BIO 285: Final Exam

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

(d) FRAP Fluorescence Recovery After Photobleaching

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.

(d) The leading strand doubles back on itself to form a primer for the lagging strand.

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

(d) all of the above

Which of the choices below represents the correct way to repair the mismatch: ------C-------new strand ------T-------template strand (a)------A------ ------T----- (b)------C------ ------G---- (c)------C------ ------A----- (d)-----G------ -----T-----

(a)------A------ ------T-----

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

(b) 5′-AUAGGCAUUCGAUCCGGAUAGCAU-3′

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

(d) protein movement is limited by the presence of a diffusion barrier

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

(d) six-carbon sugar

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

(a) are produced from a precursor miRNA transcript.

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.

(a) do not code for proteins.

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

(a) linker histones

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

(a) lysine As is conventional for nucleotide sequences, the anticodon is given reading from 5′ to 3′. The complementary base-pairing occurs between antiparallel nucleic acid sequences, and the codon recognized by this anticodon will therefore be 5′-AAG-3′.

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.

(b) Thymidine dimers are covalent links between thymidines on opposite DNA strands.

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) enzyme

(b) anchors

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

(b) arginine 5′GUUUCCCGUAUACAUGCGUGCCGGGGGC-3′ The first tRNA to bind at the A-site is the second codon of the protein, because the initiator tRNA is already bound to the P-site when translation begins. The codon that follows the binding site for the initiator tRNA is CGU, which codes for arginine.

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

(b) gene silencing

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

(b) in the endoplasmic reticulum

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

(b) inside a cavity on the protein surface

Consider the apical location of a particular protein expressed in epithelial cells, illustrated in A below. Which type of defect described below is the most likely to cause the redistribution of that protein around the entire cell, shown B? (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

(b) the deletion of a junctional protein

An individual transport vesicle ________. (a) contains only one type of protein in its lumen. (b) will fuse with only one type of membrane. (c) is endocytic if it is traveling toward the plasma membrane. (d) is enclosed by a membrane with the same lipid and protein composition as the membrane of the donor organelle.

(b) will fuse with only one type of membrane. An individual vesicle may contain more than one type of protein in its lumen [choice (a)], all of which will contain the same sorting signal (or will lack specific sorting signals). Endocytic vesicles [choice (c)] generally move away from the plasma membrane. The vesicle membrane will not necessarily contain the same lipid and protein composition as the donor organelle, because the vesicle is formed from a selected subsection of the organelle membrane from which it budded [choice (d)].

You are interested in a single-stranded DNA molecule that contains the following sequence: 5′- .....GATTGCAT.... -3′ Which molecule can be used as a probe that will hybridize to your sequence of interest? (a) 5′-GATTGCAT-3′ (b) 5′-TACGTTAG-3′ (c) 5′-CTAACGTA-3′ (d) 5′-ATGCAATC-3′

(d) 5′-ATGCAATC-3′

After isolating the rough endoplasmic reticulum from the rest of the cytoplasm, you purify the RNAs attached to it. Which of the following proteins do you expect the RNA from the rough endoplasmic reticulum to encode? (a) soluble secreted proteins (b) ER membrane proteins (c) plasma membrane proteins (d) all of the above

(d) all of the above The rough ER consists of ER membranes and polyribosomes that are in the process of translating and translocating proteins into the ER membrane and lumen. Thus, all proteins that end up in the lysosome, Golgi apparatus, or plasma membrane, or are secreted, will be encoded by the RNAs associated with the rough ER.

You are interested in understanding the gene regulation of Lkp1, a protein that is normally produced in liver and kidney cells in mice. Interestingly, you find that the LKP1 gene is not expressed in heart cells. You isolate the DNA upstream of the LKP1 gene, place it upstream of the gene for green fluorescent protein (GFP), and insert this entire piece of recombinant DNA into mice. You find GFP expressed in liver and kidney cells but not in heart cells, an expression pattern similar to the normal expression of the LKP1 gene. Further experiments demonstrate that there are three regions in the promoter, labeled A, B, and C in the figure, that contribute to this expression pattern. Assume that a single and unique transcription factor binds each site such that protein X binds site A, protein Y binds site B, and protein Z binds site C. You want to determine which region is responsible for tissue-specific expression, and create mutations in the promoter to determine the function of each of these regions. In the figure, if the site is missing, it is mutated such that it cannot bind its corresponding transcription factor. experiment |promoter region| L | K | H 1 A B C yes yes yes 2 no no yes 3 A no yes yes 4 B yes no yes 5 C no no no 6 A B yes yes yes 7 A C no yes yes 8 B C yes no no 1) Which of the following proteins are likely to act as gene repressors? (a) factor Z (b) factor Y (c) factor X (d) none of the above 2) Which of the following proteins are likely to act as gene activators? (a) factors X and Z (b) factors X and Y (c) factors Y and Z (d) factor X only

