blocks by hydrolytic enzymes and are then exported out of the lysosome for reuse.
Which of the following is a covalent modification that occurs mainly in the ER?
formation of disulfide bonds
Two major covalent modifications occur in the ER. Certain proteins need disulfide bonds to form between cysteines to stabilize their structure, and some proteins have a branched oligosaccharide added to them, which is then matured in the Golgi into the final structure glycoprotein structure.
In a fluorescence recovery after photobleaching (FRAP) experiment, a fluorescently tagged membrane protein, A, shows very little recovery of fluorescence ten minutes after photobleaching, while membrane protein B shows a rapid increase in fluorescence after bleaching, recovering nearly 80% of its original fluorescent signal by ten minutes. Based on this information, which of the following statements can be made?
Protein B is diffusing in a more fluid membrane.
The recovery of fluorescence in FRAP experiments is directly related to the amount of mobility the protein exhibits. This can be due to increased fluidity of the membrane, as well as whether the protein is relatively unconstrained by interactions that would impede on its motion.
Which type of protein binds to improperly folded or improperly assembled proteins in the ER, holding them there until proper folding occurs?
chaperones
Chaperones prevent misfolded proteins from forming aggregates, which helps steer the proteins along the path to proper folding.
Proteins that are associated with the membrane by noncovalent interactions with other membrane proteins are called ___________ proteins.
peripheral membrane
A protein that is associated with the membrane simply by virtue of interacting with another membrane protein are called peripheral membrane proteins. On the other hand, transmembrane, monolayer associated, and lipid-linked proteins are all directly associated with the membrane and are called integral membrane proteins.
In eukaryotic cells, phospholipids are synthesized by enzymes bound to which of the following?
the cytosolic face of the endoplasmic reticulum
New phospholipids are added to the ER membrane asymmetrically. Some of the newly made phospholipids are subsequently moved from the cytosolic monolayer to the other half of the bilayer so that the membrane can grow evenly.
Which type of movement is the least common for lipids in a bilayer?
flip-flop
Lipids rarely flip-flop between the different faces of the bilayer because the polar heads would have to contact the hydrophobic interior of the membrane. This only happens when catalyzed by transporter proteins.
Ricin is one of the most powerful toxins known. The protein consists of two subunits: the A chain is an enzyme that inhibits translation and the B chain is a lectin that binds to carbohydrates on the cell surface. What is the most likely mechanism by which ricin enters the cell?
The protein is internalized by endocytosis.
Ricin is taken up by endocytosis, most likely mediated by its binding to cell-surface receptors.
Proteins have to be unfolded to cross the membranes of which of these organelles?
endoplasmic reticulum
mitochondria
chloroplasts
Proteins moving from the cytosol into these organelles must pass through protein translocators located in the organelle membrane.
Proteins that lack a sorting signal remain as permanent residents of which part of a eukaryotic cell?
Cytosol
Different sorting signals direct proteins into the nucleus, mitochondria, chloroplasts (in plants), peroxisomes, and the ER. Proteins that lack such signals remain as permanent residents of the cytosol.
What is a functionally specialized region of a cell membrane, typically characterized by the presence of specific proteins, called?
membrane domain
Membrane domains are generated when cells restrict the movement of certain membrane proteins to localized areas within a cell membrane.
Which of the following is true of lysosomes?
An ATP-driven H+ pump in the lysosomal membrane maintains the organelle’s pH.
The lysosome is maintained at an acidic pH by a pump in its membrane that hydrolyzes ATP to transport H+ into the lumen.
How are newly made lipids supplied to the plasma membrane?
via the constitutive pathway of exocytosis
This steady supply of lipids enables the plasma membrane to expand prior to cell division and replaces old lipids in nonproliferating cells.
Which term correctly describes the entire phospholipid molecule?
amphipathic
Phospholipids contain both a hydrophilic and hydrophobic component and are therefore amphipathic. This property allows them to form bilayers in water, where the hydrophilic portions interact with the aqueous environment on either side of the membrane, while the hydrophobic portions are shielded from water in the bilayer’s interior.
Why do phospholipids form bilayers in water?
The hydrophilic head is attracted to water, while the hydrophobic tail shuns water
The hydrophilic head can form electrostatic attractions and hydrogen bonds with water, while the hydrophobic tails are insoluble in water.
Which organelle is the major site of new membrane synthesis in a cell?
endoplasmic reticulum
In addition to synthesizing many proteins, the ER serves as the major site for the synthesis of new membranes.
Most mitochondrial and chloroplast proteins are made within which part of the cell?
cytosol
A few mitochondrial and chloroplast proteins are synthesized inside these organelles; however, most are made in the cytosol and subsequently imported.
The low pH inside endosomes leads to what outcome?
causing many internalized receptors to release their cargo
This dissociation allows receptor proteins to be returned to the plasma membrane where they can be reused.
Which organelle is essentially a small sac of digestive enzymes that functions in degrading worn-out organelles, as well as macromolecules and particles taken into the cell by endocytosis?
lysosome
Lysosomes are membranous sacs of hydrolytic enzymes that carry out the controlled intracellular digestion of both extracellular materials and worn-out organelles. They contain about 40 types of hydrolytic enzymes, including those that degrade proteins, nucleic acids, oligosaccharides, and lipids.
