BioChem Exam 2

The enzyme that catalyzes the formation of a phosphodiester linkage at a break in a DNA strand is _____

DNA ligase

_______ gels are often used as the media for electrophoretic techniques such as SDS-PAGE and isoelectric focusing.

Polyacrylamide

Sedimentation coefficients are described as _____ units

Svedberg

In a DNA microarray, how many different oligonucleotides can be produced if each oligonucleotide is 20 nucleotides long? a. 4^20 b. 20^4 c. 80 d. 20

a. 4^20

What statement about plasmids is false? a. A bacterial cells always has plasmids b. They are circular double-stranded DNA molecules. c. Plasmids can replicate independently of the host chromosome. d. Plasmids carry genes for the inactivation of antibiotics.

a. A bacterial cells always has plasmids

Insulin is a polypeptide hormone that contains two short polypeptide chains linked by two interstrand disulfide bonds. The most logical order of events to perform in order to sequence this protein would be: A- the peptides are reduced with mercaptoethanol. B- the peptides are sequenced using Edman chemistry. C- the peptides are separated by chromatography techniques. D- the peptides are alkylated with iodoacetamide. a. A, D, C, B b. C, A, D, B c. C, B, A, D d. A, B, C, D e. A, C, D, B

a. A, D, C, B

Which statement about CRISPR-cas9 system is false? a. Cas9, CRISPR Associated Protein 9, is a polymerase that synthesizes DNA b. With CRISPR, researchers can permanently modify genes in any living cells and organisms. c. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. It is a prokaryotic immune system that confers resistance to foreign genetic elements. d. With CRISPR, it may be possible to correct mutations at precise locations in the human genome to treat genetic causes of disease.

a. Cas9, CRISPR Associated Protein 9, is a polymerase that synthesizes DNA

For a mixture of proteins shown in the Table, predict the order of emergence when subjected to a gel filtration column with a fractionation range of 1-100 kDa at pH 7? a. Protein 3, Protein 1, Protein 2 b. Protein 2, Protein 3, Protein 1 c. Protein 2, Protein 1, Protein 3 d. Protein 1, Protein 3, Protein 2

a. Protein 3, Protein 1, Protein 2

In pyrosequencing, following complementary binding of an activated nucleotide to the template strand a. Pyrophosphate is release b. adenosine 5' phosphosulfate degrades c. photons of light are release d. Luciferin is converted to oxyluciferin

a. Pyrophosphate is release

A genomic DNA library consists of a. a set of cloned fragments that collectively represent the genes of a particular organism. b. an alphabetical list of all the genes in an organism c. a set of reference books on genetics d. a collection of short fragments from nuclear DNA digestion. e. arrays of synthetic oligonucleotides used to select for a specific DNA.

a. a set of cloned fragments that collectively represent the genes of a particular organism.

Protein databases a. can identify proteins from small stretches of amino acid sequences. b. are not useful in proteomics studies due to the complexities of the proteome c. are determined from sequence data only, never deduced from genomic data d. none of these e. all of these

a. can identify proteins from small stretches of amino acid sequences.

Current DNA sequencing commonly uses ____ base analogues. a. fluorescent b. radioactive c. phosphorescent d. cross-linked e. photoreactive

a. fluorescent

_____ is used to determine protein primary structure a. mass spectrometry b. x-ray crystallography c. FTIR spectroscopy d. NMR spectroscopy

a. mass spectrometry

SDS-PAGE is used to determine the ___ of a protein a. molecular weight b. isoelectric point c. amino acid composition d. specific activity

a. molecular weight

Mass spectrometric techniques are critical in _____research because it is possible to analyze constituents of large macromolecular assemblies. a. proteomics b. genomics c. chromatography d. transcriptomics

a. proteomics

What can be used to add nucleotides to the 3' end of DNA? a. terminal transferase b. reverse transcriptase c. telomeres d. pseudogenes

a. terminal transferase

The original development of PCR did not use the Taq polymerase. What is the reason that the Taq polymerase is currently used? (check all that apply) a. the DNA melting step at 94°C would cause denaturation of most DNA polymerases from other organisms. b. the Taq polymerase is one of the most rapid DNA polymerase enzymes known and is therefore extremely useful for PCR. c. the original method of PCR required that DNA polymerase be added prior to each round of elongation, something that is not suitable for automation. d. the Taq polymerase is the only DNA polymerase that will allow production of 2n amounts of DNA (n=number of cycles).

