Molec cell - Exam 1 help (Chap 4-8, 11)

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The instructions specified by the DNA will ultimately specify the sequence of proteins. This process involves DNA, made up of ____ different nucleotides, which gets _________________ into RNA, which is then _________________into proteins, made up of _____ different amino acids. In eukaryotic cells, DNA gets made into RNA in the _________________, while proteins are produced from RNA in the _________________. The segment of DNA called a_________________ is the portion that is copied into RNA; this process is catalyzed by RNA _________________.

- 4 - transcribed - translated - 20 - nucleus - cytoplasm - gene - polymerase

Each chromosome is a single molecule of __________________ whose extraordinarily long length can be compacted by as much as __________________-fold extraordinarily long length can be compacted by as much as 1000-fold during _________________ and tenfold more during __________________. This is accomplished by binding to __________________ that help package the DNA that help package the DNA in an orderly manner so it can fit in the small space delimited by the __________________. The structure of the DNA-protein complex, called __________________, is highly __________________ over time.

- DNA - 1000 - interphase - mitosis - proteins - nuclear envelope - chromatin - dynamic

MicroRNAs are noncoding RNAs that are incorporated into a protein complex called __________________, which searches the __________________s in the cytoplasm for sequence complementary to that of the miRNA. When such a molecule is found, it is then targeted for __________________. RNAi is triggered by the presence of foreign __________________ molecules, which are digested by the __________________ enzyme into shorter fragments approximately 23 nucleotide pairs in length.

- RISC - mRNA - destruction - double-stranded RNA - Dicer

In eukaryotic cells, general transcription factors are required for the activity of all promoters transcribed by RNA polymerase II. The assembly of the general transcription factors begins with the binding of the factor __________________ to DNA, causing a marked local distortion in the DNA. This factor binds at the DNA sequence called the __________________ box, which is typically located 25 nucleotides upstream from the transcription start site.Once RNA polymerase II has been brought to the promoter DNA,it must be released to begin making transcripts. This release process is facilitated by the addition of phosphate groups to the tail of RNA polymerase by the factor __________________. It must be remembered that the general transcription factors and RNA polymerase are not sufficient to initiate transcription in the cell andare affected by proteins bound thousands of nucleotides away from the promoter. Proteins that link the distantly bound transcription regulators to RNA polymerase and the general transcription factors include the large complex of proteins called the__________________. The packing of DNA into chromatin also affects transcriptional initiation, and histone __________________ is an enzyme that can render the DNA less accessible to the general transcription factors.

- TFIID - TATA - TFIIH - mediator - deacetylase

The human immune system produces __________________ of different immunoglobulins, also called __________________, which enable the immune system to recognize and fight germs by specifically binding one or a few related __________________. The hypervariable structural element that forms the ligand-binding site is comprised of several __________________. Purified antibodies are useful for a variety of experimental purposes, including protein purification using __________________ chromatography. affinity, billions, ligands, antibodies, coiled coils, loops, antigens, hundreds, size-exclusion, Beta strands, ion-exchange

- billions - antibodies - antigens - loops - affinity

In eukaryotic __________________, DNA is complexed with proteins to form __________________. The paternal and maternal copies of human Chromosome 1 are __________________, hereas the paternal copy of Chromosome 1 and the maternal copy of Chromosome 3 are __________________. Cytogeneticists can determine large-scale chromosomal abnormalities by looking at a patient's __________________. Fluorescent molecules can be used to paint a chromosome, by a technique that employs DNA __________________, and thereby to identify each chromosome by microscopy.

- chromosomes - chromatin - homologous - non-homologous - karyotype - hybridization

he transmission of information important for gene regulation from parent to daughter cell, without altering the actual nucleotide sequence, is called_________________ inheritance. This type of inheritance is seen with the inheritance of the covalent modifications on ____________ proteins bound to DNA; these modifications are important for re-establishing the pattern of chromatin structure found on the parent chromosome. Another way to inherit chromatin structure involves DNA __________, a covalent modification that occurs on cytosine bases that typically turns off the transcription of a gene. Gene transcription patterns can also be transmitted across generations through positive _____________ loops that can involve a transcription regulator activating its own transcription in addition to other genes. These mechanisms all allow for cell ________________, a property involving the maintenance of gene expression patterns important for cell identity.

- epigenetic - histone - methylation - feedback - memory

During transcription in __________________ cells, transcriptional regulators that bind to DNA thousands of nucleotides away from a gene's promoter can affect a gene's transcription. The __________________ is a complex of proteins that links distantly bound transcription regulators with the proteins bound closer to the transcriptional start site. Transcriptional activators can also interact with histone __________________s, which alter chromatin by modifying lysines in the tail of histone proteins to allow greater accessibility to the underlying DNA. Gene repressor proteins can reduce the efficiency of transcription initiation by attracting histone __________________s. Sometimes,many contiguous genes can become transcriptionally inactive as a result of chromatin remodeling, like the __________________ found in interphase chromosomes.

- eukaryotic - mediator - actylases - deacetylases - heterochromatin

Interphase chromosomes contain both darkly staining __________________ and more lightly staining __________________. Genes that are being transcribed are thought to be packaged in a __________________ condensed type of euchromatin. Nucleosome core particles are separated from each other by stretches of __________________ DNA. A string of nucleosomes coils up with the help of __________________ to form the more compact structure of the __________________. A __________________ model describes the structure of the 30-nm fiber. The 30 nm chromatin fiber is further compacted by the formation of __________________ that emanate from a central __________________.

- heterochromatin - euchromatin - less - linker - histone H-1 - 30nm fiber - zigzags - loops - axis

Any substance that will bind to a protein is known as its__________________. Enzymes bind their __________________ at the__________________. The enzyme hexokinase is so specific that it reacts with only one of the two __________________ of glucose. Enzymes catalyze a chemical reaction by lowering the __________________, because they provide conditions favorable for the formation of a __________________ intermediate called the __________________. Once the reaction is completed, the enzyme releases the __________________ of the reaction. activation energy, inhibitors, products, active site, isomers, substrates, free energy, ligand, transition state, high-energy, low-energy

- ligand - substrates - active site - isomers - activation energy - high-energy - transition site - products

The genes of a bacterial __________________ are transcribed into a single mRNA.Many bacterial promoters contain a region known as a(n) __________________, to which a specific transcription regulator binds. Genes in which transcription is prevented are said to be __________________. The interaction of small molecules, such as tryptophan, with __________________ DNA-binding proteins, such as the tryptophan repressor, regulates bacterial genes. Genes that are being __________________ expressed are being transcribed all the time.

- operon - operator - repressed - allosteric - constitutively

The specialized functions of different membranes are largely determined by the __________________ they contain. Membrane lipids are__________________ molecules, composed of a hydrophilic portion and a hydrophobic portion. All cell membranes have the same__________________ structure, with the __________________ of the phospholipids facing into the interior of the membrane and the__________________ on the outside. The most common lipids in most cell membranes are the __________________. The head group of a glycolipid is composed of __________________.

- proteins - amphipathic - lipid bilayer - fatty acid tails - hydrophilic head groups - phospholipids - sugars

Cell-free extracts from S-strain cells of S. pneumoniae were fractionated to __________________ DNA,RNA, protein, and other cell components. Each fraction was then mixed with __________________ cells of S. pneumoniae. Its ability to change these into cells with __________________ properties resembling the __________________cells was tested by injecting the mixture into mice. Only the fraction containing __________________was able to __________________ the __________________ cells was able to transform the R-strain cells to _________________ (or __________________ ) cells that could kill mice.

- purify - R-strain - pathogenic - S-strain - DNA - transform - R-strain - pathogens - S-strain

The Alpha helices and Beta sheets are examples of protein __________________ structure. A protein such as hemoglobin, which is composed of more than one protein __________________, has __________________ structure. A protein's amino acid sequence is known as its __________________ structure. A protein __________________ is the modular unit from which many larger single-chain proteins are constructed. The three-dimensional conformation of a protein is its __________________ structure. allosteric, ligand, secondary, domain, primary, subunit, helix, quaternary, tertiary

- secondary - subunit - quaternary - primary - domain - tertiary

A newly synthesized protein generally folds up into a__________________ conformation. All the information required to determine a protein's conformation is contained in its amino acid __________________. On being heated, a protein molecule will become __________________ as a result of breakage of __________________ bonds. On removal of urea, an unfolded protein can become __________________. The final folded conformation adopted by a protein is that of __________________ energy. composition, irreversible, reversible, covalent, lowest, sequence, denatured, noncovalent, stable, highest, renatured, unstable

- stable - sequence - denatured - noncovalent - renatured - lowest

For a cell's genetic material to be used, the information is first copied from the DNA into the nucleotide sequence of RNA in a process called__________________. __________________ molecules code for proteins, __________________ molecules act as adaptors for protein synthesis, __________________ molecules are integral components of the ribosome, and__________________ molecules are important in the splicing of RNA transcripts.

- transcription - mRNA - tRNA - rRNA - snRNA

There are several ways that membrane proteins can associate with the cell membrane. Membrane proteins that extend through the lipid bilayer are called __________________ proteins and have __________________regions that are exposed to the interior of the bilayer. On the other hand,membrane-associated proteins do not span the bilayer and instead associate with the membrane through an α helix that is__________________. Other proteins are __________________ attached to lipid molecules that are inserted in the membrane.__________________ membrane proteins are linked to the membrane through noncovalent interactions with other membrane-bound proteins.

- transmembrane - hydrophobic - amphipathic - covalently - Peripheral

Name three covalent modifications that can be made to an RNA molecule in eukaryotic cells before the RNA molecule becomes a mature mRNA.

1. A poly A tail is added. 2. A 5′ cap is added. 3. Introns can be spliced out.

List three ways in which the process of eukaryotic transcription differs from the process of bacterial transcription

1. Bacterial cells contain a single RNA polymerase, whereas eukaryotic cells have three. 2. Bacterial RNA polymerase can initiate transcription without the help of additional proteins, whereas eukaryotic RNA polymerases need general transcription factors. 3. In eukaryotic cells, transcription regulators can influence transcriptional initiation thousands of nucleotides away from the promoter, whereas bacterial regulatory sequences are very close to the promoter. 4. Eukaryotic transcription is affected by chromatin structure and nucleosomes, whereas bacteria lack nucleosomes.

Give a reason why DNA makes a better material than RNA for the storage of genetic information, and explain your answer.

1. The deoxyribose sugar of DNA makes the molecule much less susceptible than RNA to breakage, because of the lack of the hydroxyl group on carbon 2 of the ribose sugar. 2. DNA is double-stranded and therefore the complementary strand provides a template from which damage can be repaired accurately. 3. The use of "T" in DNA instead of "U" (as in RNA) protects against the effect of deamination, a common form of damage. Deamination of Tproduces an aberrant base (methyl C), whereas deamination of Ugenerates C, a normal base. The presence of an abnormal base eases the cell's job of recognizing the damaged strand.

Cell membranes are fluid, and thus proteins can diffuse laterally within the lipid bilayer. However, sometimes the cell needs to localize proteins to a particular membrane domain. Name three mechanisms that a cell can use to restrict a protein to a particular place in the cell membrane.

1. The protein can be attached to the cell cortex inside the cell. 2. The protein can be attached to the extracellular matrix outside the cell. 3. The protein can be attached to other proteins on the surface of a different cell. 4. The protein can be restricted by a diffusion barrier, such as that set up by specialized junctional proteins at a tight junction.

Because hydrogen bonds hold the two strands of a DNA molecule together, the strands can be separated without breaking any covalent bonds. Every unique DNA molecule "melts" at a different temperature. In this context, Tm, melting temperature, is the point at which two strands separate, or become denatured. Order the DNA sequences listed below according to relative melting temperatures(from lowest Tm to highest Tm). Assume that they all begin as stable double stranded DNA molecules. Explain your answer. A. GGCGCACC B. TATTGTCT C. GACTCCTG D. CTAACTGG

1—B; 2—D; 3—C; 4—A All the DNA molecules are the same length, so only the A + T and G + C content determine their relative Tm. Molecules with higher G + C content will be more stable than molecules with a high A + T content. This is because there are three hydrogen bonds between each G-C base pair but only two between each A-T base pair. More energy (heat) is required to disrupt a larger number of hydrogen bonds.

Figure Q7-6 shows a ribose sugar. RNA bases are added to the part of the ribose sugar pointed to by arrow _____. (a) 3. (b) 4. (c) 5. (d) 6.

Given the sequence of one strand of a DNA helix as 5′-GCATTCGTGGGTAG-3′, give the sequence of the complementary strand and label the 5′ and 3′ ends.

5′-CTACCCACGAATGC-3′.

For each of the following indicate whether the individual folded polypeptide chain forms a globular (G) or fibrous (F) protein molecule. A. keratin B. lysozyme C. elastin D. collagen E. hemoglobin F. actin

A --> F B --> G C --> F D --> F E --> G F --> G

A. Define a gene B. Consider two different species of yeast that have similar genome sizes. Is it likely that they contain the same number of genes? A similar number of chromosomes? C. Figure 5-15 in the textbook shows the G + C content and genes found along a single chromosome. Is there any relationship between the G + C content and the locations of genes?

A gene is a segment of DNA that stores the information required to specify the particular sequence found in a protein (or, in some cases, the sequence of a structural or catalytic RNA). B. A similar genome size indicates relatively little about the number of genes and virtually nothing about the number of chromosomes. For example, the commonly studied yeasts Saccharomyces cerevisiae (Sc) and Schizosaccharomyces pombe (Sp) are separated by roughly 400 million years of evolution, and both have a genome of 14 million base pairs. Yet Sc has 6500 genes packaged into 16 chromosomes and Sp has 4800 genes in 3 chromosomes C. Regions of the chromosome with a high density of genes tend to have about 50%G + C, whereas those with few genes tend to have a lower G + C content. This is generally true in most organisms.

True or False: A. The amino acids in the interior of a protein do not interact with the ligand and do not play a role in selective binding. B. Antibodies are Y shaped and are composed of six different polypeptide chains. C. ATPases generate ATP for the cell. D. Hexokinase recognizes and phosphorylates only one of the glucose stereoisomers. E. Protein phosphorylation is another way to alter the conformation of an enzyme and serves exclusively as a mechanism to increase enzyme activity. F. GTP binding proteins typically have GTPase activity, and the hydrolysis of GTP transforms them to the "off" conformation.