1) (a) factor Z 2) (b) factors X and Y

A nucleosome contains two molecules each of histones [H1 and H2A/H2A and H2B] as well as of histones H3 and H4.

A nucleosome contains two molecules each of histones H2A and H2B, as well as histones H3 and H4.

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.

billions; antibodies; antigens; loops; affinity.

The α helices and β sheets are examples of protein ______________ structure. A protein such as hemoglobin, composed of more than one protein ____________, has _____________structure. A protein's amino acid sequence is known which is 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.

secondary; subunit; quaternary; primary; domain; tertiary.

Which of the following statements about vesicle budding from the Golgi is FALSE? (a) Clathrin molecules are important for binding to and selecting cargoes for transport. (b) Adaptins interact with clathrin. (c) Once vesicle budding occurs, clathrin molecules are released from the vesicle. (d) Clathrin molecules act at the cytosolic surface of the Golgi membrane.

(a) Clathrin molecules are important for binding to and selecting cargoes for transport. Cargo binds to cargo receptors. Adaptin molecules capture cargo receptors, which bind to the appropriate cargo molecules for incorporation into the vesicle.

A nucleosome core particle contains a core of histone with DNA wrapped around it approximately [twice/three times/four times].

A nucleosome core particle contains a core of histone with DNA wrapped around it approximately twice.

Ca2+-pumps in the plasma membrane and endoplasmic reticulum are important for _____________. (a) maintaining osmotic balance. (b) preventing Ca2+ from altering the activity of molecules in the cytosol. (c) providing enzymes in the endoplasmic reticulum with Ca2+ ions that are necessary for their catalytic activity. (d) maintaining a negative membrane potential.

(b) preventing Ca2+ from altering the activity of molecules in the cytosol.

PCR involves a heating step, followed by a cooling step, and then DNA synthesis. What is the primary reason for why this cooling step is necessary? (a) Cooling the reaction ensures the integrity of the covalent bonds holding the nucleotides together in the DNA strand. (b) Cooling the reaction gives the DNA polymerase an opportunity to rest from the previous cycle so that it will be ready for the next round of synthesis. (c) Transcription takes place during the cooling step. (d) Cooling the reaction brings the temperature down to a level that is compatible with the short primers forming stable hydrogen bonds with the DNA to be amplified.

(d) Cooling the reaction brings the temperature down to a level that is compatible with the short primers forming stable hydrogen bonds with the DNA to be amplified. During PCR, the reaction is heated to a temperature that will break the hydrogen bonds holding the strands together but should not be harmful to the covalent bonds holding the nucleotides together [choice (a)]. The DNA polymerase used in PCR is a thermostable enzyme that can tolerate the high temperatures used in PCR [choice (b)]. Transcription involves the production of RNA from DNA and does not occur during PCR [choice (c)].

K+ leak channels are found in the plasma membrane. These channels open and close in an unregulated, random fashion. What do they accomplish in a resting cell? (a) They set the K+ concentration gradient to zero. (b) They set the membrane potential to zero. (c) They disrupt the resting membrane potential. (d) They keep the electrochemical gradient for K+ near zero.

(d) They keep the electrochemical gradient for K+ near zero.

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

(d) a protein segment that folds independently

Any substance that will bind to a protein is known as its _______. Enzymes bind their _________(or ________) 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.

ligand; substrates; inhibitors; active site; isomers; activation energy; high-energy; transition state; products.

The biosynthetic pathway for the two amino acids E and H is shown schematically in the figure. 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. (a) H (b) B (c) C (d) E

(c) C

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′

(d) 5′-AAGCGCTT-3′

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.

(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.

Which of statements is TRUE (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) Ionizing radiation and oxidative damage can cause DNA double-strand breaks. (b) False. It is believed that the nicks 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.