a. the DNA melting step at 94°C would cause denaturation of most DNA polymerases from other organisms. c. the original method of PCR required that DNA polymerase be added prior to each round of elongation, something that is not suitable for automation.

Expression libraries are most often made from a. the mRNA found with a given cell or tissue. b. the genome of a given cell or tissue. c. the promoters of a given cell or tissue. d. the DNA of a single chromosome from cell type or tissue.

a. the mRNA found with a given cell or tissue.

pUC plasmids are useful for screening cells that contain recombinant DNA because they contain the _____ gene. a. β-galactosidase b. tetracycline resistance c. green fluorescent protein d. luciferase

a. β-galactosidase

Two-dimensional gel electrophoresis is the workhorse for proteomics. You have extracted a subset of proteins from the kidney of a kidney cancer patient and the same subset from a normal individual. To analyze the differences of the two protein samples you have performed a 2-D gel electrophoresis experiment using the same amount of total protein from each sample. To estimate molecular weight, you have run an SDS-PAGE and used a MW marker containing proteins with 20, 35, 50, 90, 150, and 250 kDa. The results of your experiment are shown below. What is the MW and pI of a protein that is expressed only in the diseased tissue? a. 28 kDa, 8.0 b. 75 kDa, 8.0 c. 45 kDa, 5.0 d. 48 kDa, 8.0 e. 60 kDa, 9.0

b. 75 kDa, 8.0

In a sample consisting of Lysine, Glycine, and Glutamic acid, which will be eluted first from an anion exchange resin at pH 7? a. Glutamic acid b. Lysine c. Glycine d. all three will be eluted at the same time

b. Lysine

For a mixture of proteins shown in the Table, predict the order of emergence when subjected to a cation-exchange chromatography at pH 7? a. Protein 3, Protein 1, Protein 2 b. Protein 2, Protein 3, Protein 1 c. Protein 2, Protein 1, Protein 3 d. Protein 1, Protein 3, Protein 2

b. Protein 2, Protein 3, Protein 1

Identify the restriction enzyme that would produce a "blunt end" cut. (The enzyme name is given followed by the recognition sequence. The "/" shows the cut point) a. Bgl II A/GATCT b. Scal I AGT/ACT c. Sac II CCGC/GG d. Xba I T/CTAGA

b. Scal I AGT/ACT

Which of the following best describes the state of a protein whose pI = 6, when in a solution whose pH = 9? a. The protein will have no net charge. b. The protein will have a net negative charge. c. The protein will have a net positive charge. d. The side chains of the protein's acidic residues will mostly be in their unprotonated states. e. The side chains of the protein's basic residues will mostly be in their uncharged states.

b. The protein will have a net negative charge.

Why are met and trp often used to design DNA probes from amino acid sequences? a. Met is the first amino acid in the protein chain. b. They have single codons. c. Both are used often in proteins. d. All of these. e. None of these.

b. They have single codons.

The probe used to isolate a gene from a genomic library is often a. the ligand that binds to the protein b. a portion of the mRNA of the gene c. the protein produced by the gene d. its telomere region e. its promoter region

b. a portion of the mRNA of the gene

How does RNA interference work? a. siRNA binds to genes and prevents transcription. b. a single strand of the siRNA binds to the gene transcript, promoting degradation thus preventing translation. c. siRNA is produced by RNA polymerase. d. siRNA binds to RNA polymerase preventing mRNA production.

b. a single strand of the siRNA binds to the gene transcript, promoting degradation thus preventing translation.