A. False - The interior amino acids form a structural scaffold that maintains the specific orientation for those that directly interact with the ligand. Changes to these interior amino acids can change the protein shape and render it nonfunctional. B. False. Although antibodies are Y shaped, they are composed of four, not six, polypeptide chains. There are two heavy chains and two light chains. C. False. ATPases hydrolyze ATP; they do not produce it. These enzymes enable the cell to harness the chemical energy stored in the high-energy phosphate bonds D. True E. False - Although phosphorylation of a protein can change its conformation, this modification may be either as a positive or a negative regulator of enzymes F. True

True or false: A. Generally, the total number of nonpolar amino acids has a greater effect on protein structure than the exact order of amino acids in a polypeptide chain. B. The "polypeptide backbone" refers to all atoms in a polypeptide chain, except for those that form the peptide bonds. C. The chemical properties of amino acid side chains include charged, uncharged polar, and nonpolar. D. The relative distribution of polar and nonpolar amino acids in a folded protein is determined largely by hydrophobic interactions, which favor the clustering of nonpolar side chains in the interior. E. Feedback inhibition is defined as a mechanism of down-regulating enzyme activity by the accumulation of a product earlier in the pathway. F. If an enzyme's allosteric binding site is occupied, the enzyme may adopt an alternative conformation that is not optimal for catalysis.

A. False - The order in which amino acids are linked is unique for each protein and is the most important factor in determining overall protein structure. B. False - Peptide bonds are planar amide bonds that are central to the polypeptide backbone formation. The atoms in the amino acid side chains are not considered to be part of the backbone. C. True D. True E. False - Feedback inhibition occurs when an enzyme acting early in a metabolic pathway is inhibited by the accumulation of a product late in the pathway. The inhibitory product binds to a site on the enzyme that lowers its catalytic F. True

True/False A. DNA molecules, like proteins, consist of a single, long polymeric chain that is assembled from small monomeric subunits. B. The polarity of a DNA strand results from the polarity of the nucleotide subunits. C. There are five different nucleotides that become incorporated into a DNA strand. D. Hydrogen bonds between each nucleotide hold individual DNA strands together.

A. False --> DNA is double-stranded. It is actually is made of two polymers that are complementary in sequence. B. True C. False --> There are four different nucleotides that are used to make a DNA polymer: adenine, thymine, guanine, and cytosine. A fifth nucleotide, uracil, is found exclusively in RNA molecules, replacing thymine nucleotides in the DNA sequence. D. False --> Nucleotides are linked covalently through phosphodiester bonds. Hydrogen-bonding between nucleotides from opposite strands holds the DNA molecule together.

Indicate whether the following statements are true or false. If a statement is false,explain why it is false. A. When a mouse cell is fused with a human cell, the movement of the respective membrane proteins is restricted to their original locations at the time of fusion. B. Epithelial cell membranes are asymmetric, and proteins from the apical side of the cell membrane cannot diffuse into the basal side of the membrane. C. The longest carbohydrates found on the surfaces of cells are linked to lipid molecules. D. The only role of the carbohydrate layer on the cell surface is to absorb water, which creates a slimy surface and prevents cells from sticking to each other.

A. False. After about 1 hour, the mouse and human proteins present on the surface of the fused cell are found evenly dispersed throughout the plasma membrane. B. True. C. False. The very long, branched polysaccharides that are attached to integral membrane proteins are much longer than the oligosaccharides covalently attached to membrane lipids. D. False. Although the absorption of water is an important role of the carbohydrates on the surface of the plasma membrane, a second critical role is that of cell-cell recognition, which is important in immune responses, wound healing, and other processes that rely on cell-type-specific interactions.

TRUE / FALSE A. Lipid-linked proteins are classified as peripheral membrane proteins because the polypeptide chain does not pass through the bilayer. B. A protein can be embedded on the cytosolic side of the membrane bilayer by employing a hydrophobic α helix. C. A protein that relies on protein-protein interactions to stabilize its membrane association is classified as a peripheral membrane protein because it can be dissociated without the use of detergents. D. Membrane proteins that pump ions in and out of the cell are classified as enzymes.

A. False. Lipid-linked proteins are classified as integral membrane proteins because although they are not transmembrane proteins, they are covalently bound to membrane lipids and cannot be dissociated without disrupting the membrane's integrity. B. False. An embedded protein employs an amphipathic helix. The hydrophobic side interacts with the fatty acid tails of the membrane lipids, and the hydrophilic portion interacts with the aqueous components of the cytosol. C. True. D. False. Membrane proteins that pump ions in either direction across the membrane are in the functional class of transporters.

TRUE / FALSE A. In order to study the activity of isolated transmembrane proteins, the membrane lipids must be completely stripped away. B. FRAP is a method used to study the movement of individual proteins. C. SDS is a mild detergent that is useful for the reconstitution of membrane components. D. The speed of fluorescent signal recovery during a FRAP assay is a measure of lateral mobility for the molecule of interest.

A. False. The region of the protein that normally crosses the membrane must be stabilized by the presence of phospholipids for the purified protein to be active.For this reason, purified membrane proteins are often reconstituted into artificial lipid bilayers. B. False. The FRAP method involves photobleaching of a small region of the membrane, which contains hundreds of target molecules, and follows the displacement of these molecules with neighboring molecules that have not been bleached. C. False. SDS is a strong, ionic detergent that will break up membrane bilayers andalso denature proteins. D. True.

True/False A. When DNA is being replicated inside a cell, local heating occurs, allowing the two strands to separate. B. DNA replication origins are typically rich in G-C base pairs. C. Meselson and Stahl ruled out the dispersive model for DNA replication. D. DNA replication is a bidirectional process that is initiated at multiple locations along chromosomes in eukaryotic cells.

A. False. The two strands do need to separate for replication to occur, but this is accomplished by the binding of initiator proteins at the origin of replication. B. False. DNA replication origins are typically rich in A-T base pairs, which are held together by only two hydrogen bonds (instead of three for C-G base pairs),making it easier to separate the strands at these sites. C. True D. True

True/False A. Comparing the relative number of chromosome pairs is a good way to determine whether two species are closely related. B. Chromosomes exist at different levels of condensation, depending on the stage of the cell cycle. C. Eukaryotic chromosomes contain many different sites where DNA replication can be initiated. D. The telomere is a specialized DNA sequence where microtubules from the mitotic spindle attach to the chromosome so that duplicate copies move to opposite ends of the dividing cell.

A. False. There are several examples of closely related species that have a drastically different number of chromosome pairs. Two related species of deer—Chinese and Indian muntjac—have 23 and 3, respectively. B. True. C. True. D. False. The telomere is a specialized DNA sequence, but not for the attachment of spindle microtubules. Telomeres form special caps that stabilize the ends of linear chromosomes.

Consider the structure of the DNA double helix. A. You and a friend want to split a double-stranded DNA molecule so you each have half. Is it better to cut the length of DNA in half so each person has a shorter length, or to separate the strands and each take one strand? Explain B. In the original 1953 publication describing the discovery of the structure of DNA, Watson and Crick wrote, "It has not escaped our notice that the specific pairings we have postulated immediately suggest a possible copying mechanism for the genetic material." What did they mean?

A. It is better to separate the strands and each take a single strand, because all of the information found in the original molecule is preserved in a full-length single strand but not in a half-length double-stranded molecule. B. Watson and Crick meant that the complementary base pairing of the strands allows a single strand to contain all of the information necessary to direct the synthesis of a new complementary strand.

Data for the mobility of three different proteins (X, Y, and Z) using fluorescence recovery after photobleaching (FRAP) are shown in Figure Q11-60 A. Separately,single-particle tracking (SPT) data were collected for these samples, as shown in Figure Q11-60BA. Assign an SPT profile (A, B, or C) to each of these proteins on the basis of the respective FRAP profiles. B. It is important to remember that in each of these experiments, the results reflect a real, physical difference in the way in which these proteins are situated in the plasma membrane. Provide a plausible explanation for the differences observed in proteins X, Y, and Z.

A. Protein X should have an SPT profile as shown in (B); FRAP data for protein Y correlates with SPT data shown in (A); and Z seems to have intermediate mobility, as shown in the SPT profile (C). B. Protein X is highly mobile, so it is probably a small protein that is not anchored to anything and is not part of a larger, multiprotein complex. Protein Y is relatively immobile, indicating that it is probably anchored to the cell cortex. Protein Z ismobile, but less so than protein X. If protein Z bound to other proteins as part of a complex, the higher molecular weight would retard its observed movement in the membrane.

Sodium dodecyl sulfate (SDS) and Triton X-100 are both detergents that can be used to lyse cells. A. If the goal is to study the activity of membrane proteins after cell lysis,explain why SDS would not be a good choice. B. How does Triton X-100 work in cell lysis, and why is it a better choice of detergent to help you extract proteins?

A. SDS is a strong ionic detergent. When cells are exposed to SDS, membrane proteins are not only extracted from the membrane, they are completely unfolded.After denaturation, they cannot be studied as functional molecules. B. Triton X-100 has a smaller nonpolar portion and a polar but uncharged end, allowing it to mimic more closely the type of solvation effect of the membrane lipids. Triton X-100 forms a shell around the hydrophobic portion of the protein without disrupting the existing structure. This makes it possible to then place the protein into a new, synthetic membrane bilayer for study.

You have discovered an operon in a bacterium that is turned on only when sucrose is present and glucose is absent. You have also isolated three mutants that have changes in the upstream regulatory sequences of the operon and whose behavior is summarized in the Table Q8-28. You hypothesize that there are two gene regulatory sites, A and B, in the upstream regulatory sequence that are affected by the mutations. For this question, a plus (+) indicates a normal site and a minus (-) indicates amutant site that no longer binds its transcription regulator. A. If mutant 1 has sites A- B+, which of these sites is regulated by sucrose and which by glucose? B. Give the state (+ or -) of the A and B sites in mutants 2 and 3. C. Which site is bound by a repressor and which by an activator?

A. Site A is regulated by sucrose, and site B by glucose. B. Mutant 2 (A+ B-); mutant 3 (A- B-) or (A- B+). C. Site A is bound by an activator, and site B by a repressor.

Glycolipids are found on the surface of healthy cells, and contribute to the cell's defense against chemical damage and infectious agents. A. In which organelle are sugar groups added to membrane lipids? B. By what mechanism are glycolipids transported to the plasma membrane and presented to the extracellular environment? Draw a diagram to support your answer to part B.

A. The Golgi apparatus. B. Membranes that contain newly synthesized glycolipids bud from the Golgi apparatus to form vesicles. These vesicles then fuse with the plasma membrane.The glycolipids that were facing the lumen of the Golgi will now face the extracellular environment (Figure A11-26).

The human genome comprises 23 pairs of chromosomes found in nearly every cell in the body. Answer the quantitative questions below by choosing one of the numbers in the following list: 23, 46, 69, 92, >200, >10^9 A. How many centromeres are in each cell? What is the main function of the centromere? B. How many telomeres are in each cell? What is their main function? C. How many replication origins are in each cell? What is their main function?

A. There are 46 centromeres per cell, one on each chromosome. The centromeres have a key role in the distribution of chromosomes to daughter cells during mitosis. B. There are 92 telomeres per cell, two on each chromosome. Telomeres serve to protect the ends of chromosomes and to enable complete replication of the DNA of each chromosome all the way to its tips. C. There are far more than 200 replication origins in a human cell, probably about 10,000. These DNA sequences direct the initiation of DNA synthesis needed to replicate chromosomes.

True/False A.Primase is needed to initiate DNA replication on both the leading strand and the lagging strand. B. The sliding clamp is loaded once on each DNA strand, where it remains associated until replication is complete. C. Telomerase is a DNA polymerase that carries its own RNA molecule to use as a primer at the end of the lagging strand. D. Primase requires a proofreading function that ensures there are no errors in the RNA primers used for DNA replication.

A. True B. False. Although the sliding clamp is only loaded once on the leading strand, the lagging strand needs to unload the clamp once the polymerase reaches the RNA primer from the previous segment and then reload it where a new primer has been synthesized. C. True D. False. Primase does not have a proofreading function, nor does it need one because the RNA primers are not a permanent part of the DNA. The primers are removed, and a DNA polymerase that does have a proofreading function fills in the remaining gaps.

True/False A. Ionizing radiation and oxidative damage can cause DNA double-strand breaks. B. After damaged DNA has been repaired, nicks in the phosphate backbone are maintained as a way to identify the strand that was repaired. C. Depurination of DNA is a rare event that is caused by ultraviolet irradiation. D. Nonhomologous end joining is a mechanism that ensures that DNA double-strand breaks are repaired with a high degree of fidelity to the original DNA sequence.

A. True B. False. It is believed that the knicks are generated during DNA replication as a means of easy identification of the newly synthesized strand but are sealed by DNA ligase shortly after replication is completed. C. False. Depurination occurs constantly in our cells through spontaneous hydrolysis of the bond linking the DNA base to the deoxyribose sugar. D. False. Homologous recombination can repair double-strand breaks without any change in DNA sequence, but nonhomologous end joining always involves a loss of genetic information because the ends are degraded by nucleases before they can be ligated back together.

TRUE / FALSE A. Although cholesterol is a hydrophobic molecule, it has a hydrophilic head group like all other membrane lipids. B. Phosphatidylserine is the most abundant type of phospholipid found in cell membranes. C. Glycolipids lack the glycerol component found in phospholipids. D. The highly ordered structure of the lipid bilayer makes its generation and maintenance energetically unfavorable.

A. True. B. False. Phosphatidylcholine is the most abundant phospholipid found in cell membranes. C. True. D. False. The formation of a lipid bilayer is energetically favorable.

In an attempt to define the protein domains of protein X, you treat it with a protease and use polyacrylamide gel electrophoresis to analyze the peptides produced. In the past, you have used chymotrypsin to perform this experiment, but the stock of this enzyme has been used up . You find a stock of elastase and decide to use it instead of waiting for a new stock of chymotrypsin to arrive. A. Give two reasons why elastase is a good substitute for chymotrypsin in this assay. B. Why might proteolysis of the same substrate by chymotrypsin or elastase yield different results?

A. You might assume that chymotrypsin and elastase would yield the same results because (1) they are both serine proteases and (2) they have a high degree of structural similarity. B. The slight structural differences of the substrates cause the enzymatic activity of the protease to differ. As a result, they have different substrate affinities and cleave the bond between a different set of amino acids.

For each of the following sentences, choose one of the options enclosed in square brackets to make a correct statement about nucleosomes. A. Nucleosomes are present in [prokaryotic/eukaryotic] chromosomes, but not in [prokaryotic/eukaryotic] chromosomes. B. A nucleosome contains two molecules each of histones [H1 and H2A/H2A and H2B] as well as of histones H3 and H4. C. A nucleosome core particle contains a core of histone with DNA wrapped around it approximately [twice/three times/four times]. D. Nucleosomes are aided in their formation by the high proportion of [acidic/basic/polar] amino acids in histone proteins. E. Nucleosome formation compacts the DNA into approximately [one-third/one hundredth/ one-thousandth] of its original length.