Which of the following best describes the behavior of a gated channel? (a) It stays open continuously when stimulated. (b) It opens more frequently in response to a given stimulus. (c) It opens more widely as the stimulus becomes stronger. (d) It remains closed if unstimulated.

(b) It opens more frequently in response to a given stimulus.

You have a piece of circular DNA that can be cut by the restriction nucleases XhoI and SmaI, as indicated in the figure below. If you were to cut this circular piece of DNA with both XhoI and SmaI, how many fragments of DNA would you end up with? (a) 1 (b) 2 (c) 3 (d) 4

(b) 2

Given the evolutionary relationship between higher primates shown below, which of the following statements is FALSE? (a) The last common ancestor of humans, chimpanzees, gorillas, and orangutans lived about 14 million years ago. (b) Chimpanzees are more closely related to gorillas than to humans. (c) Humans and chimpanzees diverged about 6 million years ago. (d) Orangutans are the most divergent of the four species shown in the figure.

(b) Chimpanzees are more closely related to gorillas than to humans.

The amino acid sequences below represent the sequences of transmembrane helices. The characteristics of α helices that form a channel are different from those that form a single transmembrane domain. Select the helix that forms a single transmembrane domain. (a) VGHSLSIFTLVISLGIFVFF (b) IMIVLVMLLNIGLAILFVHF (c) ILHFFHQYMMACNYFWMLCE (d) VTLHKNMFLTYILNSMIIII

(b) IMIVLVMLLNIGLAILFVHF The peptide sequences for options (a), (c), and (d) are amphipathic—that is, they contain a hydrophilic amino acid every 3-4 amino acids in the sequence. This indicates they may be part of a protein that makes a channel in the membrane, and they require hydrophobic amino acids on the surface that interacts with the lipid bilayer and a hydrophilic surface on the inside of the channel. Option (b) is the only sequence that is completely hydrophobic, indicating that it forms a helix in which all the side chains interact with the lipid bilayer.

Which of the following statements are TRUE? (a) To meet a challenge or develop a new function, evolution essentially builds from first principles, designing from scratch, to find the best possible solution. (b) Nearly every instance of DNA duplication leads to a new functional gene. (c) A pseudogene is very similar to a functional gene but cannot be expressed because of mutations. (d) Most genes in vertebrates are unique, and only a few genes are members of multigene families. (e) Horizontal transfer is very rare and thus has had little influence on the genomes of bacteria.

(c) A pseudogene is very similar to a functional gene but cannot be expressed because of mutations.

Which of the following statements about the unfolded protein response (UPR) is FALSE? (a) Activation of the UPR results in the production of more ER membrane. (b) Activation of the UPR results in the production of more chaperone proteins. (c) Activation of the UPR occurs when receptors in the cytoplasm sense misfolded proteins. (d) Activation of the UPR results in the cytoplasmic activation of gene regulatory proteins.

(c) Activation of the UPR occurs when receptors in the cytoplasm sense misfolded proteins. The receptors for the unfolded proteins are on the ER membrane, and they sense the misfolded proteins using their luminal domains.

Which of the following statements is TRUE? (a) The signal sequences on mitochondrial proteins are usually at the C-terminus. (b) Most mitochondrial proteins are not imported from the cytosol but are synthesized inside the mitochondria. (c) Chaperone proteins in the mitochondria facilitate the movement of proteins across the outer and inner mitochondrial membranes. (d) Mitochondrial proteins cross the membrane in their native, folded state.

(c) Chaperone proteins in the mitochondria facilitate the movement of proteins across the outer and inner mitochondrial membranes.

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.

(c) Disulfide bonds stabilize but do not change a protein's final conformation. (a) is incorrect, because S-S bonds are formed between cysteines. (b) is incorrect, because they are formed mainly in extracellular proteins. (d) is incorrect; the bonds are broken by mercaptoethanol, but by reduction not by oxidation.

A double-stranded DNA molecule can be separated into single strands by heating it to 90°C because _______________________. (a) heat disrupts the hydrogen bonds holding the sugar-phosphate backbone together (b) DNA is negatively charged (c) heat disrupts hydrogen bonding between complementary nucleotides (d) DNA is positively charged

(c) heat disrupts hydrogen bonding between complementary nucleotides

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.