If mRNA is converted to DNA and cloned into suitable vectors, the resultant library is called a. DNA library b. cDNA library c. mRNA library d. none of these

b. cDNA library

Which statement is false about ELISA? (check all that apply) a. primary antibody binds directly to the target protein b. secondary antibody binds directly to the target protein c. the ELISA enzyme is linked to the secondary antibody d. the ELISA enzyme is linked to the primary antibody

b. secondary antibody binds directly to the target protein d. the ELISA enzyme is linked to the primary antibody

The main difference between Western blotting and ELISA is: a. enzyme is linked to primary antibody in Western blotting but to secondary antibody in ELISA b. substrate is water soluble in ELISA but not in Western blotting c. enzyme is linked to secondary antibody in Western blotting but to first antibody in ELISA d. substrate is water soluble in Western blotting but not ELISA

b. substrate is water soluble in ELISA but not in Western blotting

Which statement about solid phase peptide synthesis is false? a. the desired product is bound to beads and excess reagents can be easily removed at each step. b. synthesis starts from N-terminus. c. there is limitation on the length of peptide chain. d. amino acid's carboxyl group must be activated with dicyclohexylcarbodiimide to facilitate peptide bond formation.

b. synthesis starts from N-terminus.

A cloning vector map is shown below. Which restriction site is best for inserting a DNA fragment for selection of chimeric plasmid containing colonies? a. BamHI b. EcoRI c. HindIII d. They're all equally good.

c. HindIII

Coronavirus is a type of ____ virus. The genome can be detected by ____. a. RNA, PCR b. DNA, PCR c. RNA, RT-PCR (Reverse transcription PCR) d. DNA, RT-PCR

c. RNA, RT-PCR (Reverse transcription PCR)

Sequencing DNA using a dideoxy method can be done by putting fluorescent tags on the ddNTPs, and then separating the DNA fragments by size using electrophoresis. A short segment is sequenced using ddNTPs tagged as shown in the Table ddNTP color ddATP ddCTP ddGTP ddTTP Green Blue Yellow red The resulting electrophoresis gel is displayed below. What is the DNA sequence of the template strand? a. AGTCCA b. TCAGGT c. TGGACT d. ACCTGA

c. TGGACT

All are characteristics of yeast artificial chromosomes (YACs) EXCEPT: a. YACs must include telomeres b. YACs must include centromere c. YACs must include operon d. YACs must include cloning site e. YACs can successfully propagate DNA molecules of 2 megabase pairs in length.

c. YACs must include operon

A single clone of interest can be distinguished from others in a mixture of clones by a. testing the clones for antibiotic resistance. b. mobility of the clones in gel electrophoresis. c. a specific probe, usually a labeled complementary DNA. d. resistance to damage by ultraviolet light.

c. a specific probe, usually a labeled complementary DNA.

What technique is used to locate disulfide bonds in protein? a. HPLC b. SDS-PAGE c. diagonal electrophoresis d. protein sequencing e. mass spectrometry

c. diagonal electrophoresis

Which of the following techniques is most useful for fractionating a heterogeneous protein mixture by size? a. affinity chromatography b. Edman degradation c. gel-filtration chromatography d. ion-exchange chromatography e. isoelectric focusing

c. gel-filtration chromatography

The typical order for the major steps of enzyme isolation would be (from first to last): a. homogenization, salt fractionation, electrophoresis, column chromatography b. salt fractionation, homogenization, electrophoresis, column chromatography c. homogenization, salt fractionation, column chromatography, electrophoresis d. homogenization, column chromatography, salt fractionation, electrophoresis e. homogenization, electrophoresis, salt fractionation, column chromatography

c. homogenization, salt fractionation, column chromatography, electrophoresis

All are true for cDNA libraries EXCEPT: a. reverse transcriptase synthesizes a DNA strand complement of the mRNA templates. b. the original RNA strands are broken down by treating with alkaline c. mRNA templates are isolated using oligo (dA)-cellulose chromatography. d. the cDNA are copies from mRNA templates.

c. mRNA templates are isolated using oligo (dA)-cellulose chromatography.