A. eukaryotic --- prokaryotic B. H2A and H2B --- H3 and H4 C. twice D. basic E. one-third

Three different membrane components are shown in Figure Q11-10. Using the list below, identify the three components, and label the chemical groups indicated

A. glycerol B. sugar C. phospholipid D. glycolipid E. sterol F. unsaturated hydrocarbon G. saturated hydrocarbon H. sterol polar head group

For each polypeptide sequence listed, choose from the options given below to indicate which secondary structure the sequence is most likely to form upon folding. The non-polar amino acids are italicized. A. Leu-Gly-Val-Leu-Ser-Leu-Phe-Ser-Gly-Leu-Met-Trp-Phe-Phe-Trp-Ile B. Leu-Leu-Gln-Ser-Ile-Ala-Ser-Val-Leu-Gln-Ser-Leu-Leu-Cys-Ala-Ile C. Thr-Leu-Asn-Ile-Ser-Phe-Gln-Met-Glu-Leu-Asp-Val-Ser-Ile-Arg-Trp -amphipathic α helix -hydrophilic α helix -hydrophobic α helix -amphipathic β sheet -hydrophilic β sheet

A. hydrophobic α helix B. Amphipathic α helix C. Amphipathic β sheet

A. Protein A binds to its DNA binding site [more tightly/less tightly] thanprotein B binds to its DNA binding site. B. Protein A is a [stronger/weaker] activator of transcription than protein B. C. Protein C is able to prevent activation by [protein A only/protein Bonly/both protein A and protein B].

A. more tightly B. weaker C. both protein A and protein B

Imagine that an RNA polymerase is transcribing a segment of DNA that contains the following sequence: 5′-AGTCTAGGCACTGA-3′ 3′-TCAGATCCGTGACT 5′ A. If the polymerase is transcribing from this segment of DNA from left to right, which strand (top or bottom) is the template? B. What will be the sequence of that RNA (be sure to label the 5′ and 3′ ends of your RNA molecule)?

A. the bottom strand B. 5′-AGUCUAGGCACUGA-3′

True/False A. Each strand of DNA contains all the information needed to create a new double-stranded DNA molecule with the same B. All functional DNA sequences inside a cell code for protein products. C. Gene expression is the process of duplicating genes during DNA replication. D. Gene sequences correspond exactly to the respective protein sequences produced

A. true B. False --> Some sequences encode only RNA molecules, some bind to specific regulatory proteins, and others are sites where specific chromosomal protein structures are built (for example, centromeric and telomeric DNA). C. False --> Gene expression is the process of going from gene sequence to RNA sequence, to protein sequence. D. False --> This statement is false for two reasons. First, genes often contain intron sequences. Second, genes always contain nucleotides flanking the protein-coding sequences that are required for the regulation of transcription and translation.

Anemia, a condition that results in individuals with a low red blood cell count,can be caused by a number of factors. Why do individuals with defects in the spectrin protein often have this condition?

Match the following types of RNA with the main polymerase that transcribes them. Types of RNAS A: most rRNA genes B: tRNA genes C: 5S rRNA genes D: protein coding genes E: mRNA genes Polymerases 1 RNA polymerase I 2 RNA polymerase II 3 RNA polymerase III

A—1; B—3; C—3; D—2; E - 2

Label the following structures in Figure Q8-35.

A—1; B—4; C—3; D—2

The classic experiments conducted by Meselson and Stahl demonstrated that DNA replication is accomplished by employing a ________________ mechanism. (a) continuous (b) semiconservative (c) dispersive (d) conservative

Which of these method(s) of controlling eukaryotic gene expression is NOT employed in prokaryotic cells? A. controlling how often a gene is transcribed B. controlling how an RNA transcript is spliced C. controlling which mRNAs are exported from the nucleus to the cytosol D. controlling which mRNAs are translated into protein by the ribosomes E. controlling how rapidly proteins are destroyed once they are made

B. controlling how an RNA transcript is spliced C. controlling which mRNAs are exported from the nucleus to the cytosol

DNA replication is considered semiconservative because____________________________. (a) after many rounds of DNA replication, the original DNA double helix is still intact (b) each daughter DNA molecule consists of two new strands copied from the parent DNA molecule (c) each daughter DNA molecule consists of one strand from the parent DNA molecule and one new strand (d) new DNA strands must be copied from a DNA template

The process of DNA replication requires that each of the parental DNA strands be used as a ___________________ to produce a duplicate of the opposing strand. (a) catalyst (b) competitor (c) template (d) copy

You wish to produce a human enzyme, protein A, by introducing its gene into bacteria. The genetically engineered bacteria make large amounts of protein A, but it is in the form of an insoluble aggregate with no enzymatic activity. Which of the following procedures might help you to obtain soluble, enzymatically active protein? Explain your reasoning. A. Make the bacteria synthesize protein A in smaller amounts. B. Dissolve the protein aggregate in urea, then dilute the solution and gradually remove the urea. C. Treat the insoluble aggregate with a protease. D. Make the bacteria overproduce chaperone proteins in addition to protein A.E. Heat the protein aggregate to denature all proteins, then cool the mixture.

Choices A, B, and D are all worth trying. Some proteins require molecular chaperones if they are to fold properly within the environment of the cell. In the absence of chaperones, a partly folded polypeptide chain has exposed amino acids that can form noncovalent bonds with other regions of the protein itself and with other proteins, thus causing nonspecific aggregation of proteins. A.) Because the protein you are expressing in bacteria is being made in large quantities, it is possible that there are not enough chaperone molecules in the bacterium to fold the protein. Expressing the protein at lower levels might increase the amount of properly folded protein. B.) Urea should solubilize the protein and completely unfold it. Removing the urea slowly and gradually often allows the protein to refold. Presumably, under less crowded conditions, the protein should be able to refold into its proper conformation. C.) Treating the aggregate with a protease, which cleaves peptide bonds, will probably solubilize the protein by trimming it into pieces that do not interact as strongly with one another; however, chopping up the protein will also destroy its enzymatic activity. D.) Overexpressing chaperone proteins might increase the amount of properly folded protein. E.) Heating can lead to the partial denaturation and aggregation of proteins to form a solid gelatinous mass, as when cooking an egg white, and rarely helps solubilize proteins.

Explain the differences between chromosome painting and the older, more traditional method of staining chromosomes being prepared for karyotyping. Highlight the way in which each method identifies chromosomes by the unique sequences they contain.

Chromosome painting relies on the specificity of DNA complementarity. Because unique sequences for each chromosome are known, short DNA molecules matching a set of these sites can be designed for each chromosome. Each set is labeled with a specific combination of fluorescent dyes and then allowed to hybridize (form base pairs) with the two homologous chromosomes that contain the unique sequences being targeted.Giemsa stain is a non-fluorescent dye that has a high affinity for DNA, and specifically accumulates in regions that are rich in A-T nucleotide pairs. This dye produces a pattern of dark and light bands, which differ for each chromosome on the basis of the distribution of A-T-rich regions.

While many prokaryotic cells have a single membrane bilayer, all eukaryotic cells have a complex system of internal membrane-bound compartments. How might it be advantageous for the cell to have these additional compartments?

Compartmentalization using intracellular membranes allows eukaryotic cells to separate a variety of cell processes. Although this requires a higher degree of coordination, the cell also gains a more stringent degree of control over these processes (examples include: the separation of transcription and translation; the separation of enzymes involved in protein modifications for secreted versus cytosolic substrates; the separation of proteolytic events in the lysosomes versus the cytosol; the separation of anaerobic metabolism in the cytosol and aerobic metabolism in the mitochondria).

One way in which an enzyme can lower the activation energy required for a reaction is to bind the substrate(s) and distort its structure so that the substrate more closely resembles the transition state of the reaction. This mechanism will be facilitated if the shape and chemical properties of the enzyme's active site are more complementary to the transition state than to the undistorted substrate; in other words, if the enzyme were to have a higher affinity for the transition state than for the substrate. Knowing this, your friend looked in an organic chemistry textbook to identify a stable chemical that closely resembles the transition state of a reaction that converts X into Y. She generated an antibody against this transition state analog and mixed the antibody with chemical X. What do you think might happen?

If your friend was lucky, she made a "catalytic antibody" that catalyzed the conversion of X into Y. Such catalytic antibodies have been isolated and shown to catalyze a variety of reactions, but with lower efficiency than genuine enzymes.

One way in which an enzyme can lower the activation energy required for a reaction is to bind the substrate(s) and distort its structure so that the substrate more closely resembles the transition state of the reaction. This mechanism will be facilitated if the shape and chemical properties of the enzyme's active site are more complementary to the transition state than to the undistorted substrate; in other words, if the enzyme were to have a higher affinity for the transition state than for the substrate. Knowing this, your friend looked in an organic chemistry textbook to identify a stable chemical that closely resembles the transition state of a reaction that converts X into Y. She generated an antibody againstthis transition state analog and mixed the antibody with chemical X. What do you think might happen?

Using the example of the p53 protein, explain how different combinations of covalent modifications can lead to a wide variety of protein functions.

In a protein with a complex regulatory protein code, such as p53, the covalent attach mentor removal of modifying groups can change the protein's behavior, its activity or stability, its binding partners, or its location within a cell. In the case of p53, there are at least 20 different locations (amino acids) that can be modified through such processes as phosphorylation, ubiquitylation, and acetylation.

Some of the enzymes that oxidize sugars to yield usable cellular energy (for example, ATP) are regulated by phosphorylation. For these enzymes, would you expect the inactive form to be the phosphorylated form or the dephosphorylated form? Explain your answer.

In general the inactive form is the phosphorylated form. The main purpose of glycolysis and the citric acid cycle is to generate ATP; thus, the enzymes are inactive when the concentration of ATP is high and active when it is low. It makes sense that cells would not want to have to phosphorylate their enzymes to turn them on when ATP levels are already low, because phosphorylation requires ATP.

Although membrane proteins contribute roughly 50% of the total mass of the membrane, there are about 50 times more lipid molecules than there are protein molecules in cellular membranes. Explain this apparent discrepancy.

Membrane proteins are much larger molecules than the membrane lipids. Thus, fewer are required to represent the same total mass contributed by the lipid components of the membrane. By this estimation, the molecular weight of the average membrane protein is 50 times that of the average membrane lipid.

Thermal motion promotes lateral position exchanges between lipid molecules within a monolayer. In an artificial bilayer, this movement has been estimated to be ~2 μm/second. This represents the entire length of a bacterial cell. Do you expect the lateral movement of a lipid molecule within a biological membrane to be equally fast? Explain your answer.

No. Although the rate of movement may be similar, it will most likely be slower in a biological membrane. An artificial bilayer is primarily phospholipids. Biological membranes contain a large number of protein components and specialized membrane domains that could limit the rate of lateral diffusion.

A small membrane vesicle containing a transmembrane protein is shown in Figure Q11-31. Assume that this membrane vesicle is in the cytoplasm of a cell. A. Label the cytosolic and non-cytosolic faces of the membrane vesicle. This membrane vesicle will undergo fusion with the plasma membrane. B. Sketch the plasma membrane after vesicle fusion, indicating the newlocations of the vesicle membrane and the transmembrane protein carried by the membrane vesicle. C. On your drawing for B, label the original cytosolic and non-cytosolic faces of the vesicle membrane as it resides in the plasma membrane. Also label the extracellular space and the cytosol. Indicate the N- and C-terminus of the inserted transmembrane protein.

See Figure A11-31A

Why is the old dogma "one gene—one protein" not always true for eukaryotic genes?

The transcripts from some genes can be spliced in more than one way to give mRNAs containing different sequences, thus encoding different proteins. A single eukaryotic gene may therefore encode more than one protein.

From the sequencing of the human genome, we believe that there are approximately 21,000 protein-coding genes in the genome, of which 1500-3000 are transcription factors. If every gene has a tissue-specific and signal- dependent transcription pattern, how can such a small number of transcriptional regulatory proteins generate a much larger set of transcriptional patterns?

Transcription regulators are generally used in combinations, thereby increasing the possible regulatory repertoire of gene expression with a limited number of proteins.

A group of membrane proteins can be extracted from membranes only by using detergents. All the proteins in this group have a similar amino acid sequence attheir C-terminus: -KKKKKXXC (where K stands for lysine, X stands for any amino acid, and C stands for cysteine). This sequence is essential for their attachment to the membrane. What is the most likely way in which the C-terminal sequence attaches these proteins to the membrane? (a) The cysteine residue is covalently attached to a membrane lipid. (b) The peptide spans the membrane as an α helix. (c) The peptide spans the membrane as part of a β sheet. (d) The positively charged lysine residues interact with an acidic integral membrane protein.

Below is the sequence from the 3′ end of an mRNA. 5′-CCGUUACCAGGCCUCAUUAUUGGUAACGGAAAAAAAAAAAAAA-3′ If you were told that this sequence contains the stop codon for the protein encoded by this mRNA, what is the anticodon on the tRNA in the P-site of the ribosome when release factor binds to the A-site? (a) 5′-CCA-3′ (b) 5′-CCG-3′ (c) 5′-UGG-3′ (d) 5′-UUA-3′

Consider the apical location of a particular protein expressed in epithelial cells,illustrated in Figure Q11-50A. When a molecule that chelates calcium is added to the cell culture medium, you observe a redistribution of that protein around the entire cell, shown in Figure Q11-50B. Which is most likely to be true about the role of calcium in maintaining an apical distribution of protein A? (a) calcium is required to maintain the structural integrity of the junctional complex (b) calcium is required for the binding of the junctional proteins to the cell cortex (c) calcium is a structural component of protein A (d) calcium inhibits intracellular transport of protein A

DNA polymerase catalyzes the joining of a nucleotide to a growing DNA strand. What prevents this enzyme from catalyzing the reverse reaction? (a) hydrolysis of PP i to P i + P i (b) release of PP i from the nucleotide (c) hybridization of the new strand to the template (d) loss of ATP as an energy source

Experiment 1 in Figure Q8-21 is the positive control, demonstrating that the region of DNA upstream of the gene for GFP results in a pattern of expression that we normally find for the LKP1 gene. Experiment 2 shows what happens when the sites for binding factors X, Y, and Z are removed. Which experiment above demonstrates that factor X alone is sufficient for expression of LPK1 inthe kidney? (a) experiment 3 (b) experiment 5 (c) experiment 6 (d) experiment 7

For some proteins, small molecules are integral to their structure and function. Enzymes can synthesize some of these small molecules, whereas others, called vitamins, must be ingested in the food we eat. Which of the following molecules is not classified as a vitamin but does require the ingestion of a vitamin for its production? (a) retinal (b) biotin (c) zinc (d) heme

Genes in eukaryotic cells often have intronic sequences coded for within the DNA. These sequences are ultimately not translated into proteins. Why? (a) Intronic sequences are removed from RNA molecules by the spliceosome, which works in the nucleus. (b) Introns are not transcribed by RNA polymerase. (c) Introns are removed by catalytic RNAs in the cytoplasm. (d) The ribosome will skip over intron sequences when translating RNA into protein.