(c) Membrane lipids diffuse within the plane of the membrane. Phospholipids form bilayers only in polar solvents. Nuclei and mitochondria are enclosed by two membranes. Membrane lipids rarely flip-flop between one monolayer and the other.

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.

(c) Misfolded proteins are delivered to the proteasome, where they are sequestered from the cytoplasm and can attempt to refold. Once proteins are sent to the proteasome, proteases degrade them. Chaperone proteins provide a place for misfolded proteins to attempt to refold.

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.

(c) Nonpolar amino acids tend to be found in the interior of proteins (a) is untrue, because some proteins also contain covalent disulfide bonds (-S-S- bonds) linking two amino acids. (b) is untrue, because the peptide bond is rigid. (d) is untrue, because the sequence of atoms in the polypeptide backbone itself is always the same from protein to protein; it is the order of the amino acid side chains that differs.

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

(c) TCT

Which one of the following is the main reason that a typical eucaryotic gene is able to respond to a far greater variety of regulatory signals than a typical procaryotic gene or operon? (a) Eucaryotes have three types of RNA polymerase. (b) Eucaryotic RNA polymerases require general transcription factors. (c) The transcription of a eucaryotic gene can be influenced by proteins that bind far from the promoter. (d) Procaryotic genes are packaged into nucleosomes. (e) The protein-coding regions of eucaryotic genes are longer than those of procaryotic genes.

(c) The transcription of a eucaryotic gene can be influenced by proteins that bind far from the promoter.

The figure below shows the orientation of the Krt1 protein on the membrane of a Golgi-derived vesicle that will fuse with the plasma membrane. Given this diagram, which of the following statements is TRUE? (a) When this vesicle fuses with the plasma membrane, the entire Krt1 protein will be secreted into the extracellular space. (b) When this vesicle fuses with the plasma membrane, the C-terminus of Krt1 will be inserted into the plasma membrane. (c) When this vesicle fuses with the plasma membrane, the N-terminus of Krt1 will be in the extracellular space. (d) When this vesicle fuses with the plasma membrane, the N-terminus of Krt1 will be cytoplasmic.

(c) When this vesicle fuses with the plasma membrane, the N-terminus of Krt1 will be in the extracellular space.

Most proteins destined to enter the endoplasmic reticulum _________. (a) are transported across the membrane after their synthesis is complete. (b) are synthesized on free ribosomes in the cytosol. (c) begin to cross the membrane while still being synthesized. (d) remain within the endoplasmic reticulum.

(c) begin to cross the membrane while still being synthesized. Proteins destined to enter the endoplasmic reticulum have an N-terminal signal sequence that leads to the docking of the ribosome synthesizing the protein onto the ER and the entry of the protein across the ER membrane as the polypeptide chain is being synthesized.

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

(c) inherited a mutation in a gene required for mismatch repair In fact, affected individuals in some families with a history of early- onset colon cancer have been found to carry mutations in mismatch repair genes. Mutations arising in somatic cells are not inherited, so (a) is incorrect. A defect in DNA synthesis or nucleotide biosynthesis would probably be lethal, so (b) and (d) are incorrect.

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

(c) recognizes promoter sites in the DNA

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

(c) template

You create a recombinant DNA molecule that fuses the coding sequence of green fluorescent protein to the regulatory DNA sequences that control the expression of your favorite genes. Which of the following pieces of information can you NOT gain by examining the expression of this reporter gene? (a) the tissue where the protein encoded by this gene is expressed (b) the cell in which the protein encoded by this gene is expressed (c) the specific location within the cell of the protein encoded by this gene (d) when, during an organism's development, this gene is expressed

(c) the specific location within the cell of the protein encoded by this gene The information for localizing proteins within a cell is found on the protein product and not in the regulatory DNA sequences. If you were to fuse your reporter gene to the DNA sequences that encode the protein to produce a GFP fusion protein, then you might determine the specific location of the protein within the cell.

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

(c) using fluorescent DNA molecules

Which of the following choices reflects the appropriate order of locations through which a protein destined for the plasma membrane travels? (a) lysosome-->endosome--->plasma membrane (b) ER--->lysosome--->plasma membrane (c) Golgi--->lysosome--->plasma membrane (d) ER--->Golgi--->plasma membrane

(d) ER--->Golgi--->plasma membrane

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.