All are steps used for construction of a chimeric plasmid EXCEPT: a. annealing the ends of the vector and foreign DNA. b. cutting the source of the foreign DNA with a restriction endonuclease. c. reannealing the ends of the vector back together. d. cutting the vector plasmid with the same restriction endonuclease.

c. reannealing the ends of the vector back together.

The typical order of differential centrifugation for organelles is (from slowest speed/lowest g to fastest speed/highest g): a. nuclei, microsomes, mitochondria & chloroplasts, cytosol, whole cells b. whole cells, cytosol, microsomes, nuclei, mitochondria & chloroplasts c. whole cells, nuclei, mitochondria & chloroplasts, microsomes, cytosol d. nuclei, mitochondria & chloroplasts, whole cells, cytosol, microsomes e. cytosol, microsomes, nuclei, mitochondria & chloroplasts, whole cells

c. whole cells, nuclei, mitochondria & chloroplasts, microsomes, cytosol

What compounds are used to reduce disulfide bonds? Select all that apply a. sodium dodecyl sulfate b. polyacrylamide c. β-mercaptoethanol d. dithiothreitol e. polyampholytes

c. β-mercaptoethanol d. dithiothreitol

The "c" in cDNA stands for _____

complementary

The following steps are all involved in genetic recombination: 1- Screening for cells that contain the recombined gene. 2- Cutting the vector with restriction enzyme. 3- Mixing the gene of interest with the vector. 4- Isolating the gene of interest from its original source. 5- Ligating the gene of interest and the vector together. The following sequence of these five steps would be typical: a. 1 → 2 → 3 → 4 → 5 b. 2 → 3 → 5 → 1 → 4 c. 5 → 4 → 3 → 2 → 1 d. 4 → 2 → 3 → 5 → 1 e. 2 → 3 → 5 → 4 → 1

d. 4 → 2 → 3 → 5 → 1

The correct sequence of procedures in the Southern blotting technique is: A- hybridization with radioactive probe. B- agarose gel electrophoresis and visualize bands. C- transfer (blot) to nitrocellulose filter. D- digest DNA with restriction nucleases. E- expose filter to X-ray film, develop and observe. a. B, A, C, E, D b. D, C, B, A, E c. C, D, B, E, A d. D, B, C, A, E e. A, B, C, D, E

d. D, B, C, A, E

This is a map of pBR322 plasmid If a recombinant plasmid were obtained inserting DNA into the BamHI site, screening for the recombinant plasmid can be done by the following technique. a. Plate on nutrient agar plates that contain ampicillin. b. Plate on nutrient agar plates that contain tetracycline. c. Plate on nutrient agar plates that contain both ampicillin and tetracycline. d. Plate on nutrient agar plates that contain ampicillin, followed by replica plating on tetracycline. e. Plate on nutrient agar plates that contain tetracycline, followed by replica plating on ampicillin.

d. Plate on nutrient agar plates that contain ampicillin, followed by replica plating on tetracycline.

Cells that contain a "blue/white screening" plasmid that has an added gene are recognized by the method: a. Ability to grow on ampicillin. b. Inability to grow on ampicillin. c. The colonies have a blue color. d. The colonies lack a blue color. e. More than one of these choices indicates that the plasmid contains recombined DNA.

d. The colonies lack a blue color.