Globular proteins fold up into compact, spherical structures that have uneven surfaces.They tend to form multisubunit complexes, which also have a rounded shape. Fibrous proteins, in contrast, span relatively large distances within the cell and in the extracellular space. Which of the proteins below is not classified as a fibrous protein? (a) elastase (b) collagen (c) keratin (d) elastin

In mammals, individuals with two X chromosomes are female, and individuals with an X and a Y chromosome are male. It had long been known that a gene located on the Y chromosome was sufficient to induce the gonads to form testes, which is the main male-determining factor in development,and researchers sought the product of this gene, the so-called testes-determining factor (TDF). For several years, the TDF was incorrectly thought to be a zinc finger protein encoded by a gene called BoY. Which of the following observations would most strongly suggest that BoY might not be the TDF? Explain your answer. (a) Some XY individuals that develop into females have mutations in a different gene, SRY, but are normal at BoY. (b) BoY is not expressed in the adult male testes. (c) Expression of BoY in adult females does not masculinize them. (d) A few of the genes that are known to be expressed only in the testes have binding sites for the BoY protein in their upstream regulatory sequences,but most do not.

Instead of studying one or two proteins or protein complexes present in the cell at any given time, we can now look at a snapshot of all proteins being expressed in cells being grown in specific conditions. This large-scale, systematic approach to the study of proteins is called _______________. (a) proteomics (b) structural biology (c) systems biology (d) genomics

Many of the breakthroughs in modern biology came after Watson and Crick published their model of DNA in 1953. In what decade did scientists first identify chromosomes? (a) 1880s (b) 1920s (c) 1940s (d) 1780s

Membrane lipids are capable of many different types of movement. Which of these does not occur spontaneously in biological membranes? (a) switching between lipid layers (b) lateral movement (c) rotation (d) flexing of hydrocarbon chains

Membrane synthesis in the cell requires the regulation of growth for both halves of the bilayer and the selective retention of certain types of lipids on one side or the other. Which group of enzymes accomplishes both of these tasks?(a) flippases(b) phospholipases(c) convertases(d) glycosylases

Methylation and acetylation are common changes made to histone H3, and the specific combination of these changes is sometimes referred to as the "histone code." Which ofthe following patterns will probably lead to gene silencing? (a) lysine 9 methylation (b) lysine 4 methylation and lysine 9 acetylation (c) lysine 14 acetylation (d) lysine 9 acetylation and lysine 14 acetylation

MicroRNAs ____________________. (a) are produced from a precursor miRNA transcript. (b) are found only in humans. (c) control gene expression by base-pairing with DNA sequences. (d) can degrade RNAs by using their intrinsic catalytic activity

Mitotic chromosomes are _____ times more compact than a DNA molecule in its extended form. (a) 10,000 (b) 100,000 (c) 1000 (d) 100

Most animal fats form a solid at room temperature, while plant fats remain liquid at room temperature. Which of the following is a feature of lipids in plant membranes that best explains this difference? (a) unsaturated hydrocarbons (b) longer hydrocarbon tails (c) higher levels of sterols (d) larger head groups

Plasma membranes are extremely thin and fragile, requiring an extensive support network of fibrous proteins. This network is called the ____________. (a) cortex. (b) attachment complex. (c) cytoskeleton. (d) spectrin.

Porin proteins form large, barrel-like channels in the membrane. Which of the following is not true about these channels? (a) They are made primarily of α helices. (b) They are made primarily of β sheets. (c) They cannot form narrow channels. (d) They have alternating hydrophobic and hydrophilic amino acids.

Several experiments were required to demonstrate how traits are inherited. Which scientist or team of scientists first demonstrated that cells contain some component that can be transferred to a new population of cells and permanently cause changes in the new cells? (a) Griffith (b) Watson and Crick (c) Avery, MacLeod, and McCarty (d) Hershey and Chase

Sometimes chemical damage to DNA can occur just before DNA replication begins, not giving the repair system enough time to correct the error before the DNA is duplicated. This gives rise to mutation. If the cytosine in the sequence TCAT is deaminated and not repaired, which of the following is the point mutation you would observe after this segment has undergone two rounds of DNA replication? (a) TTAT (b) TUAT (c) TGAT (d) TAAT

Specific regions of eukaryotic chromosomes contain sequence elements that are absolutely required for the proper transmission of genetic information from a mother cell to each daughter cell. Which of the following is not known to be one of these required elements in eukaryotes? (a) terminators of replication (b) origins of replication (c) telomeres (d) centromeres

The DNA from two different species can often be distinguished by a difference in the______________________. (a) ratio of A + T to G + C (b) ratio of A + G to C + T (c) ratio of sugar to phosphate (d) presence of bases other than A, G, C, and T

The classic "beads-on-a-string" structure is the most decondensed chromatin structure possible and is produced experimentally. Which chromatin components are not retained when this structure is generated? (a) linker histones (b) linker DNA (c) nucleosome core particles (d) core histones

The extent of complementarity of a miRNA with its target mRNA determines___________________________. (a) whether the mRNA will be immediately degraded or whether the mRNA will first be transported elsewhere in the cell before degradation. (b) whether the mRNA will be transported to the nucleus. (c) whether RISC is degraded. (d) whether the miRNA synthesizes a complementary strand.

The images of chromosomes we typically see are isolated from mitotic cells. These mitotic chromosomes are in the most highly condensed form. Interphase cells contain chromosomes that are less densely packed and __________________________. (a) occupy discrete territories in the nucleus (b) share the same nuclear territory as their homolog (c) are restricted to the nucleolus (d) are completely tangled with other chromosomes

The lateral movement of transmembrane proteins can be restricted by several different mechanisms. Which mechanism best describes the process by which a budding yeast cell designates the site of new bud formation during cell division? (a) proteins are tethered to the cell cortex (b) proteins are tethered to the extracellular matrix (c) proteins are tethered to the proteins on the surface of another cell (d) protein movement is limited by the presence of a diffusion barrier

The modular nature of the Eve gene's regulatory region means that ______. (a) there are seven regulatory elements and each element is sufficient for driving expression in a single stripe. (b) all the regulatory elements for each stripe use the same transcriptional activators. (c) the E. coli LacZ gene is normally only expressed in a single stripe—unlike Eve, which is expressed in seven stripes. (d) transcription regulators only bind to the stripe 2 regulatory DNA segment in stripe 2.

The process of generating monoclonal antibodies is labor-intensive and expensive. An alternative is to use polyclonal antibodies. A subpopulation of purified polyclonal antibodies that recognize a particular antigen can be isolated by chromatography. Which type of chromatography is used for this purpose? (a) affinity (b) ion-exchange (c) gel-filtration (d) any of the above

The repair of mismatched base pairs or damaged nucleotides in a DNA strand requires a multistep process. Which choice below describes the known sequence of events in this process? (a) DNA damage is recognized, the newly synthesized strand is identified by an existing nick in the backbone, a segment of the new strand is removed by repair proteins, the gap is filled by DNA polymerase, and the strand is sealed by DNA ligase. (b) DNA repair polymerase simultaneously removes bases ahead of it and polymerizes the correct sequence behind it as it moves along the template. DNA ligase seals the nicks in the repaired strand. (c) DNA damage is recognized, the newly synthesized strand is identified by an existing nick in the backbone, a segment of the new strand is removed by an exonuclease, and the gap is repaired by DNA ligase. (d) A nick in the DNA is recognized, DNA repair proteins switch out the wrong base and insert the correct base, and DNA ligase seals the nick.

The three-dimensional coordinates of atoms within a folded protein are determined experimentally. After researchers obtain a protein's structural details, they can use different techniques to highlight particular aspects of the structure. What visual model best displays a protein's secondary structures (α helices and β sheets)? (a) ribbon (b) space-filling (c) backbone (d) wire

Transcription in bacteria differs from transcription in a eukaryotic cell because__________________________. (a) RNA polymerase (along with its sigma subunit) can initiate transcription on its own (b) RNA polymerase (along with its sigma subunit) requires the general transcription factors to assemble at the promoter before polymerase can begin transcription (c) The sigma subunit must associate with the appropriate type of RNA polymerase to produce mRNAs (d) RNA polymerase must be phosphorylated at its C-terminal tail for transcription to proceed

Water molecules readily form hydrogen bonds with other polar molecules, and when they encounter nonpolar molecules they must form hydrogen-bonding networks with neighboring water molecules. Which of the following molecules will cause a "cage" of water to form? (a) 2-methylpropane (b) acetone (c) methanol (d) urea

When using a repeating trinucleotide sequence (such as 5′-AAC-3′) in a cell-free translation system, you will obtain: (a) three different types of peptides, each made up of a single amino acid (b) peptides made up of three different amino acids in random order (c) peptides made up of three different amino acids, each alternating with each other in a repetitive fashion (d) poly-asparagine, as the codon for asparagine is AAC

Which amino acid would you expect a tRNA with the anticodon 5′-CUU-3′ to carry? (a) lysine (b) glutamic acid (d) leucine (d) phenylalanine

Which of the following best describes the mechanism by which chromatin-remodeling complexes "loosen" the DNA wrapped around the core histones? (a) They use energy derived from ATP hydrolysis to change the relative position of the DNA and the core histone octamer. (b) They chemically modify the DNA, changing the affinity between the histone octamer and the DNA. (c) They remove histone H1 from the linker DNA adjacent to the core histone octamer. (d) They chemically modify core histones to alter the affinity between the histone octamer and the DNA.

Which of the following does not occur before a eukaryotic mRNA is exported from the nucleus? (a) The ribosome binds to the mRNA. (b) The mRNA is polyadenylated at its 3′ end. (c) 7-methyl-G is added in a 5′ to 5′ linkage to the mRNA. (d) RNA polymerase dissociates.

Which of the following is not a feature commonly observed in α helices? (a) left-handedness (b) one helical turn every 3.6 amino acids (c) cylindrical shape (d) amino acid side chains that point outward

Which of the following molecules of RNA would you predict to be the most likely to fold into a specific structure as a result of intramolecular base pairing? (a) 5′-CCCUAAAAAAAAAAAAAAAAUUUUUUUUUUUUUUUUAGGG-3′ (b) 5′-UGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUG-3′ (c) 5′-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3′ (d) 5′-GGAAAAGGAGAUGGGCAAGGGGAAAAGGAGAUGGGCAAGG-3′

Which of the following phenomena will be observed if a cell's membrane is pierced? (a) the membrane reseals (b) the membrane collapses (c) a tear is formed (d) the membrane expands

Which of the following phospholipid precursors is the most hydrophobic? (a) triacylglycerol (b) diacylglycerol (c) phosphate (d) glycerol

Which of the following proteins are likely to act as gene activators? (a) factors X and Y (b) factors X and Z (c) factors Y and Z (d) factor X only

Which of the following statements about the Lac operon is false? (a) The Lac repressor binds when lactose is present in the cell. (b) Even when the CAP activator is bound to DNA, if lactose is not present,the Lac operon will not be transcribed. (c) The CAP activator can only bind DNA when it is bound to cAMP. (d) The Lac operon only produces RNA when lactose is present and glucose is absent.

Which of the following statements about transcriptional regulators is false? (a) Transcriptional regulators usually interact with the sugar-phosphate backbone on the outside of the double helix to determine where to bind on the DNA helix. (b) Transcriptional regulators will form hydrogen bonds, ionic bonds, and hydrophobic interactions with DNA. (c) The DNA-binding motifs of transcriptional regulators usually bind in the major groove of the DNA helix. (d) The binding of transcriptional regulators generally does not disrupt the hydrogen bonds that hold the double helix together.

Which type of lipids are the most abundant in the plasma membrane? (a) phospholipids (b) glycolipids (c) sterols (d) triacylglycerides

You are studying a set of mouse genes whose expression increases when cells are exposed to the hormone cortisol, and you believe that the same cortisol-responsive transcriptional activator regulates all of these genes. Which of the following statements below should be true if your hypothesis is correct?(a) The cortisol-responsive genes share a DNA sequence in their regulatory regions that binds the cortisol-responsive transcriptional activator.(b) The cortisol-responsive genes must all be in an operon.(c) The transcriptional regulators that bind to the regulatory regions of the cortisol-responsive genes must all be the same.(d) The cortisol-responsive genes must not be transcribed in response to other hormones.

You develop a cell-free transcriptional system to study the effects of proteins G, H, and J on the transcription of gene Q. Using this system, you can examine the effects of adding these proteins to the transcriptional system in equal amounts and measuring how much gene Q is produced. When you add these proteins to the system, you get the results shown in Table Q8-29.T Which proteins are likely to act as gene repressors? (a) G (b) H (c) J (d) both H and J

You have two purified samples of protein Y: the wild-type (non mutated) protein and a mutant version with a single amino acid substitution. When washed through the same gel-filtration column, mutant protein Y runs through the column more slowly than the normal protein. Which of the following changes in the mutant protein is most likely to explain this result? (a) the loss of a binding site on the mutant protein surface through which protein Y normally forms dimers (b) a change that results in the mutant protein's acquiring an overall positive instead of a negative charge (c) a change that results in the mutant protein's being larger than the wild-type protein (d) a change that results in the mutant protein's having a slightly different shape from the wild-type protein

miRNAs, tRNAs, and rRNAs all _____________. (a) do not code for proteins. (b) act in the nucleus. (c) are packaged with other proteins to form RISC. (d) form base pairs with mRNA molecules.

You have isolated two mutants of a normally pear-shaped microorganism that have lost their distinctive shape and are now round. One of the mutants has a defect in a protein you call A and the other has a defect in a protein you call B.First, you grind up each type of mutant cell and normal cells separately and separate the plasma membranes from the cytoplasm, forming the first cell extract.Then you set aside a portion of each fraction for later testing. Next, you wash the remaining portion of the membrane fractions with a low concentration of urea (which will unfold proteins and disrupt their ability to interact with other proteins)and centrifuge the mixture. The membranes and their constituent proteins form apellet, and the proteins liberated from the membranes by the urea wash remain in the supernatant. When you check each of the fractions for the presence of A or B,you obtain the results given below.Which of the following statements are consistent with your results (more than one answer may apply)? (a) Protein A is an integral membrane protein that interacts with B, a peripheral membrane protein that is part of the cell cortex. (b) Protein B is an integral membrane protein that interacts with A, a peripheral membrane protein that is part of the cell cortex. (c) Proteins A and B are both integral membrane proteins. (d) The mutation in A affects its ability to interact with B.

a & d

Since the first nucleotides cannot be linked in a newly synthesized strand in DNA replication, ___________ is required for initiation

an RNA primer

A bacterium is suddenly expelled from a warm human intestine into the coldworld outside. Which of the following adjustments might the bacterium make to maintain the same level of membrane fluidity? (a) Produce lipids with hydrocarbon tails that are longer and have fewer double bonds. (b) Produce lipids with hydrocarbon tails that are shorter and have more double bonds. (c) Decrease the amount of cholesterol in the membrane. (d) Decrease the amount of glycolipids in the membrane.