(d) It was synthesized from multiple origins by a mixture of continuous and discontinuous DNA synthesis. Each newly synthesized strand in a daughter duplex was synthesized by a mixture of continuous and discontinuous DNA synthesis from multiple origins. Consider a single replication origin. The fork moving in one direction synthesizes a daughter strand continuously as part of leading-strand synthesis; the fork moving in the opposite direction synthesizes a portion of the same daughter strand discontinuously as part of lagging-strand synthesis.

You 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.

(d) It will be more likely to generate mismatched base pairs.

Which of the following statements about differentiated cells is TRUE? (a) Cells of distinct types express nonoverlapping 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.

(d) Some of the proteins found in differentiated cells are found in all cells of a multicellular organism. The housekeeping proteins are proteins common to all cells and are used in processes important to the basic function of cells. Some transcription factors, particularly those used to regulate housekeeping genes, are found in all cell types (choice (a)). Even though a cell is differentiated, it may be able to respond to changes in its environment by changing its gene expression pattern (choices (b) and (c)). A differentiated cell usually continues to express genes and make new proteins (choice (c)).

Match the type of phenotypic change below with the type of genetic change most likely to cause it. Each type of genetic change may be used more than once, or may not be used at all. Phenotypic changes: 1. A protein normally localized in the nucleus is now localized in the cytoplasm. _________ 2. A protein acquires a DNA-binding domain. _________ 3. Tandem copies of a gene are found in the genome. _________ 4. A copy of a bacterial gene is now found integrated on a human chromosome. _________ 5. A protein becomes much more unstable. _________ 6. A protein normally expressed only in the liver is now expressed in blood cells. ________ Types of genetic change: A. mutation within a gene B. gene duplication C. mutation in a regulatory region D. exon shuffling E. horizontal gene transfer

1—A; 2—D; 3—B; 4—E; 5—A; 6—C

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′

Indicate whether the statements below are true or false. If a statement is false, explain why it is false. A. Gap junctions are large pores that connect the cytosol to the extracellular space. B. Aquaporin channels are found in the plasma membrane, and allow the rapid passage of water molecules and small ions in and out of cells. C. The ion selectivity of a channel depends solely on the charge of the amino acids lining the pore inside the channel. D. Most ion channels are gated, which allows them to open and close in response to a specific stimulus, rather than allowing the constant, unregulated flow of ions.

A. False. Gap junctions are used to connect the cytosol of adjacent cells, allowing the sharing of ions and small metabolites. Because gap junctions are large channels, if they were open while facing the extracellular environment, the ability of the plasma membrane to serve as a permeability barrier would be greatly reduced. B. False. Charged molecules (even protons, which are very small) are not able to pass through aquaporins. C. False. Selectivity depends on three parameters: the diameter, shape, and charge of the ion trying to pass through the pore of the channel. D. True.

Indicate whether the statements below are true or false. If a statement is false, explain why it is false. A. Neurotransmitters are small molecules released into the synaptic cleft after the fusion of synaptic vesicles with the presynaptic membrane. B. Action potentials are usually mediated by voltage-gated Ca2+ channels. C. Voltage-gated Na+ channels become automatically inactivated shortly after opening, which ensures that the action potential cannot move backward along the axon. D. Voltage-gated K+ channels also open immediately in response to local depolarization, reducing the magnitude of the action potential.

A. True. B. False. Action potentials are usually mediated by voltage-gated Na+ channels. C. True. D. False. Voltage-gated K+ channels respond more slowly than the voltage-gated Na+ channels. Because voltage-gated K+ channels do not open until the action potential reaches its peak, they do not affect its magnitude. Instead, they help to restore the local membrane potential quickly while the voltage-gated Na+ channels are in the inactivated conformation.

What is the most abundant cation outside a typical mammalian cell?

Sodium (Na+)

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. A. GGCGCACC B. TATTGTCT C. GACTCCTG D. CTAACTGG

The order in which the DNA molecules would denature as the temperature increases is: 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.

If you remove the ER retention signal from a protein that normally resides in the ER lumen, where do you predict the protein will ultimately end up? Explain your reasoning.

The protein would end up in the extracellular space. Normally, the protein would go from the ER to the Golgi apparatus, get captured because of its ER retention signal, and return to the ER. However, without the ER retention signal, the protein would evade capture, ultimately leave the Golgi via the default pathway, and become secreted into the extracellular space. The protein would not be retained anywhere else along the secretory pathway: it presumably has no signals to promote such localization because it normally resides in the ER lumen.