If DNA fragments of about 20 kb are to be cloned, which vector would be most useful? a. plasmid b. cosmid c. YACs (yeast artificial chromosomes) d. bacteriophage lambda e. E. coli chromosome

d. bacteriophage lambda

On the quantitative PCR diagram, CT shows the a. number of copies of the original cDNA template b. fluorescence intensity c. number of copies of the original template d. cycle number at which fluorescence becomes detectable e. starting quantity of DNA

d. cycle number at which fluorescence becomes detectable

The chain terminator used in Sanger's DNA sequencing is _______. It works due to ______. a. dNTP; lack of 2'OH b. ddNTP; lack of 2'OH c. dNTP; lack of 3'OH d. ddNTP; lack of 3'OH

d. ddNTP; lack of 3'OH

What is shown in the figure? a. plasmid pUC18 b. cloning vector c. lambda phage d. expression vector e. cosmid

d. expression vector

Which statement is false about peptide mass fingerprinting? a. it is a high throughput protein identification technique b. it does not depend on protein sequencing for identification c. it uses mass spectrometry to generate a peak list of proteolytic fragments d. it does not require database to have similar protein that is already characterized

d. it does not require database to have similar protein that is already characterized

Which of the following would be a possible amino acid sequence for an oligopeptide given the experimental data below? 1. The amino acid composition is found to be [val, lys, phe, met, cys, plus some decomposition products]. 2. the peptide has a molecular weight about 700 Da and absorbs at 280 nm 3. treatment with carboxypeptidase results in tryptophan and a peptide 4. CNBr treatment yields two tripeptides 5. trypsin digestion produces an amino acid and a pentapeptide with cys on the amino end 6. chymotrypsin digestion produces a tetrapeptide and a dipeptide a. trp-lys-met-cys-met-val b. lys-val-cys-phe-met-trp c. trp-val-phe-cys-met-lys d. lys-cys-met-phe-val-trp e. lys-met-cys-val-phe-trp

d. lys-cys-met-phe-val-trp

In vitro ____ makes it possible to alter the nucleotide sequence of a cloned gene systematically. a. protein synthesis b. mRNA synthesis c. hybridization d. mutagenesis

d. mutagenesis

The DNA fragment was inserted into a specific plasmid. What do the plasmid and the DNA fragment have in common? a. both act as vectors b. identical restriction sites c. same molecular weight d. same sticky ends

d. same sticky ends

The predominance of protein sequence information is now derived from: a. chemical sequencing (Edman method). b. mass spectrometry. c. tandem mass spectrometry. d. translating the nucleotide sequence of genes into codons, and thus amino acid sequence.

d. translating the nucleotide sequence of genes into codons, and thus amino acid sequence.

Which of the following are methods by which cells can be induced to take up recombinant DNA molecules? a. liposome. b. DNA "guns" which spray the DNA at very high speeds. c. Electroporation. d. Phage or virus infection. e. All of these are used.

e. All of these are used.

The method that reveals the atomic structure of proteins in a solution is: a. MALDI b. electrophoresis c. x-ray crystallography d. ion-exchange chromatography e. NMR

e. NMR

What is not a step in cassette mutagenesis? a. DNA is cleaved at a pair of unique restriction sites b. The short segment is removed from the plasmid c. the cassette is ligated into the plasmid d. in the end, we get the desired mutation e. The short segment connects with the cassette

e. The short segment connects with the cassette

Due to what mechanism do many genes encode more than one protein? a. adenylation b. mutagenesis c. translation d. transcription e. alternative splicing

e. alternative splicing

Which statement about gene disruption is false? a. gene disruption can be used to determine the function of a gene. b. gene disruption can be achieved by RNA interference. c. gene disruption can be achieved by CRISPR-Cas9 system. d. gene disruption is also known as gene knockout. e. gene disruption cannot be done at a precise location

e. gene disruption cannot be done at a precise location

Another name for an antigenic determinant is _____

epitope

What enzyme is used to create DNA from RNA?

reverse transcriptase

The ratio of enzyme activity relative to total protein is called ______

specific activity