A mutation in the tRNA for the amino acid lysine results in the anticodon sequence 5′-UAU-3′ (instead of 5′-UUU-3′). Which of the following aberrations in protein synthesis might this tRNA cause? (a) read-through of stop codons (b) substitution of lysine for isoleucine (c) substitution of lysine for tyrosine (d) substitution of lysine for phenylalanine

A poison added to an in vitro translation mixture containing mRNA molecules with the sequence 5′-AUGAAAAAAAAAAAAUAA-3′ has the following effect: the only product made is a Met-Lys dipeptide that remains attached to the ribosome. What is the most likely way in which the poison acts to inhibit protein synthesis? (a) It inhibits peptidyl transferase activity. (b) It inhibits movement of the small subunit relative to the large subunit. (c) It inhibits release factor. (d) It mimics release factor.

Combinatorial control of gene expression __________________________. (a) involves every gene using a different combination of transcriptional regulators for its proper expression. (b) involves groups of transcriptional regulators working together to determine the expression of a gene. (c) involves only the use of gene activators used together to regulate genes appropriately. (d) is seen only when genes are arranged in operons.

Consider the apical location of a particular protein expressed in epithelial cells,illustrated in Figure Q11-49A. Which type of defect described below is the most likely to cause the redistribution of that protein around the entire cell, shown in Figure Q11-49B? (a) a nonfunctional protein glycosylase (b) the deletion of a junctional protein (c) the truncation of a protein found in the extracellular matrix (d) a nonfunctional flippase

DNA polymerases are processive, which means that they remain tightly associated with the template strand while moving rapidly and adding nucleotides to the growing daughter strand. Which piece of the replication machinery accounts for this characteristic? (a) helicase (b) sliding clamp (c) single-strand binding protein (d) primase

Figure Q5-45 clearly depicts the nucleolus, a nuclear structure that looks like a large, dark region when stained. The other dark, speckled regions in this image are the locations of particularly compact chromosomal segments called ____________. (a) euchromatin. (b) heterochromatin. (c) nuclear pores. (d) nucleosomes.

Formation of a lipid bilayer is energetically favorable. How does this arrangement result in higher entropy for the system, and thus make bilayer formation energetically favorable? (a) Polar head groups form a hydrogen-bonding network at the interface with water. (b) Water molecules form cage like structures around hydrophobic molecules. (c) Hydrogen bonds form between neighboring polar head groups in the bilayer. (d) Fatty acid tails are highly saturated and flexible.

Fred Griffith studied two strains of Streptococcus pneumonia, one that causes a lethal infection when injected into mice, and a second that is harmless. He observed that pathogenic bacteria that have been killed by heating can no longer cause an infection. But when these heat-killed bacteria are mixed with live, harmless bacteria, this mixture is capable of infecting and killing a mouse. What did Griffith conclude from this experiment? (a) The infectious strain cannot killed by heating. (b) The heat-killed pathogenic bacteria "transformed" the harmless strain into a lethal one. (c) The harmless strain somehow revived the heat-killed pathogenic bacteria. (d) The mice had lost their immunity to infection with S. pneumoniae.

Homologous recombination is an important mechanism in which organisms use a "back-up" copy of the DNA as a template to fix double-strand breaks without loss of genetic information. Which of the following is not necessary for homologous recombination to occur? (a) 3′ DNA strand overhangs (b) 5′ DNA strand overhangs (c) a long stretch of sequence similarity (d) nucleases

How are most eukaryotic transcription regulators able to affect transcription when their binding sites are far from the promoter? (a) by binding to their binding site and sliding to the site of RNA polymerase assembly (b) by looping out the intervening DNA between their binding site and the promoter (c) by unwinding the DNA between their binding site and the promoter (d) by attracting RNA polymerase and modifying it before it can bind to the promoter

In eukaryotes, but not in prokaryotes, ribosomes find the start site of translation by____________________________. (a) binding directly to a ribosome-binding site preceding the initiation codon (b) scanning along the mRNA from the 5′ end (c) recognizing an AUG codon as the start of translation (d) binding an initiator tRNA

In the photosynthetic archaean Halobacterium halobium, a membrane transport protein called bacteriorhodopsin captures energy from sunlight and uses it to pump protons out of the cell. The resulting proton gradient serves as an energystore that can later be tapped to generate ATP. Which statement best describes how bacteriorhodopsin operates? (a) The absorption of sunlight triggers a contraction of the β barrel that acts as the protein's central channel, squeezing a proton out of the cell. (b) The absorption of sunlight triggers a shift in the conformation of the protein's seven, membrane spanning α helices, allowing a proton to leave the cell. (c) The absorption of sunlight triggers a restructuring of bacteriorhodopsin's otherwise unstructured core to form the channel through which a proton can exit the cell. (d) The absorption of sunlight triggers the activation of an enzyme that generates ATP.

Initiator proteins bind to replication origins and disrupt hydrogen bonds between the two DNA strands being copied. Which of the factors below does not contribute to the relative ease of strand separation by initiator proteins? a. replication origins are rich in A-T base pairs b. the reaction can occur at room temperature c. they only separate a few base pairs at a time d. once opened, other proteins of the DNA replication machinery bind to the origin

Interphase chromosomes are about______ times less compact than mitotic chromosomes,but still are about______ times more compact than a DNA molecule in its extended form. (a) 10; 1000 (b) 20; 500 (c) 5; 2000 (d) 50; 200

Investigators performed nuclear transplant experiments to determine whether DNA is altered irreversibly during development. Which of the following statements about these experiments is true? (a) Because the donor nucleus is taken from an adult animal, the chromosomes from the nucleus must undergo recombination with the DNA in the egg for successful development to occur. (b) The embryo that develops from the nuclear transplant experiment is genetically identical to the donor of the nucleus. (c) The meiotic spindle of the egg must interact with the chromosomes of the injected nuclei for successful nuclear transplantation to occur. (d) Although nuclear transplantation has been successful in producing embryos in some mammals with the use of foster mothers, evidence of DNA alterations during differentiation has not been obtained for plants.

It is possible to follow the movement of a single molecule or a small group of molecules. This requires the use of antibodies linked to small particles of gold,which appear as dark spots when tracked through video microscopy. What is this method called? What does the abbreviation stand for? (a) SDS (b) SPT (c) GFP (d) FRAP

Membrane proteins, like membrane lipids, can move laterally by exchanging positions with other membrane components. Which type of membrane proteins is expected to be the least mobile, based on their function? (a) channels (b) anchors (c) receptors (d) enzymes

Mitotic chromosomes were first visualized in the 1880s with the use of very simple tools: a basic light microscope and some dyes. Which of the following characteristics of mitotic chromosomes reflects how they were named? (a) motion (b) color (c) shape (d) location

Proteins bind selectively to small molecule targets called ligands. The selection of one ligand out of a mixture of possible ligands depends on the number of weak, noncovalent interactions in the protein's ligand-binding site. Where is the binding site typically located in the protein structure? (a) on the surface of the protein (b) inside a cavity on the protein surface (c) buried in the interior of the protein (d) forms on the surface of the protein in the presence of ligand

Proteins can assemble to form large complexes that work coordinately, like moving parts inside a single machine. Which of the following steps in modulating the activity of a complex protein machine is least likely to be directly affected by ATP or GTP hydrolysis? a. conformational change of protein components b. translation of protein components c. complex assembly d. complex disassembly

Sickle-cell anemia is an example of an inherited disease. Individuals with this disorder have misshapen (sickle-shaped) red blood cells caused by a change in the sequence of theβ-globin gene. What is the nature of the change? (a) chromosome loss (b) base-pair change (c) gene duplication (d) base-pair insertion

Stepwise condensation of linear DNA happens in five different packing processes. Which of the following four processes has a direct requirement for histone H1? (a) formation of "beads-on-a-string" (b) formation of the 30 nm fiber (c) looping of the 30 nm fiber (d) packing of loops to form interphase chromosomes

Studies conducted with a lysozyme mutant that contains an Asp→Asn change at position 52 and a Glu→Gln change at position 35 exhibited almost a complete loss in enzymatic activity. What is the most likely explanation for the decrease in enzyme activity in the mutant? (a) increased affinity for substrate (b) absence of negative charges in the active site (c) change in the active site scaffold (d) larger amino acids in the active site decrease the affinity for substrate

The N-terminal tail of histone H3 can be extensively modified, and depending on the number, location, and combination of these modifications, these changes may promote the formation of heterochromatin. What is the result of heterochromatin formation? (a) increase in gene expression (b) gene silencing (c) recruitment of remodeling complexes (d) displacement of histone H1

The distinct characteristics of different cell types in a multicellular organism result mainly from the differential regulation of the _________________. (a) replication of specific genes. (b) transcription of genes transcribed by RNA polymerase II. (c) transcription of housekeeping genes. (d) proteins that directly bind the TATA box of eukaryotic genes.

The information stored in the DNA sequences is used directly as a template to make ___________. (a) lipids. (b) RNA. (c) polypeptides. (d) carbohydrates.

The lateral movement of transmembrane proteins can be restricted by several different mechanisms. Which mechanism best describes the process by which focal adhesions are formed to promote cell motility? (a) proteins are tethered to the cell cortex (b) proteins are tethered to the extracellular matrix (c) proteins are tethered to the proteins on the surface of another cell (d) protein movement is limited by the presence of a diffusion barrier

The manner in which a gene sequence is related to its respective protein sequence is referred to as the _________ code. (a) protein (b) genetic (c) translational (d) expression

The owners of a local bakery ask for your help in improving a special yeast strain they use to make bread. They would like you to help them design experiments using RNA interference to turn off genes, to allow them to test their hypothesis that certain genes are important for the good flavors found in their bread. Of the components in the following list, which is the most important to check for in this yeast strain if you'd like this project to succeed? (a) the presence of foreign double-stranded RNA (b) the presence of genes in the genome that code for RISC proteins (c) the presence of miRNA genes in the genome (d) the presence of single-stranded siRNAs within the cell

The phosphorylation of a protein is typically associated with a change in activity, the assembly of a protein complex, or the triggering of a downstream signaling cascade. The addition of ubiquitin, a small polypeptide, is another type of covalent modification that can affect the protein function. Ubiquitylation often results in ______________. (a) membrane association (b) protein degradation (c) protein secretion (d) nuclear translocation

The piece of RNA below includes the region that codes the binding site for the initiator tRNA needed in translation. 5′-GUUUCCCGUAUACAUGCGUGCCGGGGGC-3′ Which amino acid will be on the tRNA that is the first to bind to the A-site of the ribosome? (a) methionine (b) arginine (c) cystine (d) valine

The plasma membrane serves many functions, many of which depend on the presence of specialized membrane proteins. Which of the following roles of the plasma membrane could still occur if the bilayer were lacking these proteins? (a) intercellular communication (b) selective permeability (c) cellular movement (d) import/export of molecules

The tryptophan operator ___________________________. (a) is an allosteric protein. (b) binds to the tryptophan repressor when the repressor is bound to tryptophan. (c) is required for production of the mRNA encoded by the tryptophan operon. (d) is important for the production of the tryptophan repressor.

There are several reasons why the primase used to make the RNA primer for DNA replication is not suitable for gene transcription. Which of the statements below is not one of those reasons? (a) Primase initiates RNA synthesis on a single-stranded DNA template. (b) Primase can initiate RNA synthesis without the need for a base-paired primer. (c) Primase synthesizes only RNAs of about 5-20 nucleotides in length. (d) The RNA synthesized by primase remains base-paired to the DNA template.

There are two properties of phospholipids that affect how tightly they pack together: the length of the hydrocarbon chain and the number of double bonds.The degree of packing, in turn, influences the relative mobility of these molecules in the membrane. Which of the following would yield the most highly mobile phospholipid (listed as number of carbons and number of double bonds,respectively)? (a) 24 carbons with 1 double bond (b) 15 carbons with 2 double bonds (c) 20 carbons with 2 double bonds (d) 16 carbons with no double bonds

To study how proteins fold, scientists must be able to purify the protein of interest, use solvents to denature the folded protein, and observe the process of refolding at successive time points. What is the effect of the solvents used in the denaturation process? (a) The solvents break all covalent interactions. (b) The solvents break all noncovalent interactions. (c) The solvents break some of the non covalent interactions, resulting in a misfolded protein. (d) The solvents create a new protein conformation.

We know the detailed molecular structure and mechanism of action of the transmembrane protein bacteriorhodopsin. This protein uses sunlight as the source of energy to pump ______ out of the cell. (a) ATP (b) H+ (c) K+ (d) Na+

What do you predict would happen if you created a tRNA with an anticodon of 5′-CAA-3′ that is charged with methionine, and added this modified tRNA to a cell-free translation system that has all the normal components required for translating RNAs? (a) methionine would be incorporated into proteins at some positions where glutamine should be (b) methionine would be incorporated into proteins at some positions where leucine should be (c) methionine would be incorporated into proteins at some positions where valine should be (d) translation would no longer be able to initiate

What do you predict would happen if you replace the Lac operator DNA from the Lac operon with the DNA from the operator region from the tryptophan operon? (a) The presence of lactose will not cause allosteric changes to the Lac repressor. (b) The Lac operon will not be transcribed when tryptophan levels are high. (c) The lack of glucose will no longer allow CAP binding to the DNA. (d) RNA polymerase will only bind to the Lac promoter when lactose is present.

Where does most new membrane synthesis take place in a eukaryotic cell? (a) in the Golgi apparatus (b) in the endoplasmic reticulum (c) in the plasma membrane (d) in the mitochondria (e) on ribosomes

Which of the following DNA sequences is not commonly carried on mobile genetic elements? You may choose more than one option. (a) transposase gene (b) Holliday junction (c) recognition site for transposase (d) antibiotic resistance gene

Which of the following is not a chemical modification commonly found on core histone N-terminal tails? (a) methylation (b) hydroxylation (c) phosphorylation (d) acetylation

Which of the following is not a feature commonly observed in β sheets? (a) antiparallel regions (b) coiled-coil patterns (c) extended polypeptide backbone (d) parallel regions

Which of the following proteins are likely to act as gene repressors? (a) MetA only (b) MetB only (c) MetC only (d) Both MetA and MetC

Which of the following statements about RNA splicing is false? (a) Conventional introns are not found in bacterial genes. (b) For a gene to function properly, every exon must be removed from the primary transcript in the same fashion on every mRNA molecule produced from the same gene. (c) Small RNA molecules in the nucleus perform the splicing reactions necessary for the removal of introns. (d) Splicing occurs after the 5′ cap has been added to the end of the primary transcript.

Which of the following statements about RNAi is true? (a) The RNAi mechanism is found only in plants and animals. (b) RNAi is induced when double-stranded, foreign RNA is present in the cell. (c) RISC uses the siRNA duplex to locate complementary foreign RNA molecules. (d) siRNAs bind to miRNAs to induce RNAi.