Voltage-gated channels contain charged protein domains, which are sensitive to changes in membrane potential. By responding to a threshold in the membrane potential, these voltage sensors trigger the opening of the channels. Which of the following best describes the behavior of a population of channels exposed to such a threshold? (a) Some channels remain closed and some open completely. (b) All channels open completely. (c) All channels open partly, to the same degree. (d) All channels open partly, each to a different degree.

(a) Some channels remain closed and some open completely. Individual channels are either completely open or completely closed. However, in a given population, there will be a mixture of open and closed channels.

Which of the following statements about nuclear transport is TRUE? (a) mRNAs and proteins transit the nucleus through different types of nuclear pores. (b) Nuclear import receptors bind to proteins in the cytosol and bring the proteins to the nuclear pores, where the proteins are released from the receptors into the pores for transit into the nucleus. (c) Nuclear pores have water-filled passages that small, water-soluble molecules can pass through in a nonselective fashion. (d) Nuclear pores are made up of many copies of a single protein.

(c) Nuclear pores have water-filled passages that small, water-soluble molecules can pass through in a nonselective fashion. mRNAs and proteins can move through the same nuclear pore [choice (a)]. Nuclear import receptors bind to proteins in the cytosol and transit with them across the nuclear pore into the nucleus [choice (b)]. Nuclear pores are made up of many copies of multiple proteins [choice (d)].

Signal sequences that direct proteins to the correct compartment are _________. (a) added to proteins through post-translational modification. (b) added to a protein by a protein translocator. (c) encoded in the amino acid sequence and sufficient for targeting a protein to its correct destination. (d) always removed once a protein is at the correct destination.

(c) encoded in the amino acid sequence and sufficient for targeting a protein to its correct destination. Signal sequences are found within the amino acid sequence of proteins. They are sometimes removed when the protein is at the correct destination [choice (d)], but not all are removed. For example, nuclear import signals are not removed once a protein is inside the nucleus. A protein translocator resides in the membrane and helps transport soluble proteins across the membrane [choice (b)], but does not add signal sequences to proteins.

Nucleosomes are aided in their formation by the high proportion of [acidic/basic/polar] amino acids in histone proteins.

Nucleosomes are aided in their formation by the high proportion of basic amino acids in histone proteins.

Nucleosomes are present in [procaryotic/eucaryotic] chromosomes, but not in [procaryotic/eucaryotic] chromosomes.

Nucleosomes are present in eucaryotic chromosomes, but not in procaryotic chromosomes.

What is the most abundant cation inside a typical mammalian cell?

Potassium (K+)

You want to amplify the DNA between the two stretches of sequence shown in the figure below. Of the listed primers, choose the pair that will allow you to amplify the DNA by PCR. DNA to be amplified: 5'-GACCTGTGGAAGC--------CATACGGGATTGA-3' 3'-CTGGACACCTTCG--------GTATGCCCTAACT-5' Primers: 1. 5'-GACCTGTGGAAGC-3' 2. 5'-CTGGACACCTTCG-3' 3. 5'-CGAAGGTGTCCAG-3' 4. 5'-GCTTCCACAGGTC-3' 5. 5'-CATACGGGATTGA-3' 6. 5'-GTATGCCCTAACT-3' 7. 5'-TGTTAGGGCATAC-3' 8. 5'-TCAATCCCGTATG-3'

The appropriate PCR primers are primer 1 (5′-GACCTGTGGAAGC-3′) and primer 8 (5′- TCAATCCCGTATG-3′). The first primer will hybridize to the bottom strand and prime synthesis in the rightward direction. The second primer will hybridize to the top strand and prime synthesis in the leftward direction. (Remember that strands pair antiparallel.) The middle two primers in each list (primers 2, 3, 6, and 7) would not hybridize to either strand. The remaining pair of primers (4 and 5) would hybridize, but would prime synthesis in the wrong direction—that is, outward, away from the central segment of DNA. Each wrong choice has been made at one time or another in most laboratories that use PCR. In most cases the confusion arises because the conventions for writing nucleotide sequences have been ignored. By convention, nucleotide sequences are written 5′ to 3′, with the 5′ end on the left. For double- stranded DNA, the 5′ end of the top strand is on the left.