Which organelle receives proteins and lipids from the endoplasmic reticulum, modifies them, and then dispatches them to other destinations in the cell?
Golgi apparatus
Soluble proteins and pieces of membrane enter the Golgi network via transport vesicles derived from the ER. Proteins exit from the Golgi network in transport vesicles destined for either the cell surface or another organelle of the endomembrane system.
Proteins destined for the Golgi apparatus, endosomes, lysosomes, and even the cell surface must pass through which organelle?
ER
The ER serves as an entry point for proteins destined for many of the cell’s organelles, as well as for those that remain in the ER itself.
A phospholipid is inserted into the cytosolic side of the ER membrane. Which of the following could randomly reposition this phospholipid to the other (lumen) side of the ER membrane?
scramblase
Scramblase is an enzyme that randomly mixes phospholipids from one face of the ER membrane to the other. Flippases selectively move phospholipids from one face to another.
Which cellular compartment acts as the main sorting station for extracellular cargo molecules taken up by endocytosis?
Endosomes
Endosomes can send material back to the plasma membrane, to a different domain of the plasma membrane, or on to lysosomes for degradation.
Proteins enter which organelle through pores in its membrane?
nucleus
The pores function as selective gates that actively transport specific macromolecules but also allow free diffusion of smaller molecules.
What would happen to a protein that is engineered to contain both a nuclear localization signal and a nuclear export signal?
It would shuttle in and out of the nucleus.
A number of proteins naturally contain both of these signals—for example, proteins that escort mature mRNAs from the nucleus to the cytosol need an export signal to leave the nucleus and a localization signal to re-enter.
Membrane-bound ribosomes and free ribosomes are structurally and functionally identical; they differ only in ..
in the proteins they are making at a particular time.
How does the inclusion of cholesterol affect animal cell membranes?
It tends to make the lipid bilayer less fluid.
Vesicle budding is driven by which of the following?
assembly of a protein coat
After budding from its parent organelle, the vesicle sheds this coat, allowing its membrane to interact directly with the target membrane with which it will fuse.
Which organelle contains enzymes used in a variety of oxidative reactions that break down lipids and destroy toxic molecules?
peroxisome
Peroxisomes are packed with enzymes that digest toxins and synthesize certain phospholipids, including those present in the myelin sheath surrounding nerve cell axons.
The ER signal sequence on a growing polypeptide chain is recognized by a signal-recognition particle (SRP) in the cytosol. What does this interaction accomplish?
It guides the ribosome and its polypeptide to the ER.
The SRP (brown) binds to both the exposed ER signal sequence and the ribosome. This SRP–ribosome complex then binds to an SRP receptor in the ER membrane.
In the α helices of transmembrane proteins, the hydrophobic side chains face which direction?
the outside of the membrane-spanning helix
This arrangement allows the exposed hydrophobic side chains of the α helix to interact with the hydrophobic tails of the lipid bilayer.
When the transport vesicle shown below fuses with the plasma membrane, which monolayer will face the cell cytosol?
The orange monolayer will face the cytosol.
The cytosolic monolayer will always face the cytosol, whether the vesicle is moving between organelles or fusing with the plasma membrane.
You have attached green fluorescent protein (GFP) to the carboxy terminal end of a secreted yeast protein. You express this protein in normal yeast cells, secretory mutant A cells, and secretory mutant B cells (see image).
Using fluorescent microscopy, you observe the expected results, with protein secretion in normal cells, ER accumulation in mutant A, and Golgi apparatus accumulation in mutant B. You also express the GFP-fusion protein in double-mutant yeast cells containing mutations in both the gene underlying mutant A and the gene underlying mutant B. What is the correct location and explanation for where the GFP-fusion protein will accumulate in these A and B double-mutant yeast cells?
The protein will accumulate in the ER because that is an earlier step in the secretory pathway.
If proteins cannot leave the ER, they will never make it to the Golgi apparatus. The double-mutant yeast cells will have the same phenotype as secretory mutant A.
How are proteins destined to function in the ER retained there?
They contain a C-terminal ER retention signal.
This retention signal is recognized by a membrane-bound receptor protein in the ER and Golgi apparatus.
In a lipid bilayer, where do lipids rapidly diffuse?
within the plane of their own monolayer
The lipid bilayer is a two-dimensional fluid in which phospholipids rapidly diffuse within the plane of their own monolayer.
Which of these organelles are surrounded by a double membrane?
mitochondria
chloroplasts
nucleus
The nuclear membranes most likely originated by invagination of the plasma membrane to form a two-layered envelope that surrounds the cell’s DNA; mitochondria and chloroplasts evolved from bacteria that were engulfed by primitive eukaryotic cells.
Which organelle sorts ingested molecules and recycles some of them back to the plasma membrane?
endosome
Eukaryotic cells continually ingest bits of their plasma membrane, along with small amounts of extracellular fluid, in the process of pinocytosis. Most material taken up by cells in this manner is rapidly delivered to endosomes, which serve as sorting stations for ingested material.