Which of the following statements about iPS cells is false? (a) iPS cells are created by adding a combination of transcription regulators toa fibroblast. (b) iPS cells created from mouse cells can differentiate into almost any human cell type. (c) Stimulation by extracellular signal molecules causes iPS cells to differentiate. (d) During the de-differentiation process to become an iPS, the fibroblast will undergo changes to its gene expression profile.

Which of the following statements about mRNA half-life is false? (a) The half-life of mRNAs produced from different genes will vary more than the half-life of mRNAs produced from the same gene. (b) The half-life of most eukaryotic-cell mRNAs is >24 hours. (c) The half-life of most bacterial mRNAs is shorter than the half-life of atypical eukaryotic mRNA. (d) The 5′ and 3′ untranslated regions of an mRNA often contain specific sequences that determine the lifetime of the mRNA molecule

Which of the following statements about prokaryotic mRNA molecules is false? (a) A single prokaryotic mRNA molecule can be translated into several proteins. (b) Ribosomes must bind to the 5′ cap before initiating translation. (c) mRNAs are not polyadenylated. (d) Ribosomes can start translating an mRNA molecule before transcription is complete.

Which of the following statements about the Ey transcriptional regulator isfalse? (a) Expression of Ey in cells that normally form legs in the fly will lead to the formation of an eye in the middle of the legs. (b) The Ey transcription factor must bind to the promoter of every eye-specific gene in the fly. (c) Positive feedback loops ensure that Ey expression remains switched on in the developing eye. (d) A homolog of Ey is found in vertebrates; this homolog is also used during eye development.

Which of the following statements about the genetic code is correct? (a) All codons specify more than one amino acid. (b) The genetic code is redundant. (c) All amino acids are specified by more than one codon. (d) All codons specify an amino acid.

Which of the following statements is not an accurate statement about thymidine dimers? (a) Thymidine dimers can cause the DNA replication machinery to stall. (b) Thymidine dimers are covalent links between thymidines on opposite DNA strands. (c) Prolonged exposure to sunlight causes thymidine dimers to form. (d) Repair proteins recognize thymidine dimers as a distortion in the DNA backbone.

You are studying a disease that is caused by a virus, but when you purify the virus particles and analyze them you find they contain no trace of DNA. Which of the following molecules are likely to contain the genetic information of the virus? (a) high-energy phosphate groups (b) RNA (c) lipids (d) carbohydrates

You have a bacterial strain with a mutation that removes the transcription termination signal from the Abd operon. Which of the following statements describes the most likely effect of this mutation on Abd transcription? (a) The Abd RNA will not be produced in the mutant strain. (b) The Abd RNA from the mutant strain will be longer than normal. (c) Sigma factor will not dissociate from RNA polymerase when the Abdoperon is being transcribed in the mutant strain. (d) RNA polymerase will move in a backwards fashion at the Abd operon inthe mutant strain.

You have a piece of DNA that includes the following sequence: 5′-ATAGGCATTCGATCCGGATAGCAT-3′3′-TATCCGTAAGCTAGGCCTATCGTA-5′ Which of the following RNA molecules could be transcribed from this piece of DNA? (a) 5′-UAUCCGUAAGCUAGGCCUAUGCUA-3′ (b) 5′-AUAGGCAUUCGAUCCGGAUAGCAU-3′ (c) 5′-UACGAUAGGCCUAGCUUACGGAUA-3′ (d) none of the above

You have discovered a protein that inhibits translation. When you add this inhibitor to a mixture capable of translating human mRNA and centrifuge the mixture to separate polyribosomes and single ribosomes, you obtain the results shown in Figure Q7-57. Which of the following interpretations is consistent with these observations? (a) The protein binds to the small ribosomal subunit and increases the rate of initiation of translation. (b) The protein binds to sequences in the 5′ region of the mRNA and inhibits the rate of initiation of translation. (c) The protein binds to the large ribosomal subunit and slows down elongation of the polypeptide chain. (d) The protein binds to sequences in the 3′ region of the mRNA and prevents termination of translation.

A strain of yeast translates mRNA into protein inaccurately. Individual molecules of a particular protein isolated from this yeast have variations in the first 11 amino acids compared with the sequence of the same protein isolated from normal yeast cells, as listed in Figure Q7-36. What is the most likely cause of this variation in protein sequence? Figure Q7-36 (a) a mutation in the DNA coding for the protein (b) a mutation in the anticodon of the isoleucine tRNA (tRNA Ile) (c) a mutation in the isoleucyl-tRNA synthetase that decreases its ability to distinguish between different amino acids (d) a mutation in the isoleucyl-tRNA synthetase that decreases its ability to distinguish between different tRNA molecules

Although the chromatin structure of interphase and mitotic chromosomes is very compact, DNA-binding proteins and protein complexes must be able to gain access to the DNA molecule. Chromatin-remodeling complexes provide this access by__________________. (a) recruiting other enzymes (b) modifying the N-terminal tails of core histones (c) using the energy of ATP hydrolysis to move nucleosomes (d) denaturing the DNA by interfering with hydrogen-bonding between base pairs

Beside the distortion in the DNA backbone caused by a mismatched base pair, what additional mark is there on eukaryotic DNA to indicate which strand needs to be repaired? (a) a nick in the template strand (b) a chemical modification of the new strand (c) a nick in the new strand (d) a sequence gap in the new strand

Both glycoproteins and proteoglycans contribute to the carbohydrate layer on the surface of the cell. Which of the following is not true of glycoproteins? (a) They can be secreted into the extracellular environment. (b) They have only one transmembrane domain. (c) They have long carbohydrate chains. (d) They are recognized by lectins.

Consider two genes that are next to each other on a chromosome, as arranged in Figure Q7-3. Which of the following statements is true? (a) The two genes must be transcribed into RNA using the same strand of DNA. (b) If gene A is transcribed in a cell, gene B cannot be transcribed. (c) Gene A and gene B can be transcribed at different rates, producing different amounts of RNA within the same cell. (d) If gene A is transcribed in a cell, gene B must be transcribed.

Figure Q7-6 shows a ribose sugar. The part of the ribose sugar that is different from the deoxyribose sugar used in DNA is pointed to by arrow ____. (a) 1. (b) 4. (c) 5. (d) 6.

Figure Q7-6 shows a ribose sugar. The part of the ribose sugar where a new ribonucleotide will attach in an RNA molecule is pointed to by arrow ____. (a) 1. (b) 3. (c) 4. (d) 5.

Fully folded proteins typically have polar side chains on their surfaces, where electrostatic attractions and hydrogen bonds can form between the polar group on the amino acid and the polar molecules in the solvent. In contrast, some proteins have a polar side chain in their hydrophobic interior. Which of following would not occur to help accommodate an internal, polar side chain? (a) A hydrogen bond forms between two polar side chains. (b) A hydrogen bond forms between a polar side chain and protein backbone. (c) A hydrogen bond forms between a polar side chain and an aromatic side chain. (d) Hydrogen bonds form between polar side chains and a buried water molecule.

How do changes in histone modifications lead to changes in chromatin structure? (a) They directly lead to changes in the positions of the core histones. (b) They change the affinity between the histone octamer and the DNA. (c) They help recruit other proteins to the chromatin. (d) They cause the histone N-terminal tails to become hyperextended.

In addition to the repair of DNA double-strand breaks, homologous recombination is a mechanism for generating genetic diversity by swapping segments of parental chromosomes. During which process does swapping occur? (a) DNA replication (b) DNA repair (c) meiosis (d) transposition

In principle, how many different cell types can an organism having four different types of transcription regulator and thousands of genes create? (a) up to 4 (b) up to 8 (c) up to 16 (d) thousands

In what tissue is factor Z normally present and bound to the DNA? (a) kidney (b) liver (c) heart (d) none of the above

New membrane phospholipids are synthesized by enzymes bound to the_____________ side of the _________________ membrane. (a) cytosolic, mitochondrial (b) luminal, Golgi (c) cytosolic, endoplasmic reticulum (d) extracellular, plasma

Nucleosomes are formed when DNA wraps _____ times around the histone octamer in a______ coil. (a) 2.0; right-handed (b) 2.5; left-handed (c) 1.7; left-handed (d) 1.3; right-handed

Operons ___________________________. (a) are commonly found in eukaryotic cells. (b) are transcribed by RNA polymerase II. (c) contain a cluster of genes transcribed as a single mRNA. (d) can only be regulated by gene activator proteins.

RNA in cells differs from DNA in that ___________________. (a) it contains the base uracil, which pairs with cytosine (b) it is single-stranded and cannot form base pairs (c) it is single-stranded and can fold up into a variety of structures (d) the sugar ribose contains fewer oxygen atoms than does deoxyribose

RNA in cells differs from DNA in that ___________________. (a) it contains the base uracil, which pairs with cytosine. (b) it is single-stranded and cannot form base pairs. (c) it is single-stranded and can fold up into a variety of structures. (d) the sugar ribose contains fewer oxygen atoms than does deoxyribose.

Ribozymes catalyze which of the following reactions? (a) DNA synthesis (b) transcription (c) RNA splicing (d) protein hydrolysis

Several members of the same family were diagnosed with the same kind of cancer when they were unusually young. Which one of the following is the most likely explanation for this phenomenon? It is possible that the individuals with the cancer have_______________________. (a) inherited a cancer-causing gene that suffered a mutation in an ancestor's somatic cells (b) inherited a mutation in a gene required for DNA synthesis (c) inherited a mutation in a gene required for mismatch repair (d) inherited a mutation in a gene required for the synthesis of purine nucleotides

Sometimes chemical damage to DNA can occur just before DNA replication begins, not giving the repair system enough time to correct the error before the DNA is duplicated.This gives rise to mutation. If the adenosine in the sequence TCAT is depurinated and not repaired, which of the following is the point mutation you would observe after this segment has undergone two rounds of DNA replication? (a) TCGT (b) TAT (c) TCT (d) TGTT

The MyoD transcriptional regulator is normally found in differentiating muscle cells and participates in the transcription of genes that produce muscle-specific proteins, such as those needed in contractile tissue. Amazingly, expression of MyoD in fibroblasts causes these cells derived from skin connective tissue to produce proteins normally only seen in muscles.However, some other cell types do not transcribe muscle-specific genes when MyoD is expressed in them. Which of the following statements below is the best explanation of why MyoD can cause fibroblasts to express muscle-specific genes? (a) Unlike some other cell types, fibroblasts have not lost the muscle-specific genes from their genome. (b) The muscle-specific genes must be in heterochromatin in fibroblasts. (c) During their developmental history, fibroblasts have accumulated some transcriptional regulators in common with differentiating muscle cells. (d) The presence of MyoD is sufficient to activate the transcription of muscle-specific genes in all cell types.

The biosynthetic pathway for the two amino acids E and H is shown schematically in Figure Q4-60. You are able to show that E inhibits enzyme V, and H inhibits enzyme X. Enzyme T is most likely to be subject to feedback inhibition by __________________ alone. Figure Q4-60 a. B b. H c. C d. E

The chromatin structure in eukaryotic cells is much more complicated than that observed in prokaryotic cells. This is thought to be the reason that DNA replication occurs much faster in prokaryotes. How much faster is it? (a) 2× (b) 5× (c) 10× (d) 100×

The concentration of a particular protein X in a normal human cell rises gradually from a low point, immediately after cell division, to a high point, just before cell division, and then drops sharply. The level of its mRNA in the cell remains fairly constant throughout this time. Protein X is required for cell growth and survival,but the drop in its level just before cell division is essential for division to proceed. You have isolated a line of human cells that grow in size in culture but cannot divide, and on analyzing these mutants, you find that levels of X mRNA inthe mutant cells are normal. Which of the following mutations in the gene for X could explain these results? (a) the introduction of a stop codon that truncates protein X at the fourth amino acid (b) a change of the first ATG codon to CCA (c) the deletion of a sequence that encodes sites at which ubiquitin can be attached to the protein (d) a change at a splice site that prevents splicing of the RNA

The core histones are small, basic proteins that have a globular domain at the C-terminus and a long extended conformation at the N-terminus. Which of the following is not true of the N terminal "tail" of these histones? (a) It is subject to covalent modifications, (b) It extends out of the nucleosome core. (c) It binds to DNA in a sequence-specific manner. (d) It helps DNA pack tightly.

The expression of the BRF1 gene in mice is normally quite low, but mutations in a gene called BRF2 lead to increased expression of BRF1. You have a hunch that nucleosomes are involved in the regulation of BRF1 expression and soyou investigate the position of nucleosomes over the TATA box of BRF1 in normal mice and in mice that lack either the BRF2 protein (BRF2-) or part of histone H4 (HHF-) (histone H4 is encoded by the HHF gene). Table Q8-37 summarizes your results. A normal functional gene is indicated by a plus sign(+). Which of the following conclusions cannot be drawn from your data? Explain your answer. (a) BRF2 is required for the repression of BRF1. (b) BRF2 is required for the specific pattern of nucleosome positions over the BRF1 upstream region. (c) The specific pattern of nucleosome positioning over the BRF1 upstream region is required for BRF1 repression. (d) The part of histone H4 missing in HHF-mice is not required for the formation of nucleosomes.

The human genome encodes about 21,000 protein-coding genes.Approximately how many such genes does the typical differentiated human cell express at any one time? (a) 21,000—all of them (b) between 18,900 and 21,000—at least 90% of the genes (c) between 5000 and 15,000 (d) less than 2100

The lateral movement of transmembrane proteins can be restricted by several different mechanisms. Which mechanism best describes the process by which an antigen-presenting cell triggers an adaptive immune response? (a) proteins are tethered to the cell cortex (b) proteins are tethered to the extracellular matrix (c) proteins are tethered to the proteins on the surface of another cell (d) protein movement is limited by the presence of a diffusion barrier

The lateral movement of transmembrane proteins can be restricted by several different mechanisms. Which mechanism best describes the process by which neutrophils are recruited by endothelial cells? (a) proteins are tethered to the cell cortex (b) proteins are tethered to the extracellular matrix (c) proteins are tethered to the proteins on the surface of another cell (d) protein movement is limited by the presence of a diffusion barrier

The process of sorting human chromosomes pairs by size and morphology is called karyotyping. A modern method employed for karyotyping is called chromosome painting. How are individual chromosomes "painted"? (a) with a laser (b) using fluorescent antibodies (c) using fluorescent DNA molecules (d) using green fluorescent protein

The ribosome is important for catalyzing the formation of peptide bonds. Which of the following statements is true? Select one: a. The number of rRNA molecules that make up a ribosome greatly exceeds the number of protein molecules found in the ribosome. b. The large subunit of the ribosome is important for binding to the mRNA. c. The catalytic site for peptide bond formation is formed primarily from an rRNA. d. Once the large and small subunits of the ribosome assemble, they will not separate from each other until degraded by the proteasome.

The sigma subunit of bacterial RNA polymerase ___________________. (a) contains the catalytic activity of the polymerase (b) remains part of the polymerase throughout transcription (c) recognizes promoter sites in the DNA (d) recognizes transcription termination sites in the DNA

Three phospholipids X, Y, and Z are distributed in the plasma membrane as indicated in Figure Q11-14. For which of these phospholipids does a flippase probably exist? (a) X only (b) Z only (c) X and Y (d) Y and Z

Unlike soluble, cytosolic proteins, membrane proteins are more difficult to purify.Which of the following substances is most commonly used to help purify a membrane protein? (a) high salt solution (b) sucrose (c) detergent (d) ethanol

What type of macromolecule helps package DNA in eukaryotic chromosomes? (a) lipids (b) carbohydrates (c) proteins (d) RNA

When there is a well-established segment of heterochromatin on an interphase chromosome, there is usually a special barrier sequence that prevents the heterochromatin from expanding along the entire chromosome. Gene A, which is normally expressed, has been moved by DNA recombination near an area of heterochromatin. None of the daughter cells produced after this recombination event express gene A, even though its DNA sequence is unchanged. What is this the best way to describe what has happened to the function of gene A in these cells? (a) barrier destruction (b) heterochromatization (c) epigenetic inheritance (d) euchromatin depletion

Which DNA base pair is represented in Figure Q5-18? (a) A-T (b) T-A (c) G-C (d) C-G

Which of the following is not involved in post-transcriptional control? (a) the spliceosome (b) Dicer (c) Mediator (d) RISC

Which of the following mechanisms best describes the manner in which lysozyme lowers the energy required for its substrate to reach its transition state conformation? (a) by binding two molecules and orienting them in a way that favors a reaction between them (b) by altering the shape of the substrate to mimic the conformation of the transition state (c) by speeding up the rate at which water molecules collide with the substrate (d) by binding irreversibly to the substrate so that it cannot dissociate

Which of the following methods used to study proteins is limited to proteins with a molecular weight of 50 kD or less? (a) x-ray crystallography (b) fingerprinting (c) nuclear magnetic resonance (d) mass spectroscopy

Which of the following molecules is thought to have arisen first during evolution? (a) protein (b) DNA (c) RNA (d) All came to be at the same time.

Which of the following pairs of codons might you expect to be read by the same tRNA as a result of wobble? (a) CUU and UUU (b) GAU and GAA (c) CAC and CAU (d) AAU and AGU

Which of the following proteins is likely to act as a gene repressor? (a) factor X (b) factor Y (c) factor Z (d) none of the above

Which of the following statements about allostery is true? a. Binding of allosteric molecules usually locks an enzyme in its current conformation, such that the enzyme cannot adopt a different conformation. b. Enzymes are the only types of proteins that are subject to allosteric regulation. c. Allosteric regulators are often products of other chemical reactions in the same biochemical pathway. d. Allosteric regulation is always used for negative regulation of enzyme activity.

Which of the following statements about how fruit flies can develop an eye in the middle of a leg is true? (a) When the Ey gene is expressed in adult leg cells, these cells de-differentiate and become eye cells. (b) The Ey gene encodes a transcription regulator that is the only transcription regulator used to produce a fruit-fly eye. (c) When the Ey gene is introduced into cells that would normally give rise to a leg, the transcription regulators used to control its expression in the legare different from those that are normally used to control Ey expression in the eye. (d) All the eye cells found in the adult leg are a single cell type and have identical characteristics.

Which of the following statements about miRNAs is false? (a) One miRNA can regulate the expression of many genes. (b) miRNAs are transcribed in the nucleus from genomic DNA. (c) miRNAs are produced from rRNAs. (d) miRNAs are made by RNA polymerase.

Which of the following statements about nucleosomes is true? (a) Nucleosomes activate transcription when bound to the promoter. (b) Although RNA polymerase can access DNA packed within nucleosomes,the general transcription factors and transcriptional regulators cannot. (c) Histone acetyltransferases affect transcription by both altering chromatin structure to allow accessibility to the DNA and by adding acetyl groups to histones that can bind proteins that promote transcription. (d) Histone deacetylases remove lysines from histone tails.

Which of the following statements about the carbohydrate coating of the cell surface is false? (a) It is not usually found on the cytosolic side of the membrane. (b) It can play a role in cell-cell adhesion. (c) The arrangement of the oligosaccharide side chains is highly ordered,much like the peptide bonds of a polypeptide chain. (d) Specific oligosaccharides can be involved in cell-cell recognition.

Which of the following statements about the proteasome is false? (a) Ubiquitin is a small protein that is covalently attached to proteins to mark them for delivery to the proteasome. (b) Proteases reside in the central cylinder of a proteasome. (c) Misfolded proteins are delivered to the proteasome, where they are sequestered from the cytoplasm and can attempt to refold. (d) The protein stoppers that surround the central cylinder of the proteasome use the energy from ATP hydrolysis to move proteins into the proteasome inner chamber.

Which of the following statements is true? (a) Disulfide bonds are formed by the cross-linking of methionine residues. (b) Disulfide bonds are formed mainly in proteins that are retained within the cytosol. (c) Disulfide bonds stabilize but do not change a protein's final conformation. (d) Agents such as mercaptoethanol can break disulfide bonds through oxidation.

Which of the following statements is true? (a) Peptide bonds are the only covalent bonds that can link together two amino acids in proteins. (b) The polypeptide backbone is free to rotate about each peptide bond. (c) Nonpolar amino acids tend to be found in the interior of proteins. (d) The sequence of the atoms in the polypeptide backbone varies between different proteins.

Which of the following statements is true? (a) Phospholipids will spontaneously form liposomes in nonpolar solvents. (b) In eukaryotes, all membrane-enclosed organelles are surrounded by one lipid bilayer. (c) Membrane lipids diffuse within the plane of the membrane. (d) Membrane lipids frequently flip-flop between one monolayer and the other.

Which of the following statements is true? (a) Ribosomes are large RNA structures composed solely of rRNA. (b) Ribosomes are synthesized entirely in the cytoplasm. (c) rRNA contains the catalytic activity that joins amino acids together. (d) A ribosome binds one tRNA at a time.

Which of the following structural characteristics is not normally observed in a DNA duplex? (a) purine-pyrimidine pairs (b) external sugar-phosphate backbone (c) uniform left-handed twist (d) antiparallel strands

Which one of the following is the main reason that a typical eukaryotic gene is able to respond to a far greater variety of regulatory signals than a typical prokaryotic gene or operon? (a) Eukaryotes have three types of RNA polymerase. (b) Eukaryotic RNA polymerases require general transcription factors. (c) The transcription of a eukaryotic gene can be influenced by proteins that bind far from the promoter. (d) Procaryotic genes are packaged into nucleosomes.

Which proteins do you predict are bound to the promoter in experiment #8? (a) only H and J (b) only G and H (c) only G and J (d) only J

Which transcription factors are normally bound to the Psf promoter in the presence of both Mg2+ and Ca2+? (a) MetA and MetB (b) MetB and MetC (c) MetA and MetC (d) MetA, MetB, and MetC

You are a virologist interested in studying the evolution of viral genomes. You are studying two newly isolated viral strains and have sequenced their genomes. You find that the genome of strain 1 contains 25% A, 55% G, 20% C, and 10% T. You report that you have isolated a virus with a single-stranded DNA genome. Based on what evidence can you make this conclusion?( a) single-stranded genomes always have a large percentage of purines (b) using the formula: G - A = C + T (c) Double-stranded genomes have equal amounts of A and T (d) Single-stranded genomes have a higher rate of mutation

You have discovered a gene (Figure Q7-36A) that is alternatively spliced to produce several forms of mRNA in various cell types, three of which are shown in Figure Q7-36B. The lines connecting the exons that are included in the mRNA indicate the splicing. From your experiments, you know that protein translation begins in exon 1. For all forms of the mRNA, the encoded protein sequence is the same in the regions of the mRNA that correspond to exons 1 and 10. Exons 2 and 3 are alternative exons used in different mRNA, as are exons 7 and 8. Which of the following statements about exons 2 and 3 is the most accurate? (a) Exons 2 and 3 must have the same number of nucleotides. (b) Exons 2 and 3 must contain an integral number of codons (that is, the number of nucleotides divided by 3 must be an integer). (c) Exons 2 and 3 must contain a number of nucleotides that when divided by 3, leaves the same remainder (that is, 0, 1, or 2). (d) Exons 2 and 3 must have different numbers of nucleotides.

Your colleague looks at your data above and predicts that protein G will bind more strongly to the DNA at site A, compared to protein H. Which experiment above is critical for this prediction? (a) #2 (b) #3 (c) #5 (d) #6

neuron and a white blood cell have very different functions. For example, a neuron can receive and respond to electrical signals while a white blood cell defends the body against infection. This is because ______. (a) the proteins found in a neuron are completely different from the proteins found in a white blood cell. (b) the neuron and the white blood cell within an individual have the same genome. (c) the neuron expresses some mRNAs that the white blood cell does not. (d) neurons and white blood cells are differentiated cells and thus no longer need to transcribe and translate genes.

A molecule of bacterial DNA introduced into a yeast cell is imported into the nucleus but fails to replicate the yeast DNA. Where do you think the block to replication arises?Choose the protein or protein complex below that is most probably responsible for the failure to replicate bacterial DNA. Give an explanation for your answer. (a) primase (b) helicase (c) DNA polymerase (d) initiator proteins

According to current thinking, the minimum requirement for life to have originated on Earth was the formation of a _______________. (a) molecule that could provide a template for the production of a complementary molecule (b) double-stranded DNA helix (c) molecule that could direct protein synthesis (d) molecule that could catalyze its own replication

Although all protein structures are unique, there are common structural building blocks that are referred to as regular secondary structures. Some have α helices, some have βsheets, and still others have a combination of both. What makes it possible for proteins to have these common structural elements? (a) specific amino acid sequences (b) side-chain interactions (c) the hydrophobic core interactions (d) hydrogen bonds along the protein backbone

An extraterrestrial organism (ET) is discovered whose basic cell biology seems pretty much the same as that of terrestrial organisms except that it uses a different genetic code to translate RNA into protein. You set out to break the code by translation experiments using RNAs of known sequence and cell-free extracts of ET cells to supply the necessary protein-synthesizing machinery. In experiments using the RNAs below, the following results were obtained when the 20 possible amino acids were added either singly or in different combinations of two or three: RNA 1: 5′-GCGCGCGCGCGCGCGCGCGCGCGCGCGC-3′ RNA 2: 5′-GCCGCCGCCGCCGCCGCCGCCGCCGCCGCC-3′ Using RNA 1, a polypeptide was produced only if alanine and valine were added to the reaction mixture. Using RNA 2, a polypeptide was produced only if leucine and serine and cysteine were added to the reaction mixture. Assuming that protein synthesis can start anywhere on the template, that the ET genetic code is nonoverlapping and linear, and that each codon is the same length (like the terrestrial triplet code), how many nucleotides does an ET codon contain? (a) 2 (b) 3 (c) 4 (d) 5 (e) 6

Cholesterol serves several essential functions in mammalian cells. Which of the following is not influenced by cholesterol? (a) membrane permeability (b) membrane fluidity (c) membrane rigidity (d) membrane thickness

Diversity among the oligosaccharide chains found in the carbohydrate coating of the cell surface can be achieved in which of the following ways? (a) varying the types of sugar monomers used (b) varying the types of linkages between sugars (c) varying the number of branches in the chain (d) all of the above

Energy required by the cell is generated in the form of ATP. ATP is hydrolyzed to powermany of the cellular processes, increasing the pool of ADP. ADP molecules then bind to glycolytic enzymes, which will lead to the production of more ATP. The best way to describe how oxidation energy is converted to ATP energy during glycolysis is by___________. (a) feedback inhibition (b) allosteric conformation (c) allosteric activation (d) substrate-level phosphorylation

Even though DNA polymerase has a proofreading function, it still introduces errors in the newly synthesized strand at a rate of 1 per 10 7 nucleotides. To what degree does the mismatch repair system decrease the error rate arising from DNA replication? (a) 2-fold (b) 5-fold (c) 10-fold (d) 100-fold

Hershey and Chase used radiolabeled macromolecules to identify the material that contains heritable information. What radioactive material was used to track DNA during this experiment? (a) 3H (b) 14C (c) 35S (d) 32P

How does the total number of replication origins in bacterial cells compare with the number of origins in human cells? (a) 1 versus 100 (b) 5 versus 500 (c) 10 versus 1000 (d) 1 versus 10,000

If the genome of the bacterium E. coli requires about 20 minutes to replicate itself, how can the genome of the fruit fly Drosophila be replicated in only 3 minutes? (a) The Drosophila genome is smaller than the E. coli genome. (b) EuKaryotic DNA polymerase synthesizes DNA at a much faster rate than proKaryotic DNA polymerase. (c) The nuclear membrane keeps the Drosophila DNA concentrated in one place inthe cell, which increases the rate of polymerization. (d) Drosophila DNA contains more origins of replication than E. coli DNA.

In a DNA double helix, _____________________. (a) the two DNA strands are identical (b) purines pair with purines (c) thymine pairs with cytosine (d) the two DNA strands run antiparallel

In the 1940s, proteins were thought to be the more likely molecules to house genetic information. What was the primary reason that DNA was not originally believed to be the genetic material? (a) DNA has a high density of negative charges. (b) Nucleotides were known to be a source of chemical energy for the cell. (c) Both protein and nucleic acids were found to be components of chromosomes. (d) DNA was found to contain only four different chemical building blocks.

Lysozyme is an enzyme that specifically recognizes bacterial polysaccharides, which renders it an effective antibacterial agent. Into what classification of enzymes does lysozyme fall? (a) isomerase (b) protease (c) nuclease (d) hydrolase

Membrane curvature is influenced by the differential lipid composition of the twomembrane monolayers. Which factor do you think has the largest impact on the curvature of biological membranes? (a) amount of cholesterol (b) charge of the lipid head group (c) length of the hydrocarbon tails (d) size of the lipid head group

Mobile genetic elements are sometimes called "jumping genes," because they move from place to place throughout the genome. The exact mechanism by which they achieve this mobility depends on the genes contained within the mobile element. Which of the following mobile genetic elements carry both a transposase gene and a reverse transcriptase gene? (a) L1 (b) B1 (c) Alu (d) Tn3

Motor proteins use the energy in ATP to transport organelles, rearrange elements of the cytoskeleton during cell migration, and move chromosomes during cell division. Which of the following mechanisms is sufficient to ensure the unidirectional movement of a motor protein along its substrate? (a) A conformational change is coupled to the release of a phosphate (Pi). (b) The substrate on which the motor moves has a conformational polarity. (c) A conformational change is coupled to the binding of ADP. d) A conformational change is linked to ATP hydrolysis.