Fluorescence recovery after photobleaching (FRAP) is used to monitor the movement of fluorescently labeled molecules within the plane of a cell membrane. The molecules labeled are often proteins, but lipids can be labeled too.
How would the curve that represents FRAP for labeled proteins compare to the curve representing labeled lipids?
The FRAP curve for lipids would show a much more rapid recovery to initial levels of fluorescence.
Name the organelle that proteins can enter as they are being synthesized.
ER
Most of the proteins that enter the ER begin to be threaded across the ER membrane before the polypeptide chain has been released from the ribosome.
Which proteins play a central role in the fusion of a vesicle with a target membrane?
SNAREs
SNARE proteins on the vesicle interact with SNARE proteins in the target membrane to help vesicles dock. By winding around each other tightly, SNARE proteins pull the membrane bilayers close enough to allow their lipids to flow together.
Which is a mechanism for restricting the movement of proteins in the plasma membrane?
tethering proteins to the extracellular matrix
tethering proteins to the surface of another cell
using barriers such as tight junctions
tethering proteins to the cell cortex
To restrict the movement of proteins in the plasma membrane, the proteins can be tethered to structures outside the cell, such as molecules in the extracellular matrix or on an adjacent cell, or to relatively immobile structures inside the cell, such as the cell cortex.
They can also be corralled within barriers, such as those created by tight junctions that seal adjacent epithelial cells.
Which of the following would produce the most fluid lipid bilayer?
phospholipids with tails of 18 carbon atoms and two double bonds
A shorter chain length and double bonds both reduce the tendency of the phospholipid tails to interact with one another, thereby increasing the fluidity of the membrane.
Viruses such as influenza and HIV enter cells via which of these processes?
receptor-mediated endocytosis
Some viruses can bind to cell-surface receptors and be taken in by clathrin-coated vesicles.
What enables proteins destined for nuclear import to pass through the nuclear pore?
They are recognized by receptors that interact with repeated amino acid sequences in proteins lining the nuclear pore.
The nuclear localization signal on proteins destined for the nucleus is recognized by cytosolic proteins called nuclear import receptors. These receptors help direct a newly synthesized protein to a nuclear pore by interacting with the tentacle-like fibrils that extend from the rim of the pore; the receptors then interact with short, repeated amino acid sequences within the tangle of nuclear pore proteins that fill the center of the pore.
Eukaryotic cells continually ingest bits of their plasma membrane, along with small amounts of extracellular fluid. The lost pieces of membrane are replaced by what process?
exocytosis
As much membrane is added to the cell surface by exocytosis as is removed by pinocytosis.
All of the carbohydrates in the plasma membrane face the cell exterior. Which direction do the carbohydrates on internal cell membranes face?
the lumen of the vesicle or organelle
Glycolipids are located only in the noncytosolic half of the bilayer; the same orientation holds true for glycoproteins. For the plasma membrane, this means that sugars face the cell exterior. For internal membranes, any sugars will face the lumen of the vesicle or organelle.
See Hint
Investigators have engineered a gene that encodes a protein bearing an ER signal sequence followed by a nuclear localization signal. What would be the likely fate of that protein?
The protein will be recognized by an SRP and enter the ER.
Because proteins enter the ER while they are being made, the N-terminal ER signal sequence will likely be recognized by an SRP before the nuclear localization signal has even been synthesized.
On what side of the plasma membrane are the carbohydrate chains of glycoproteins, proteoglycans, and glycolipids located?
the extracellular side
The sugars on plasma membrane glycolipids, glycoproteins, and proteoglycans all face the cell exterior, where they form a carbohydrate layer or glycocalyx that coats the surface of the cell.
Which of the following correctly describe steps required for protein transport into the rough ER?
- recognition and binding of the protein signal sequence by SRP
- passing of the protein to a protein translocation channel in the ER membrane
- cleavage of the signal sequence from the protein by signal peptidase
Which of the following would be most likely to disrupt lipid bilayer formation?
addition of a phosphate to the end of the lipid tail
Imagine you collected bacteria from the sediment in a frozen lake in Minnesota in January and compared the membranes to membranes from bacteria collected from a lake in Texas in June. Consider how the membranes would likely differ.
The membranes in bacteria from the Minnesota lake would most likely have which of the following?
more unsaturated lipid tails than membranes in Texas bacteria
ATP is important for chaperone protein function. Why would protein import into mitochondria be disrupted if ATP were depleted from inside mitochondria?
The protein could slip back out of the mitochondria during transport.
The FRAP technique occurs in a series of steps. Select every statement that correctly describes a step in the FRAP procedure.
The relative mobility of the fluorescently labeled molecule is measured.
The molecule of interest is fluorescently labeled.
How are misfolded proteins and incompletely assembled proteins retained in the ER?
Chaperone proteins bind them and prevent their entry into vesicles.
Misfolded proteins or incompletely assembled protein complexes are bound by chaperone proteins that help guide their proper folding. This prevents them from leaving the ER or from aggregating and causing issues while folding is attempted.