Protein structures have several different levels of organization. The primary structure of a protein is its amino acid sequence. The secondary and tertiary structures are more complicated. Consider the definitions below and select the one that best fits the term"protein domain." (a) a small cluster of α helices and β sheets (b) the tertiary structure of a substrate-binding pocket (c) a complex of more than one polypeptide chain (d) a protein segment that folds independently

Red blood cells have been very useful in the study of membranes and the protein components that provide structural support. Which of the following proteins is the principal fibrous protein in the cortex of the red blood cell? (a) tubulin (b) attachment proteins (c) actin (d) spectrin

Several experiments were required to demonstrate how traits are inherited. Which scientist or team of scientists obtained definitive results demonstrating that DNA is the genetic molecule? (a) Griffith (b) Watson (c) Crick (d) Hershey and Chase

Some lipases are able to cleave the covalent bonds between the glycerol backbone and the attached fatty acid. What final products do you expect to accumulate through the action of the enzyme monoacylglycerol lipase? (a) phosphoglycerol and free fatty acid (b) sterol and glycerol (c) free phosphate and glycerol (d) glycerol and free fatty acid

Telomeres serve as caps at the ends of linear chromosomes. Which of the following is not true regarding the replication of telomeric sequences? (a) The lagging strand telomeres are not completely replicated by DNA polymerase. (b) Telomeres are made of repeating sequences. (c) Additional repeated sequences are added to the template strand. (d) The leading strand doubles back on itself to form a primer for the lagging strand.

The Ras protein is a GTPase that functions in many growth-factor signaling pathways. In its active form, with GTP bound, it transmits a downstream signal that leads to cell proliferation. Its inactive form, with GDP bound, the signal is not transmitted. Mutations in the gene for Ras are found in many cancers. Of the choices below, which alteration of Ras activity is most likely to contribute to the uncontrolled growth of cancer cells? (a) a change that prevents Ras from being made (b) a change that increases the affinity of Ras for GDP (c) a change that decreases the affinity of Ras for GTP (d) a change that decreases the rate of hydrolysis of GTP by Ras

The complete set of information found in a given organism's DNA is called its____________. (a) genetic code (b) coding sequence (c) gene (d) genome

The correct folding of proteins is necessary to maintain healthy cells and tissues. Unfolded proteins are responsible for such neurodegenerative disorders as Alzheimer's,Huntington's, and Creutzfeld-Jacob disease (the specific faulty protein is different for each disease). What is the ultimate fate of these disease-causing, unfolded proteins? (a) They are degraded. (b) They bind a different target protein. (c) They form structured filaments. (d) They form protein aggregates.

The events listed below are all necessary for homologous recombination to occur properly: A. Holliday junction cut and ligated B. strand invasion C. DNA synthesis D. DNA ligation E. double-strand break F. nucleases create uneven strands Which of the following is the correct order of events during homologous recombination? (a) E, B, F, D, C, A (b) B, E, F, D, C, A (c) C, E, F, B, D, A (d) E, F, B, C, D, A

The human genome has enough DNA to stretch more than 2 m. However, this DNA is not contained in a single molecule; it is divided into linear segments and packaged into structures called chromosomes. What is the total number of chromosomes found in each of the somatic cells in your body? (a) 22 (b) 23 (c) 44 (d) 46

The inactivation of one X chromosome is established by the directed spreading of heterochromatin. The silent state of this chromosome is _______________ in the subsequent cell divisions. (a) completed (b) switched (c) erased (d) maintained

The lateral movement of transmembrane proteins can be restricted by several different mechanisms. Which mechanism best describes the process by which nutrients are taken up at the apical surface of the epithelial cells that line the gut and released from their basal and lateral surfaces? (a) proteins are tethered to the cell cortex (b) proteins are tethered to the extracellular matrix (c) proteins are tethered to the proteins on the surface of another cell (d) protein movement is limited by the presence of a diffusion barrier

The octameric histone core is composed of four different histone proteins, assembled in a stepwise manner. Once the core octamer has been formed, DNA wraps around it to form a nucleosome core particle. Which of the following histone proteins does not form part of the octameric core? (a) H4 (b) H2A (c) H3 (d) H1

Total nucleic acids are extracted from a culture of yeast cells and are then mixed with resin beads to which the polynucleotide 5′-TTTTTTTTTTTTTTTTTTTTTTTTT-3′ has been covalently attached. After a short incubation, the beads are then extracted from the mixture. When you analyze the cellular nucleic acids that have stuck to the beads, which of the following is most abundant? (a) DNA (b) tRNA (c) rRNA (d) mRNA

Transcription is similar to DNA replication in that ___________________. (a) an RNA transcript is synthesized discontinuously and the pieces are then joined together (b) it uses the same enzyme as that used to synthesize RNA primers during DNA replication (c) the newly synthesized RNA remains paired to the template DNA (d) nucleotide polymerization occurs only in the 5′-to-3′ direction

Transcription is similar to DNA replication in that ___________________. (a) an RNA transcript is synthesized discontinuously and the pieces are then joined together. (b) it uses the same enzyme as that used to synthesize RNA primers during DNA replication. (c) the newly synthesized RNA remains paired to the template DNA. (d) nucleotide polymerization occurs only in the 5′-to-3′ direction.

Unlike DNA, which typically forms a helical structure, different molecules of RNA can fold into a variety of three-dimensional shapes. This is largely because ___________________. (a) RNA contains uracil and uses ribose as the sugar. (b) RNA bases cannot form hydrogen bonds with each other. (c) RNA nucleotides use a different chemical linkage between nucleotides compared to DNA. (d) RNA is single-stranded.

Using genetic engineering techniques, you remove the sequences that code for the ribosome-binding sequences of the bacterial LacZ gene. The removal of these sequences will lead to ___________. (a) more LacZ protein produced due to faster ribosome movement across the LacZ mRNA. (b) transcriptional repression, resulting in fewer mRNA molecules produced from this gene. (c) a longer half-life for the LacZ mRNA. (d) translational inhibition of the LacZ mRNA.

We can estimate the relative mobility of a population of molecules along the surface of a living cell by fluorescently labeling the molecules of interest,bleaching the label in one small area, and then measuring the speed of signal recovery as molecules migrate back into the bleached area. What is this method called? What does the abbreviation stand for? (a) SDS (b) SPT (c) GFP (d) FRAP

Which of the following chemical groups is not used to construct a DNA molecule? (a) five-carbon sugar (b) phosphate (c) nitrogen-containing base (d) six-carbon sugar

Which of the following is not a general mechanism that cells use to maintain stable patterns of gene expression as cells divide? (a) a positive feedback loop, mediated by a transcriptional regulator that activates transcription of its own gene in addition to other cell-type-specific genes (b) faithful propagation of condensed chromatin structures as cells divide (c) inheritance of DNA methylation patterns when cells divide (d) proper segregation of housekeeping proteins when cells divide

Which of the following is not a good example of a housekeeping protein? (a) DNA repair enzymes (b) histones (c) ATP synthase (d) hemoglobin

Which of the following is true of a retrovirus but not of the Alu retrotransposon? (a) It requires cellular enzymes to make copies. (b) It can be inserted into the genome. (c) It can be excised and moved to a new location in the genome. (d) It encodes its own reverse transcriptase.

Which of the following membrane lipids does not contain a fatty acid tail? (a) phosphatidylcholine (b) a glycolipid (c) phosphatidylserine (d) cholesterol

Which of the following methods is not used by cells to regulate the amount of a protein in the cell? (a) Genes can be transcribed into mRNA with different efficiencies. (b) Many ribosomes can bind to a single mRNA molecule. (c) Proteins can be tagged with ubiquitin, marking them for degradation. (d) Nuclear pore complexes can regulate the speed at which newly synthesized proteins are exported from the nucleus into the cytoplasm.

Which of the following might decrease the transcription of only one specific gene in a bacterial cell? (a) a decrease in the amount of sigma factor (b) a decrease in the amount of RNA polymerase (c) a mutation that introduced a stop codon into the DNA that precedes the gene's coding sequence (d) a mutation that introduced extensive sequence changes into the DNA that precedes the gene's transcription start site

Which of the following proteins are likely to act as gene activators? (a) MetA only (b) MetB only (c) MetC only (d) Both MetA and MetC

Which of the following questions would not be answered by using karyotyping? (a) Is the individual genetically female or male? (b) Do any of the chromosomes contain pieces that belong to other chromosomes? (c) Does the individual have an extra chromosome? (d) Do any chromosomes contain point mutations?

Which of the following sequences can fully base-pair with itself? (a) 5′-AAGCCGAA-3′ (b) 5′-AAGCCGTT-3′ (c) 5′-AAGCGCAA-3′ (d) 5′-AAGCGCTT-3′

Which of the following statements about DNA methylation in eukaryotes is false? (a) Appropriate inheritance of DNA methylation patterns involves maintenance methyltransferase. (b) DNA methylation involves a covalent modification of cytosine bases. (c) Methylation of DNA attracts proteins that block gene expression. (d) Immediately after DNA replication, each daughter helix contains one methylated DNA strand, which corresponds to the newly synthesized strand.

Which of the following statements about differentiated cells is true? (a) Cells of distinct types express non-overlapping sets of transcription factors. (b) Once a cell has differentiated, it can no longer change its gene expression. (c) Once a cell has differentiated, it will no longer need to transcribe RNA. (d) Some of the proteins found in differentiated cells are found in all cells of a multicellular organism.

Which of the following statements about the newly synthesized strand of a human chromosome is true? (a) It was synthesized from a single origin solely by continuous DNA synthesis. (b) It was synthesized from a single origin by a mixture of continuous and discontinuous DNA synthesis. (c) It was synthesized from multiple origins solely by discontinuous DNA synthesis. (d) It was synthesized from multiple origins by a mixture of continuous and discontinuous DNA synthesis.

Which of the following statements is false? (a) A new RNA molecule can begin to be synthesized from a gene before the previous RNA molecule's synthesis is completed. (b) If two genes are to be expressed in a cell, these two genes can be transcribed with different efficiencies. (c) RNA polymerase is responsible for both unwinding the DNA helix and catalyzing the formation of the phosphodiester bonds between nucleotides. (d) Unlike DNA, RNA uses a uracil base and a deoxyribose sugar.

You are examining the DNA sequences that code for the enzyme phosphofructokinase inskinks and Komodo dragons. You notice that the coding sequence that actually directs the sequence of amino acids in the enzyme is very similar in the two organisms but that the surrounding sequences vary quite a bit. What is the most likely explanation for this? (a) Coding sequences are repaired more efficiently. (b) Coding sequences are replicated more accurately. (c) Coding sequences are packaged more tightly in the chromosomes to protect them from DNA damage. (d) Mutations in coding sequences are more likely to be deleterious to the organism than mutations in noncoding sequences.

You develop a cell-free transcriptional system to study the effects of proteins G, H, and J on the transcription of gene Q. Using this system, you can examine the effects of adding these proteins to the transcriptional system in equal amounts and measuring how much gene Q is produced. When you add these proteins to the system, you get the results shown in Table Q8-29. Which proteins are likely to act as gene activators? (a) G (b) H (c) J (d) both H and J

You have a segment of DNA that contains the following sequence: 5′-GGACTAGACAATAGGGACCTAGAGATTCCGAAA-3′ 3′-CCTGATCTGTTATCCCTGGATCTCTAAGGCTTT-5′ If you know that the RNA transcribed from this segment contains the following sequence: 5′-GGACUAGACAAUAGGGACCUAGAGAUUCCGAAA-3′ Which of the following choices best describes how transcription occurs? (a) The top strand is the template strand; RNA polymerase moves along this strand from 5′ to 3′. (b) The top strand is the template strand; RNA polymerase moves along this strand from 3′ to 5′. (c) The bottom strand is the template strand; RNA polymerase moves along this strand from 5′ to 3′. (d) The bottom strand is the template strand; RNA polymerase moves along this strand from 3′ to 5′.

You have discovered an alien life-form that surprisingly uses DNA as its genetic material, makes RNA from DNA, and reads the information from RNA to make protein using ribosomes and tRNAs, which read triplet codons. Because it is your job to decipher the genetic code for this alien, you synthesize some artificial RNA molecules and examine the protein products produced from these RNA molecules in a cell-free translation system using purified alien tRNAs and ribosomes. You obtain the results shown in Table Q7-68.From this information, which of the following peptides can be produced from poly UAUC? (a) Ile-Phe-Val-Tyr (b) Tyr-Ser-Phe-Ala (c) Ile-Lys-His-Tyr (d) Cys-Pro-Lys-Ala

ou have discovered an "Exo - " mutant form of DNA polymerase in which the 3′-to-5′exonuclease function has been destroyed but the ability to join nucleotides together is unchanged. Which of the following properties do you expect the mutant polymerase to have? (a) It will polymerize in both the 5′-to-3′ direction and the 3′-to-5′ direction. (b) It will polymerize more slowly than the normal Exo + polymerase. (c) It will fall off the template more frequently than the normal Exo + polymerase. (d) It will be more likely to generate mismatched base pairs.

ou know that Gip1 is only expressed in adult liver cells and not in the liver of embryos. You also know that Jk8 and Pa5 behave similarly on other promoters in the embryo or in the adult, in terms of whether they act as repressors or gene activators. Given the data, use of which of the following mechanisms would make the most sense for regulating the Jk8 and Pa5 proteins: (a) Jk8 is ubiquitylated and targeted for destruction in adult cells. (b) Jk8, but not Pa5, is transcribed in embryonic liver cells. (c) Jk8 binds to the promoter of the gene that encodes Jk8 in embryonic liver cells. (d) Pa5 binds to the promoter of the gene that encodes Jk8 in embryonic liver cells.

snRNAs ___________________. (a) are translated into snRNPs. (b) are important for producing mature mRNA transcripts in bacteria. (c) are removed by the spliceosome during RNA splicing. (d) can bind to specific sequences at intron-exon boundaries through complementary base-pairing.

Match the basic protein functions in the left column with a specific example of that type of protein in the column on the right. ___ gene regulatory A. insulin ___ motor B. carboxylase ___ storage C. rhodopsin ___ enzyme D. hemoglobin ___ transport E. ferritin ___ structural F. myosin ___ special purpose G. green fluorescent protein ___ receptor H. tubulin ___ signal I. homeodomain proteins

gene regulatory --> I motor --> F storage --> E enzyme --> B transport --> D structural --> H special purpose --> G receptor --> C signal --> A

Even though proteins can form channels across biological membranes using eitherα helices or β sheets, channels made of α helices are more versatile. Explain the physical constraints on β-barrel structures and why these constraints do not apply to channels made of α helices.

β-Barrel structures are composed of individual β strands that form a β sheet that needs to be curved to make the structure of a pore in the membrane. The physical constraints are due to very specific positioning of each strand to maintain the necessary hydrogen-bonding network within the sheet. The relative positions of α helices can vary and still form strong interactions with other helices in the transmembrane region of a protein.

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